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Delvenne A, Gobom J, Schindler SE, Kate MT, Reus LM, Dobricic V, Tijms BM, Benzinger TLS, Cruchaga C, Teunissen CE, Ramakers I, Martinez-Lage P, Tainta M, Vandenberghe R, Schaeverbeke J, Engelborghs S, Roeck ED, Popp J, Peyratout G, Tsolaki M, Freund-Levi Y, Lovestone S, Streffer J, Barkhof F, Bertram L, Blennow K, Zetterberg H, Visser PJ, Vos SJB. CSF proteomic profiles of neurodegeneration biomarkers in Alzheimer's disease. Alzheimers Dement 2024. [PMID: 38970402 DOI: 10.1002/alz.14103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 06/05/2024] [Accepted: 06/06/2024] [Indexed: 07/08/2024]
Abstract
INTRODUCTION We aimed to unravel the underlying pathophysiology of the neurodegeneration (N) markers neurogranin (Ng), neurofilament light (NfL), and hippocampal volume (HCV), in Alzheimer's disease (AD) using cerebrospinal fluid (CSF) proteomics. METHODS Individuals without dementia were classified as A+ (CSF amyloid beta [Aβ]42), T+ (CSF phosphorylated tau181), and N+ or N- based on Ng, NfL, or HCV separately. CSF proteomics were generated and compared between groups using analysis of covariance. RESULTS Only a few individuals were A+T+Ng-. A+T+Ng+ and A+T+NfL+ showed different proteomic profiles compared to A+T+Ng- and A+T+NfL-, respectively. Both Ng+ and NfL+ were associated with neuroplasticity, though in opposite directions. Compared to A+T+HCV-, A+T+HCV+ showed few proteomic changes, associated with oxidative stress. DISCUSSION Different N markers are associated with distinct neurodegenerative processes and should not be equated. N markers may differentially complement disease staging beyond amyloid and tau. Our findings suggest that Ng may not be an optimal N marker, given its low incongruency with tau pathophysiology. HIGHLIGHTS In Alzheimer's disease, neurogranin (Ng)+, neurofilament light (NfL)+, and hippocampal volume (HCV)+ showed differential protein expression in cerebrospinal fluid. Ng+ and NfL+ were associated with neuroplasticity, although in opposite directions. HCV+ showed few proteomic changes, related to oxidative stress. Neurodegeneration (N) markers may differentially refine disease staging beyond amyloid and tau. Ng might not be an optimal N marker, as it relates more closely to tau.
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Affiliation(s)
- Aurore Delvenne
- Department of Psychiatry and Neuropsychology, Alzheimer Centrum Limburg, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands
| | - Johan Gobom
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
| | - Suzanne E Schindler
- Department of Neurology, Washington University School of Medicine, St. Louis, Missouri, USA
- Knight Alzheimer's Disease Research Center, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Mara Ten Kate
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
- Department of Radiology and Nuclear Medicine, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
| | - Lianne M Reus
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
| | - Valerija Dobricic
- Lübeck Interdisciplinary Platform for Genome Analytics, University of Lübeck, Lübeck, Germany
| | - Betty M Tijms
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
| | - Tammie L S Benzinger
- Department of Radiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Charlotte E Teunissen
- Neurochemistry Laboratory, Department of Clinical Chemistry, Amsterdam University Medical Centers (AUMC), Amsterdam Neuroscience, Amsterdam, the Netherlands
| | - Inez Ramakers
- Department of Psychiatry and Neuropsychology, Alzheimer Centrum Limburg, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands
| | | | - Mikel Tainta
- Fundación CITA-Alzhéimer Fundazioa, Donostia, Spain
| | - Rik Vandenberghe
- Neurology Service, University Hospitals Leuven, Leuven, Belgium
- Laboratory for Cognitive Neurology, Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Jolien Schaeverbeke
- Neurology Service, University Hospitals Leuven, Leuven, Belgium
- Laboratory for Cognitive Neurology, Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Sebastiaan Engelborghs
- Reference Center for Biological Markers of Dementia (BIODEM), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- Department of Neurology and Bru-BRAIN, Universitair Ziekenhuis Brussel and NEUR Research Group, Center for Neurosciences (C4N), Vrije Universiteit Brussel, Brussels, Belgium
| | - Ellen De Roeck
- Reference Center for Biological Markers of Dementia (BIODEM), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- Department of Neurology and Memory Clinic, Hospital Network Antwerp (ZNA) Middelheim and Hoge Beuken, Antwerp, Belgium
| | - Julius Popp
- Old Age Psychiatry, University Hospital Lausanne, Lausanne, Switzerland
- Department of Psychiatry, Psychotherapy and Psychosomatics, Psychiatry University Hospital Zürich, Zürich, Switzerland
| | | | - Magda Tsolaki
- 1st Department of Neurology, AHEPA University Hospital, Medical School, Faculty of Health Sciences, Aristotle University of Thessaloniki, Makedonia, Thessaloniki, Greece
| | - Yvonne Freund-Levi
- Department of Neurobiology, Caring Sciences and Society (NVS), Division of Clinical Geriatrics, Karolinska Institutet, Huddinge, Stockholm, Sweden
- Department of Psychiatry in Region Örebro County and School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
- Department of Old Age Psychiatry, Psychology & Neuroscience, King's College, London, UK
| | - Simon Lovestone
- University of Oxford, United Kingdom (currently at Johnson and Johnson Medical Ltd., Oxford, UK
| | - Johannes Streffer
- Reference Center for Biological Markers of Dementia (BIODEM), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- H. Lundbeck A/S, Valby, Denmark
| | - Frederik Barkhof
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
- Queen Square Institute of Neurology and Centre for Medical Image Computing, University College London, London, UK
| | - Lars Bertram
- Lübeck Interdisciplinary Platform for Genome Analytics, University of Lübeck, Lübeck, Germany
| | - Kaj Blennow
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
- Paris Brain Institute, ICM, Pitié-Salpêtrière Hospital, Sorbonne University, Paris, France
- Neurodegenerative Disorder Research Center, Division of Life Sciences and Medicine, and Department of Neurology, Institute on Aging and Brain Disorders, University of Science and Technology of China and First Affiliated Hospital of USTC, Hefei, P.R. China
| | - Henrik Zetterberg
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, UK
- UK Dementia Research Institute at UCL, London, UK
- Hong Kong Center for Neurodegenerative Diseases, Clear Water Bay, Hong Kong, China
- Wisconsin Alzheimer's Disease Research Center, University of Wisconsin School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Pieter Jelle Visser
- Department of Psychiatry and Neuropsychology, Alzheimer Centrum Limburg, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Stephanie J B Vos
- Department of Psychiatry and Neuropsychology, Alzheimer Centrum Limburg, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands
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Yoshida H. Dissecting the Immune System through Gene Regulation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1444:219-235. [PMID: 38467983 DOI: 10.1007/978-981-99-9781-7_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
The immune system plays a dual role in human health, functioning both as a protector against pathogens and, at times, as a contributor to disease. This feature emphasizes the importance to uncover the underlying causes of its malfunctions, necessitating an in-depth analysis in both pathological and physiological conditions to better understand the immune system and immune disorders. Recent advances in scientific technology have enabled extensive investigations into gene regulation, a crucial mechanism governing cellular functionality. Studying gene regulatory mechanisms within the immune system is a promising avenue for enhancing our understanding of immune cells and the immune system as a whole. The gene regulatory mechanisms, revealed through various methodologies, and their implications in the field of immunology are discussed in this chapter.
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Affiliation(s)
- Hideyuki Yoshida
- YCI Laboratory for Immunological Transcriptomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
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Russell ND, Jorde LB, Chow CY. Characterizing genetic variation in the regulation of the ER stress response through computational and cis-eQTL analyses. G3 (BETHESDA, MD.) 2023; 13:jkad229. [PMID: 37792690 PMCID: PMC10700025 DOI: 10.1093/g3journal/jkad229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 08/17/2023] [Accepted: 09/27/2023] [Indexed: 10/06/2023]
Abstract
Misfolded proteins in the endoplasmic reticulum (ER) elicit the ER stress response, a large transcriptional response driven by 3 well-characterized transcription factors (TFs). This transcriptional response is variable across different genetic backgrounds. One mechanism in which genetic variation can lead to transcriptional variability in the ER stress response is through altered binding and activity of the 3 main TFs: XBP1, ATF6, and ATF4. This work attempts to better understand this mechanism by first creating a computational pipeline to identify potential binding sites throughout the human genome. We utilized GTEx data sets to identify cis-eQTLs that fall within predicted TF binding sites (TFBSs). We also utilized the ClinVar database to compare the number of pathogenic vs benign variants at different positions of the binding motifs. Finally, we performed a cis-eQTL analysis on human cell lines experiencing ER stress to identify cis-eQTLs that regulate the variable ER stress response. The majority of these cis-eQTLs are unique to a given condition: control or ER stress. Some of these stress-specific cis-eQTLs fall within putative binding sites of the 3 main ER stress response TFs, providing a potential mechanism by which these cis-eQTLs might be impacting gene expression under ER stress conditions through altered TF binding. This study represents the first cis-eQTL analysis on human samples experiencing ER stress and is a vital step toward identifying the genetic components responsible for the variable ER stress response.
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Affiliation(s)
- Nikki D Russell
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Lynn B Jorde
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Clement Y Chow
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
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Delvenne A, Gobom J, Tijms B, Bos I, Reus LM, Dobricic V, Kate MT, Verhey F, Ramakers I, Scheltens P, Teunissen CE, Vandenberghe R, Schaeverbeke J, Gabel S, Popp J, Peyratout G, Martinez-Lage P, Tainta M, Tsolaki M, Freund-Levi Y, Lovestone S, Streffer J, Barkhof F, Bertram L, Blennow K, Zetterberg H, Visser PJ, Vos SJB. Cerebrospinal fluid proteomic profiling of individuals with mild cognitive impairment and suspected non-Alzheimer's disease pathophysiology. Alzheimers Dement 2023; 19:807-820. [PMID: 35698882 DOI: 10.1002/alz.12713] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 04/06/2022] [Accepted: 05/12/2022] [Indexed: 11/09/2022]
Abstract
BACKGROUND Suspected non-Alzheimer's disease pathophysiology (SNAP) is a biomarker concept that encompasses individuals with neuronal injury but without amyloidosis. We aim to investigate the pathophysiology of SNAP, defined as abnormal tau without amyloidosis, in individuals with mild cognitive impairment (MCI) by cerebrospinal fluid (CSF) proteomics. METHODS Individuals were classified based on CSF amyloid beta (Aβ)1-42 (A) and phosphorylated tau (T), as cognitively normal A-T- (CN), MCI A-T+ (MCI-SNAP), and MCI A+T+ (MCI-AD). Proteomics analyses, Gene Ontology (GO), brain cell expression, and gene expression analyses in brain regions of interest were performed. RESULTS A total of 96 proteins were decreased in MCI-SNAP compared to CN and MCI-AD. These proteins were enriched for extracellular matrix (ECM), hemostasis, immune system, protein processing/degradation, lipids, and synapse. Fifty-one percent were enriched for expression in the choroid plexus. CONCLUSION The pathophysiology of MCI-SNAP (A-T+) is distinct from that of MCI-AD. Our findings highlight the need for a different treatment in MCI-SNAP compared to MCI-AD.
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Affiliation(s)
- Aurore Delvenne
- Department of Psychiatry and Neuropsychology, Alzheimer Centrum Limburg, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands
| | - Johan Gobom
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
| | - Betty Tijms
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, the Netherlands
| | - Isabelle Bos
- Department of Psychiatry and Neuropsychology, Alzheimer Centrum Limburg, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, the Netherlands
| | - Lianne M Reus
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, the Netherlands
| | - Valerija Dobricic
- Lübeck Interdisciplinary Platform for Genome Analytics, University of Lübeck, Lübeck, Germany
| | - Mara Ten Kate
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, the Netherlands
- Department of Radiology and Nuclear Medicine, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
| | - Frans Verhey
- Department of Psychiatry and Neuropsychology, Alzheimer Centrum Limburg, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands
| | - Inez Ramakers
- Department of Psychiatry and Neuropsychology, Alzheimer Centrum Limburg, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands
| | - Philip Scheltens
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, the Netherlands
| | - Charlotte E Teunissen
- Neurochemistry Laboratory, Department of Clinical Chemistry, Amsterdam University Medical Centers (AUMC), Amsterdam Neuroscience, the Netherlands
| | - Rik Vandenberghe
- Neurology Service, University Hospitals Leuven, Leuven, Belgium
- Laboratory for Cognitive Neurology, Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Jolien Schaeverbeke
- Neurology Service, University Hospitals Leuven, Leuven, Belgium
- Laboratory for Cognitive Neurology, Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Silvy Gabel
- Neurology Service, University Hospitals Leuven, Leuven, Belgium
- Laboratory for Cognitive Neurology, Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Julius Popp
- Old Age Psychiatry, University Hospital Lausanne, Lausanne, Switzerland
- Department of Geriatric Psychiatry, Psychiatry University Hospital Zürich, Zürich, Switzerland
| | | | | | - Mikel Tainta
- Fundación CITA-Alzhéimer Fundazioa, San Sebastian, Spain
| | - Magda Tsolaki
- 1st Department of Neurology, AHEPA University Hospital, Medical School, Faculty of Health Sciences, Aristotle University of Thessaloniki, Makedonia, Thessaloniki, Greece
| | - Yvonne Freund-Levi
- Department of Neurobiology, Caring Sciences and Society (NVS), Division of Clinical Geriatrics, Karolinska Institutet, Stockholm, Sweden
- Department of Psychiatry in Region Örebro County and School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
- Department of Old Age Psychiatry, Psychology & Neuroscience, King's College, London, UK
| | - Simon Lovestone
- University of Oxford, Oxford, United Kingdom (currently at Johnson and Johnson Medical Ltd.), London, UK
| | - Johannes Streffer
- Institute Born-Bunge, Reference Center for Biological Markers of Dementia (BIODEM), Institute Born-Bunge, University of Antwerp, Belgium
- UCB Biopharma SPRL, Brain-l'Alleud, Belgium
| | - Frederik Barkhof
- Department of Radiology and Nuclear Medicine, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
- Institutes of Neurology & Healthcare Engineering, UCL London, London, UK
| | - Lars Bertram
- Lübeck Interdisciplinary Platform for Genome Analytics, University of Lübeck, Lübeck, Germany
- Center for Lifespan Changes in Brain and Cognition, Department of Psychology, University of Oslo, Oslo, Norway
| | - Kaj Blennow
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
| | - Henrik Zetterberg
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, UK
- UK Dementia Research Institute at UCL, London, UK
| | - Pieter Jelle Visser
- Department of Psychiatry and Neuropsychology, Alzheimer Centrum Limburg, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, the Netherlands
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Karolinska Institutet, Stockholm, Sweden
| | - Stephanie J B Vos
- Department of Psychiatry and Neuropsychology, Alzheimer Centrum Limburg, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands
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Impact of Maternal Feed Restriction at Different Stages of Gestation on the Proteomic Profile of the Newborn Skeletal Muscle. Animals (Basel) 2022; 12:ani12081011. [PMID: 35454257 PMCID: PMC9031497 DOI: 10.3390/ani12081011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 04/08/2022] [Accepted: 04/11/2022] [Indexed: 11/17/2022] Open
Abstract
We aimed to investigate the effects of the maternal plane of nutrition during gestation on the proteome profile of the skeletal muscle of the newborn. Pregnant goats were assigned to the following experimental treatments: restriction maintenance (RM) where pregnant dams were fed at 50% of their maintenance requirements from 8−84 days of gestation, and then feed of 100% of the maintenance requirements was supplied from 85—parturition (n = 6); maintenance restriction (MR) where pregnant dams were fed at 100% of their maintenance requirements from 8−84 days of gestation, and then experienced feed restriction of 50% of the maintenance requirements from 85—parturition (n = 8). At birth, newborns were euthanized and samples of the Longissimus dorsi muscle were collected and used to perform HPLC-MS/MS analysis. The network analyses were performed to identify the biological processes and KEGG pathways of the proteins identified as differentially abundant protein and were deemed significant when the adjusted p-value (FDR) < 0.05. Our results suggest that treatment RM affects the energy metabolism of newborns’ skeletal muscle by changing the energy-investment phase of glycolysis, in addition to utilizing glycogen as a carbon source. Moreover, the RM plane of nutrition may contribute to fatty acid oxidation and increases in the cytosolic α-KG and mitochondrial NADH levels in the skeletal muscle of the newborn. On the other hand, treatment MR likely affects the energy-generation phase of glycolysis, contributing to the accumulation of mitochondrial α-KG and the biosynthesis of glutamine.
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Pimsler ML, Hjelmen CE, Jonika MM, Sharma A, Fu S, Bala M, Sze SH, Tomberlin JK, Tarone AM. Sexual Dimorphism in Growth Rate and Gene Expression Throughout Immature Development in Wild Type Chrysomya rufifacies (Diptera: Calliphoridae) Macquart. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.696638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Reliability of forensic entomology analyses to produce relevant information to a given case requires an understanding of the underlying arthropod population(s) of interest and the factors contributing to variability. Common traits for analyses are affected by a variety of genetic and environmental factors. One trait of interest in forensic investigations has been species-specific temperature-dependent growth rates. Recent work indicates sexual dimorphism may be important in the analysis of such traits and related genetic markers of age. However, studying sexual dimorphic patterns of gene expression throughout immature development in wild-type insects can be difficult due to a lack of genetic tools, and the limits of most sex-determination mechanisms. Chrysomya rufifacies, however, is a particularly tractable system to address these issues as it has a monogenic sex determination system, meaning females have only a single-sex of offspring throughout their life. Using modified breeding procedures (to ensure single-female egg clutches) and transcriptomics, we investigated sexual dimorphism in development rate and gene expression. Females develop slower than males (9 h difference from egg to eclosion respectively) even at 30°C, with an average egg-to-eclosion time of 225 h for males and 234 h for females. Given that many key genes rely on sex-specific splicing for the development and maintenance of sexually dimorphic traits, we used a transcriptomic approach to identify different expression of gene splice variants. We find that 98.4% of assembled nodes exhibited sex-specific, stage-specific, to sex-by-stage specific patterns of expression. However, the greatest signal in the expression data is differentiation by developmental stage, indicating that sexual dimorphism in gene expression during development may not be investigatively important and that markers of age may be relatively independent of sex. Subtle differences in these gene expression patterns can be detected as early as 4 h post-oviposition, and 12 of these nodes demonstrate homology with key Drosophila sex determination genes, providing clues regarding the distinct sex determination mechanism of C. rufifacies. Finally, we validated the transcriptome analyses through qPCR and have identified five genes that are developmentally informative within and between sexes.
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Costa TC, Mendes TA, Fontes MM, Lopes MM, Du M, Serão NV, Sanglard LM, Bertolini F, Rothschild MF, Silva FF, Gionbelli MP, Duarte M. Transcriptome changes in newborn goats’ skeletal muscle as a result of maternal feed restriction at different stages of gestation. Livest Sci 2021. [DOI: 10.1016/j.livsci.2021.104503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Suresh NT, Ravindran VE, Krishnakumar U. A Computational Framework to Identify Cross Association Between Complex Disorders by Protein-protein Interaction Network Analysis. Curr Bioinform 2021. [DOI: 10.2174/1574893615999200724145434] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Objective:
It is a known fact that numerous complex disorders do not happen in
isolation indicating the plausible set of shared causes common to several different sicknesses.
Hence, analysis of comorbidity can be utilized to explore the association between several
disorders. In this study, we have proposed a network-based computational approach, in which
genes are organized based on the topological characteristics of the constructed Protein-Protein
Interaction Network (PPIN) followed by a network prioritization scheme, to identify distinctive
key genes and biological pathways shared among diseases.
Methods:
The proposed approach is initiated from constructed PPIN of any randomly chosen
disease genes in order to infer its associations with other diseases in terms of shared pathways, coexpression,
co-occurrence etc. For this, initially, proteins associated to any disease based on
random choice were identified. Secondly, PPIN is organized through topological analysis to define
hub genes. Finally, using a prioritization algorithm a ranked list of newly predicted
multimorbidity-associated proteins is generated. Using Gene Ontology (GO), cellular pathways
involved in multimorbidity-associated proteins are mined.
Result and Conclusion:
: The proposed methodology is tested using three disorders, namely
Diabetes, Obesity and blood pressure at an atomic level and the results suggest the comorbidity of
other complex diseases that have associations with the proteins included in the disease of present
study through shared proteins and pathways. For diabetes, we have obtained key genes like
GAPDH, TNF, IL6, AKT1, ALB, TP53, IL10, MAPK3, TLR4 and EGF with key pathways like
P53 pathway, VEGF signaling pathway, Ras Pathway, Interleukin signaling pathway, Endothelin
signaling pathway, Huntington disease etc. Studies on other disorders such as obesity and blood
pressure also revealed promising results.
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Affiliation(s)
- Nikhila T. Suresh
- Department of Computer Science and IT, Amrita School of Arts and Sciences, Amrita Vishwa Vidyapeetham, Kochi Campus, Kochi, India
| | - Vimina E. Ravindran
- Department of Computer Science and IT, Amrita School of Arts and Sciences, Amrita Vishwa Vidyapeetham, Kochi Campus, Kochi, India
| | - Ullattil Krishnakumar
- Department of Computer Science and IT, Amrita School of Arts and Sciences, Amrita Vishwa Vidyapeetham, Kochi Campus, Kochi, India
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Mitterboeck TF, Liu S, Adamowicz SJ, Fu J, Zhang R, Song W, Meusemann K, Zhou X. Positive and relaxed selection associated with flight evolution and loss in insect transcriptomes. Gigascience 2018; 6:1-14. [PMID: 29020740 PMCID: PMC5632299 DOI: 10.1093/gigascience/gix073] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 08/01/2017] [Indexed: 12/31/2022] Open
Abstract
The evolution of powered flight is a major innovation that has facilitated the success of insects. Previously, studies of birds, bats, and insects have detected molecular signatures of differing selection regimes in energy-related genes associated with flight evolution and/or loss. Here, using DNA sequences from more than 1000 nuclear and mitochondrial protein-coding genes obtained from insect transcriptomes, we conduct a broader exploration of which gene categories display positive and relaxed selection at the origin of flight as well as with multiple independent losses of flight. We detected a number of categories of nuclear genes more often under positive selection in the lineage leading to the winged insects (Pterygota), related to catabolic processes such as proteases, as well as splicing-related genes. Flight loss was associated with relaxed selection signatures in splicing genes, mirroring the results for flight evolution. Similar to previous studies of flight loss in various animal taxa, we observed consistently higher nonsynonymous-to-synonymous substitution ratios in mitochondrial genes of flightless lineages, indicative of relaxed selection in energy-related genes. While oxidative phosphorylation genes were not detected as being under selection with the origin of flight specifically, they were most often detected as being under positive selection in holometabolous (complete metamorphosis) insects as compared with other insect lineages. This study supports some convergence in gene-specific selection pressures associated with flight ability, and the exploratory analysis provided some new insights into gene categories potentially associated with the gain and loss of flight in insects.
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Affiliation(s)
- T Fatima Mitterboeck
- Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1 Canada.,Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1 Canada
| | - Shanlin Liu
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong Province, 518083 China.,Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Sarah J Adamowicz
- Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1 Canada.,Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1 Canada
| | - Jinzhong Fu
- Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1 Canada
| | - Rui Zhang
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong Province, 518083 China
| | - Wenhui Song
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong Province, 518083 China
| | - Karen Meusemann
- University of Freiburg, Department for Biology I (Zoology), Evolutionary Biology and Ecology, Hauptstr. 1, D-79104 Freiburg, Germany.,Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 53113 Bonn, Germany.,Australian National Insect Collection CSIRO, Natl Collections & Marine Infrastructure, Clunies Ross Street, ACTON, 2601 ACT, Canberra, Australia
| | - Xin Zhou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, 2 West Yuanmingyuan Rd., Haidian District, Beijing 100193, China.,College of Plant Protection, China Agricultural University, 2 West Yuanmingyuan Rd., Haidian District, Beijing 100193, China
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10
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Pita-Juárez Y, Altschuler G, Kariotis S, Wei W, Koler K, Green C, Tanzi RE, Hide W. The Pathway Coexpression Network: Revealing pathway relationships. PLoS Comput Biol 2018; 14:e1006042. [PMID: 29554099 PMCID: PMC5875878 DOI: 10.1371/journal.pcbi.1006042] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Revised: 03/29/2018] [Accepted: 02/19/2018] [Indexed: 02/02/2023] Open
Abstract
A goal of genomics is to understand the relationships between biological processes. Pathways contribute to functional interplay within biological processes through complex but poorly understood interactions. However, limited functional references for global pathway relationships exist. Pathways from databases such as KEGG and Reactome provide discrete annotations of biological processes. Their relationships are currently either inferred from gene set enrichment within specific experiments, or by simple overlap, linking pathway annotations that have genes in common. Here, we provide a unifying interpretation of functional interaction between pathways by systematically quantifying coexpression between 1,330 canonical pathways from the Molecular Signatures Database (MSigDB) to establish the Pathway Coexpression Network (PCxN). We estimated the correlation between canonical pathways valid in a broad context using a curated collection of 3,207 microarrays from 72 normal human tissues. PCxN accounts for shared genes between annotations to estimate significant correlations between pathways with related functions rather than with similar annotations. We demonstrate that PCxN provides novel insight into mechanisms of complex diseases using an Alzheimer’s Disease (AD) case study. PCxN retrieved pathways significantly correlated with an expert curated AD gene list. These pathways have known associations with AD and were significantly enriched for genes independently associated with AD. As a further step, we show how PCxN complements the results of gene set enrichment methods by revealing relationships between enriched pathways, and by identifying additional highly correlated pathways. PCxN revealed that correlated pathways from an AD expression profiling study include functional clusters involved in cell adhesion and oxidative stress. PCxN provides expanded connections to pathways from the extracellular matrix. PCxN provides a powerful new framework for interrogation of global pathway relationships. Comprehensive exploration of PCxN can be performed at http://pcxn.org/. Genes do not function alone, but interact within pathways to carry out specific biological processes. Pathways, in turn, interact at a higher level to affect major cellular activities such as motility, growth and development. We present a pathway coexpression network (PCxN) that systematically maps and quantifies these high-level interactions and establishes a unifying reference for pathway relationships. The method uses 3,207 human microarrays from 72 normal human tissues and 1,330 of the most well established pathway annotations to describe global relationships between pathways. PCxN accounts for shared genes to estimate correlations between pathways with related functions rather than with redundant pathway definitions. PCxN can be used to discover and explore pathways correlated with a pathway of interest. We applied PCxN to identify key processes related to Alzheimer’s disease (AD), interpreting a mixed genetic association and experimental derived set of disease genes in the context of gene co-expression. We expand the known relationships between pathways identified by gene set enrichment analysis in brain tissues affected with AD. PCxN provides a high-level overview of pathway relationships. PCxN is available as a webtool at http://pcxn.org/, and as a Bioconductor package at http://bioconductor.org/packages/pcxn/.
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Affiliation(s)
- Yered Pita-Juárez
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, United States of America
| | - Gabriel Altschuler
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, Sheffield, United Kingdom
| | - Sokratis Kariotis
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, Sheffield, United Kingdom
| | - Wenbin Wei
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, Sheffield, United Kingdom
| | - Katjuša Koler
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, Sheffield, United Kingdom
| | - Claire Green
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, Sheffield, United Kingdom
| | - Rudolph E. Tanzi
- Genetics and Aging Research Unit, MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts, United States of America
| | - Winston Hide
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, United States of America
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, Sheffield, United Kingdom
- Harvard Stem Cell Institute, Cambridge, Massachusetts, United States of America
- National Institute Health Research, Sheffield Biomedical Research Centre, Sheffield, United Kingdom
- * E-mail:
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11
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Cantini L, Calzone L, Martignetti L, Rydenfelt M, Blüthgen N, Barillot E, Zinovyev A. Classification of gene signatures for their information value and functional redundancy. NPJ Syst Biol Appl 2017; 4:2. [PMID: 29263798 PMCID: PMC5736638 DOI: 10.1038/s41540-017-0038-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 11/15/2017] [Accepted: 11/21/2017] [Indexed: 12/21/2022] Open
Abstract
Gene signatures are more and more used to interpret results of omics data analyses but suffer from compositional (large overlap) and functional (correlated read-outs) redundancy. Moreover, many gene signatures rarely come out as significant in statistical tests. Based on pan-cancer data analysis, we construct a restricted set of 962 signatures defined as informative and demonstrate that they have a higher probability to appear enriched in comparative cancer studies. We show that the majority of informative signatures conserve their weights for the genes composing the signature (eigengenes) from one cancer type to another. We finally construct InfoSigMap, an interactive online map of these signatures and their cross-correlations. This map highlights the structure of compositional and functional redundancies between informative signatures, and it charts the territories of biological functions. InfoSigMap can be used to visualize the results of omics data analyses and suggests a rearrangement of existing gene sets. An informative collection of gene signatures for transcriptomic data analysis is constructed. The number of transcriptomic signatures grows fast and their collections are highly redundant that hampers omics data analyses interpretation. A computational biology team from Institut Curie led by Andrei Zinovyev selected a collection of 962 gene signatures shown to be informative for cancer studies and reflecting mechanisms of cancer progression. The signatures were filtered from a large compendium without requiring any manual curation by experts through a large-scale unbiased analysis of pancancer data. They have much higher chance to obtain significant enrichment scores in a comparative trancriptomic study. The authors integrated the 962 signatures into InfoSigMap, a new data visualization resource for the interpretation of the results of omics data analyses, which facilitates getting an insight into the mechanisms driving cancer.
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Affiliation(s)
- Laura Cantini
- Institut Curie, PSL Research University, INSERM U900, Mines ParisTech, 26, rue d'Ulm, F-75248 Paris, France
| | - Laurence Calzone
- Institut Curie, PSL Research University, INSERM U900, Mines ParisTech, 26, rue d'Ulm, F-75248 Paris, France
| | - Loredana Martignetti
- Institut Curie, PSL Research University, INSERM U900, Mines ParisTech, 26, rue d'Ulm, F-75248 Paris, France
| | - Mattias Rydenfelt
- Institute of Pathology, Charite Universitätsmedizin Berlin, Chariteplatz 1, 10117 Berlin, Germany.,IRI Life Sciences and Institute for Theoretical Biology, Humboldt University, Philippstr. 13, Haus 18, 10115 Berlin, Germany
| | - Nils Blüthgen
- Institute of Pathology, Charite Universitätsmedizin Berlin, Chariteplatz 1, 10117 Berlin, Germany.,IRI Life Sciences and Institute for Theoretical Biology, Humboldt University, Philippstr. 13, Haus 18, 10115 Berlin, Germany
| | - Emmanuel Barillot
- Institut Curie, PSL Research University, INSERM U900, Mines ParisTech, 26, rue d'Ulm, F-75248 Paris, France
| | - Andrei Zinovyev
- Institut Curie, PSL Research University, INSERM U900, Mines ParisTech, 26, rue d'Ulm, F-75248 Paris, France
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12
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Meijer RJ, Goeman JJ. Multiple Testing of Gene Sets from Gene Ontology: Possibilities and Pitfalls. Brief Bioinform 2015; 17:808-18. [DOI: 10.1093/bib/bbv091] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Indexed: 11/14/2022] Open
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13
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Tan Y, Wu F, Tamayo P, Haining WN, Mesirov JP. Constellation Map: Downstream visualization and interpretation of gene set enrichment results. F1000Res 2015; 4:167. [PMID: 26594333 PMCID: PMC4648224 DOI: 10.12688/f1000research.6644.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/19/2015] [Indexed: 12/17/2022] Open
Abstract
Summary: Gene set enrichment analysis (GSEA) approaches are widely used to identify coordinately regulated genes associated with phenotypes of interest. Here, we present Constellation Map, a tool to visualize and interpret the results when enrichment analyses yield a long list of significantly enriched gene sets. Constellation Map identifies commonalities that explain the enrichment of multiple top-scoring gene sets and maps the relationships between them. Constellation Map can help investigators take full advantage of GSEA and facilitates the biological interpretation of enrichment results. Availability: Constellation Map is freely available as a GenePattern module at
http://www.genepattern.org.
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Affiliation(s)
- Yan Tan
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Bioinformatics Program, Boston University, Boston, MA, 02215, USA
| | - Felix Wu
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Pablo Tamayo
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - W Nicholas Haining
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, 02215, USA.,Division of Hematology/Oncology, Children's Hospital, Harvard Medical School, Boston, MA, 02215, USA
| | - Jill P Mesirov
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Bioinformatics Program, Boston University, Boston, MA, 02215, USA
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14
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Cao J, Zhang S. A Bayesian extension of the hypergeometric test for functional enrichment analysis. Biometrics 2013; 70:84-94. [PMID: 24320951 DOI: 10.1111/biom.12122] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2012] [Revised: 09/01/2013] [Accepted: 10/01/2013] [Indexed: 11/28/2022]
Abstract
Functional enrichment analysis is conducted on high-throughput data to provide functional interpretation for a list of genes or proteins that share a common property, such as being differentially expressed (DE). The hypergeometric P-value has been widely used to investigate whether genes from pre-defined functional terms, for example, Gene Ontology (GO), are enriched in the DE genes. The hypergeometric P-value has three limitations: (1) computed independently for each term, thus neglecting biological dependence; (2) subject to a size constraint that leads to the tendency of selecting less-specific terms; (3) repeated use of information due to overlapping annotations by the true-path rule. We propose a Bayesian approach based on the non-central hypergeometric model. The GO dependence structure is incorporated through a prior on non-centrality parameters. The likelihood function does not include overlapping information. The inference about enrichment is based on posterior probabilities that do not have a size constraint. This method can detect moderate but consistent enrichment signals and identify sets of closely related and biologically meaningful functional terms rather than isolated terms. We also describe the basic ideas of assumption and implementation of different methods to provide some theoretical insights, which are demonstrated via a simulation study. A real application is presented.
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Affiliation(s)
- Jing Cao
- Department of Statistical Science, Southern Methodist University, Dallas, Texas 75275, U.S.A
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15
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Heng SSJ, Chan OYW, Keng BMH, Ling MHT. Glucan Biosynthesis Protein G Is a Suitable Reference Gene in Escherichia coli K-12. ISRN MICROBIOLOGY 2011; 2011:469053. [PMID: 23724305 PMCID: PMC3658596 DOI: 10.5402/2011/469053] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Accepted: 10/13/2011] [Indexed: 11/24/2022]
Abstract
The expressions of reference genes used in gene expression studies are assumed to be stable under most circumstances. However, a number of studies had demonstrated that such genes were found to vary under experimental conditions. In addition, genes that are stably expressed in an organ may not be stably expressed in other organs or other organisms, suggesting the need to identify reference genes for each organ and organism. This study aims at identifying stably expressed genes in Escherichia coli. Microarray datasets from E. coli substrain MG1655 and 1 dataset from W3110 were analysed. Coefficient of variance (COV) of was calculated and 10% of the lowest COV from 4631 genes common in the 3 MG1655 sets were analysed using NormFinder. Glucan biosynthesis protein G (mdoG), which is involved in cell wall synthesis, displayed the lowest weighted COV and weighted NormFinder Stability Index for the MG1655 datasets, while also showing to be the most stable in the dataset for substrain W3110, suggesting that mdoG is a suitable reference gene for E. coli K-12. Gene ontology over-representation analysis on the 39 genes suggested an over-representation of cell division, carbohydrate metabolism, and protein synthesis which supports the short generation time of E. coli.
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Affiliation(s)
- Sean S J Heng
- Raffles Institution, One Raffles Institution Lane, Singapore 575954
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16
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Ponomarenko EA, Il'gisonis EV, Lisitsa AV. [Knowledge-based technologies in proteomics]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2011; 37:190-8. [PMID: 21721252 DOI: 10.1134/s1068162011020129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Proteomic technologies enable to identify thousands of proteins in biological samples. These data require appropriate means for storage, dissemination and analytical processing to decipher the new knowledge. Automatic processing of high-efficient experiment results is powered by the controlled vocabularies, such as Medical Subjects Headings and GeneOntology. While ontology and vocabularies undergo constant evolution, it is necessary to provide the centralized storage of proteomic data for further revision in accordance with the updated knowledge domain. Proteomic repositories like PRIDE, The Global Proteome Machine, PeptideAtlas etc. are available to harbor the wealth of mass spectral data and appropriate protein identifications. The existing repositories facilitate the development of knowledge extraction technologies to compare the list of identified proteins with the GeneOntology annotations, Medical Subjects Headings, metabolic and regulatory pathways. This paper reviews modern analytical tools that exploit the knowledge-based technologies for proteome research.
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17
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Abe D, Kubota T, Morozumi T, Shimizu T, Nakasone N, Itagaki M, Yoshie H. Altered gene expression in leukocyte transendothelial migration and cell communication pathways in periodontitis-affected gingival tissues. J Periodontal Res 2011; 46:345-53. [PMID: 21382035 DOI: 10.1111/j.1600-0765.2011.01349.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
BACKGROUND AND OBJECTIVE Gene expression is related to the pathogenesis of periodontitis and plays a crucial role in local tissue destruction and disease susceptibility. The aims of the present study were to identify the expression of specific genes and biological pathways in periodontitis-affected gingival tissue using microarray and quantitative real-time RT-PCR analyses. MATERIAL AND METHODS Healthy and periodontitis-affected gingival tissues were taken from three patients with severe chronic periodontitis. Total RNAs from six gingival tissue samples were used for microarray analyses. Data-mining analyses, such as comparisons, gene ontology and pathway analyses, were performed and biological pathways with a significant role in periodontitis were identified. In addition, quantitative real-time RT-PCR analysis was performed on samples obtained from 14 patients with chronic periodontitis and from 14 healthy individuals in order to confirm the results of the pathway analysis. RESULTS Comparison analyses found 15 up-regulated and 13 down-regulated genes (all of which showed a change of more than twofold in expression levels) in periodontitis-affected gingival tissues. Pathway analysis identified 15 up-regulated biological pathways, including leukocyte transendothelial migration, and five down-regulated pathways, including cell communication. Quantitative real-time RT-PCR verified that five genes in the leukocyte transendothelial migration pathway were significantly up-regulated, and four genes in the cell communication pathway were significantly down-regulated, which was consistent with pathway analysis. CONCLUSION We identified up-regulated genes (ITGB-2, MMP-2, CXCL-12, CXCR-4 and Rac-2) and down-regulated genes (connexin, DSG-1, DSC-1 and nestin) in periodontitis-affected gingival tissues; these genes may be related to the stimulation of leukocyte transendothelial migration and to the the impairment of cell-to-cell communication in periodontitis.
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Affiliation(s)
- D Abe
- Division of Periodontology, Department of Oral Biological Science, Niigata University Graduate School of Medical and Dental Sciences, Japan
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18
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Merico D, Isserlin R, Stueker O, Emili A, Bader GD. Enrichment map: a network-based method for gene-set enrichment visualization and interpretation. PLoS One 2010; 5:e13984. [PMID: 21085593 PMCID: PMC2981572 DOI: 10.1371/journal.pone.0013984] [Citation(s) in RCA: 1572] [Impact Index Per Article: 112.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2010] [Accepted: 10/20/2010] [Indexed: 12/13/2022] Open
Abstract
Background Gene-set enrichment analysis is a useful technique to help functionally characterize large gene lists, such as the results of gene expression experiments. This technique finds functionally coherent gene-sets, such as pathways, that are statistically over-represented in a given gene list. Ideally, the number of resulting sets is smaller than the number of genes in the list, thus simplifying interpretation. However, the increasing number and redundancy of gene-sets used by many current enrichment analysis software works against this ideal. Principal Findings To overcome gene-set redundancy and help in the interpretation of large gene lists, we developed “Enrichment Map”, a network-based visualization method for gene-set enrichment results. Gene-sets are organized in a network, where each set is a node and edges represent gene overlap between sets. Automated network layout groups related gene-sets into network clusters, enabling the user to quickly identify the major enriched functional themes and more easily interpret the enrichment results. Conclusions Enrichment Map is a significant advance in the interpretation of enrichment analysis. Any research project that generates a list of genes can take advantage of this visualization framework. Enrichment Map is implemented as a freely available and user friendly plug-in for the Cytoscape network visualization software (http://baderlab.org/Software/EnrichmentMap/).
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Affiliation(s)
- Daniele Merico
- Department of Molecular Genetics, Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- * E-mail: (GDB); (DM)
| | - Ruth Isserlin
- Department of Molecular Genetics, Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Oliver Stueker
- Department of Molecular Genetics, Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Andrew Emili
- Department of Molecular Genetics, Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Gary D. Bader
- Department of Molecular Genetics, Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- * E-mail: (GDB); (DM)
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19
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Functional analysis: evaluation of response intensities--tailoring ANOVA for lists of expression subsets. BMC Bioinformatics 2010; 11:510. [PMID: 20942918 PMCID: PMC2964684 DOI: 10.1186/1471-2105-11-510] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Accepted: 10/13/2010] [Indexed: 02/06/2023] Open
Abstract
Background Microarray data is frequently used to characterize the expression profile of a whole genome and to compare the characteristics of that genome under several conditions. Geneset analysis methods have been described previously to analyze the expression values of several genes related by known biological criteria (metabolic pathway, pathology signature, co-regulation by a common factor, etc.) at the same time and the cost of these methods allows for the use of more values to help discover the underlying biological mechanisms. Results As several methods assume different null hypotheses, we propose to reformulate the main question that biologists seek to answer. To determine which genesets are associated with expression values that differ between two experiments, we focused on three ad hoc criteria: expression levels, the direction of individual gene expression changes (up or down regulation), and correlations between genes. We introduce the FAERI methodology, tailored from a two-way ANOVA to examine these criteria. The significance of the results was evaluated according to the self-contained null hypothesis, using label sampling or by inferring the null distribution from normally distributed random data. Evaluations performed on simulated data revealed that FAERI outperforms currently available methods for each type of set tested. We then applied the FAERI method to analyze three real-world datasets on hypoxia response. FAERI was able to detect more genesets than other methodologies, and the genesets selected were coherent with current knowledge of cellular response to hypoxia. Moreover, the genesets selected by FAERI were confirmed when the analysis was repeated on two additional related datasets. Conclusions The expression values of genesets are associated with several biological effects. The underlying mathematical structure of the genesets allows for analysis of data from several genes at the same time. Focusing on expression levels, the direction of the expression changes, and correlations, we showed that two-step data reduction allowed us to significantly improve the performance of geneset analysis using a modified two-way ANOVA procedure, and to detect genesets that current methods fail to detect.
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20
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Zhang S, Cao J, Kong YM, Scheuermann RH. GO-Bayes: Gene Ontology-based overrepresentation analysis using a Bayesian approach. ACTA ACUST UNITED AC 2010; 26:905-11. [PMID: 20176581 DOI: 10.1093/bioinformatics/btq059] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
MOTIVATION A typical approach for the interpretation of high-throughput experiments, such as gene expression microarrays, is to produce groups of genes based on certain criteria (e.g. genes that are differentially expressed). To gain more mechanistic insights into the underlying biology, overrepresentation analysis (ORA) is often conducted to investigate whether gene sets associated with particular biological functions, for example, as represented by Gene Ontology (GO) annotations, are statistically overrepresented in the identified gene groups. However, the standard ORA, which is based on the hypergeometric test, analyzes each GO term in isolation and does not take into account the dependence structure of the GO-term hierarchy. RESULTS We have developed a Bayesian approach (GO-Bayes) to measure overrepresentation of GO terms that incorporates the GO dependence structure by taking into account evidence not only from individual GO terms, but also from their related terms (i.e. parents, children, siblings, etc.). The Bayesian framework borrows information across related GO terms to strengthen the detection of overrepresentation signals. As a result, this method tends to identify sets of closely related GO terms rather than individual isolated GO terms. The advantage of the GO-Bayes approach is demonstrated with a simulation study and an application example.
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Affiliation(s)
- Song Zhang
- Department of Clinical Sciences, U.T. Southwestern Medical Center, 5323 Harry Hines Boulevard Dallas, TX 75390-9072, USA.
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21
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Huang WL, Tung CW, Huang HL, Ho SY. Predicting protein subnuclear localization using GO-amino-acid composition features. Biosystems 2009; 98:73-9. [DOI: 10.1016/j.biosystems.2009.06.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2009] [Revised: 06/10/2009] [Accepted: 06/26/2009] [Indexed: 10/20/2022]
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22
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van den Berg BHJ, Thanthiriwatte C, Manda P, Bridges SM. Comparing gene annotation enrichment tools for functional modeling of agricultural microarray data. BMC Bioinformatics 2009; 10 Suppl 11:S9. [PMID: 19811693 PMCID: PMC3226198 DOI: 10.1186/1471-2105-10-s11-s9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The widespread availability of microarray technology has driven functional genomics to the forefront as scientists seek to draw meaningful biological conclusions from their microarray results. Gene annotation enrichment analysis is a functional analysis technique that has gained widespread attention and for which many tools have been developed. Unfortunately, most of these tools have limited support for agricultural species. Here, we evaluate and compare four publicly available computational tools (Onto-Express, EasyGO, GOstat, and DAVID) that support analysis of gene expression datasets in agricultural species. We use AgBase as the functional annotation reference for agricultural species. The selected tools were evaluated based on i) available features, usage and accessibility, ii) implemented statistical computational methods, and iii) annotation and enrichment performance analysis. Annotation was assessed using a randomly selected test gene annotation set and an experimental differentially expressed gene-set – both from chicken. The experimental set was also used to evaluate identification of enriched functional groups. Comparison of the tools shows that they produce different sets of annotations for the two datasets and different functional groups for the experimental dataset. While DAVID, GOstat and Onto-Express annotate comparable numbers of genes, DAVID provides by far the most annotations per gene. However, many of DAVID's annotations appear to be redundant or are at very high levels in the GO hierarchy. The GOSlim distribution of annotations shows that GOstat, Onto-Express and EasyGO provide similar GO distributions to those found in AgBase while annotations from DAVID show a different GOSlim distribution, again probably due to duplication and many non-specific terms. No consistent trends were found in results of GO term over/under representation analysis applied to the experimental data using different tools. While GOstat, David and Onto-Express could retrieve some significantly enriched terms, EasyGO did not show any significantly enriched terms. There was little agreement about the enriched terms identified by the tools. Conclusion Different tools for functionally annotating gene sets and identifying significantly enriched GO categories differ widely in their results when applied to a test annotation gene set and an experimental dataset from chicken. These results emphasize the need for care when interpreting the results of such analysis and the lack of standardization of approaches.
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Affiliation(s)
- Bart H J van den Berg
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Starkville, MS 39762, USA.
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23
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Ackermann M, Strimmer K. A general modular framework for gene set enrichment analysis. BMC Bioinformatics 2009; 10:47. [PMID: 19192285 PMCID: PMC2661051 DOI: 10.1186/1471-2105-10-47] [Citation(s) in RCA: 250] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2008] [Accepted: 02/03/2009] [Indexed: 11/17/2022] Open
Abstract
Background Analysis of microarray and other high-throughput data on the basis of gene sets, rather than individual genes, is becoming more important in genomic studies. Correspondingly, a large number of statistical approaches for detecting gene set enrichment have been proposed, but both the interrelations and the relative performance of the various methods are still very much unclear. Results We conduct an extensive survey of statistical approaches for gene set analysis and identify a common modular structure underlying most published methods. Based on this finding we propose a general framework for detecting gene set enrichment. This framework provides a meta-theory of gene set analysis that not only helps to gain a better understanding of the relative merits of each embedded approach but also facilitates a principled comparison and offers insights into the relative interplay of the methods. Conclusion We use this framework to conduct a computer simulation comparing 261 different variants of gene set enrichment procedures and to analyze two experimental data sets. Based on the results we offer recommendations for best practices regarding the choice of effective procedures for gene set enrichment analysis.
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Affiliation(s)
- Marit Ackermann
- Biotechnology Center, Technical University Dresden, 01062 Dresden, Germany
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Huang DW, Sherman BT, Lempicki RA. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 2008; 37:1-13. [PMID: 19033363 PMCID: PMC2615629 DOI: 10.1093/nar/gkn923] [Citation(s) in RCA: 10891] [Impact Index Per Article: 680.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Functional analysis of large gene lists, derived in most cases from emerging high-throughput genomic, proteomic and bioinformatics scanning approaches, is still a challenging and daunting task. The gene-annotation enrichment analysis is a promising high-throughput strategy that increases the likelihood for investigators to identify biological processes most pertinent to their study. Approximately 68 bioinformatics enrichment tools that are currently available in the community are collected in this survey. Tools are uniquely categorized into three major classes, according to their underlying enrichment algorithms. The comprehensive collections, unique tool classifications and associated questions/issues will provide a more comprehensive and up-to-date view regarding the advantages, pitfalls and recent trends in a simpler tool-class level rather than by a tool-by-tool approach. Thus, the survey will help tool designers/developers and experienced end users understand the underlying algorithms and pertinent details of particular tool categories/tools, enabling them to make the best choices for their particular research interests.
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Affiliation(s)
- Da Wei Huang
- Laboratory of Immunopathogenesis and Bioinformatics, Clinical Services Program, SAIC-Frederick, Inc., National Cancer Institute at Frederick, Frederick, MD 21702, USA
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Trajkovski I, Lavrač N, Tolar J. SEGS: Search for enriched gene sets in microarray data. J Biomed Inform 2008; 41:588-601. [DOI: 10.1016/j.jbi.2007.12.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2007] [Revised: 10/08/2007] [Accepted: 12/04/2007] [Indexed: 01/21/2023]
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Abstract
The essence of a living cell is adaptation to a changing environment, and a central goal of modern cell biology is to understand adaptive change under normal and pathological conditions. Because the number of components is large, and processes and conditions are many, visual tools are useful in providing an overview of relations that would otherwise be far more difficult to assimilate. Historically, representations were static pictures, with genes and proteins represented as nodes, and known or inferred correlations between them (links) represented by various kinds of lines. The modern challenge is to capture functional hierarchies and adaptation to environmental change, and to discover pathways and processes embedded in known data, but not currently recognizable. Among the tools being developed to meet this challenge is VisANT (freely available at http://visant.bu.edu) which integrates, mines and displays hierarchical information. Challenges to integrating modeling (discrete or continuous) and simulation capabilities into such visual mining software are briefly discussed.
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Affiliation(s)
- Zhenjun Hu
- Bioinformatics Program, Boston University, 24 Cummington Street, Boston, MA 02115, USA
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Huang WL, Tung CW, Ho SW, Hwang SF, Ho SY. ProLoc-GO: utilizing informative Gene Ontology terms for sequence-based prediction of protein subcellular localization. BMC Bioinformatics 2008; 9:80. [PMID: 18241343 PMCID: PMC2262056 DOI: 10.1186/1471-2105-9-80] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2007] [Accepted: 02/01/2008] [Indexed: 11/10/2022] Open
Abstract
Background Gene Ontology (GO) annotation, which describes the function of genes and gene products across species, has recently been used to predict protein subcellular and subnuclear localization. Existing GO-based prediction methods for protein subcellular localization use the known accession numbers of query proteins to obtain their annotated GO terms. An accurate prediction method for predicting subcellular localization of novel proteins without known accession numbers, using only the input sequence, is worth developing. Results This study proposes an efficient sequence-based method (named ProLoc-GO) by mining informative GO terms for predicting protein subcellular localization. For each protein, BLAST is used to obtain a homology with a known accession number to the protein for retrieving the GO annotation. A large number n of all annotated GO terms that have ever appeared are then obtained from a large set of training proteins. A novel genetic algorithm based method (named GOmining) combined with a classifier of support vector machine (SVM) is proposed to simultaneously identify a small number m out of the n GO terms as input features to SVM, where m <<n. The m informative GO terms contain the essential GO terms annotating subcellular compartments such as GO:0005634 (Nucleus), GO:0005737 (Cytoplasm) and GO:0005856 (Cytoskeleton). Two existing data sets SCL12 (human protein with 12 locations) and SCL16 (Eukaryotic proteins with 16 locations) with <25% sequence identity are used to evaluate ProLoc-GO which has been implemented by using a single SVM classifier with the m = 44 and m = 60 informative GO terms, respectively. ProLoc-GO using input sequences yields test accuracies of 88.1% and 83.3% for SCL12 and SCL16, respectively, which are significantly better than the SVM-based methods, which achieve < 35% test accuracies using amino acid composition (AAC) with acid pairs and AAC with dipedtide composition. For comparison, ProLoc-GO using known accession numbers of query proteins yields test accuracies of 90.6% and 85.7%, which is also better than Hum-PLoc (85.0%) and Euk-OET-PLoc (83.7%) using ensemble classifiers with hybridization of GO terms and amphiphilic pseudo amino acid composition for SCL12 and SCL16, respectively. Conclusion The growth of Gene Ontology in size and popularity has increased the effectiveness of GO-based features. GOmining can serve as a tool for selecting informative GO terms in solving sequence-based prediction problems. The prediction system using ProLoc-GO with input sequences of query proteins for protein subcellular localization has been implemented (see Availability).
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Affiliation(s)
- Wen-Lin Huang
- Institute of Bioinformatics, National Chiao Tung University, Hsinchu, Taiwan.
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Yang D, Li Y, Xiao H, Liu Q, Zhang M, Zhu J, Ma W, Yao C, Wang J, Wang D, Guo Z, Yang B. Gaining confidence in biological interpretation of the microarray data: the functional consistence of the significant GO categories. ACTA ACUST UNITED AC 2007; 24:265-71. [PMID: 18006543 DOI: 10.1093/bioinformatics/btm558] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
MOTIVATION In microarray studies, numerous tools are available for functional enrichment analysis based on GO categories. Most of these tools, due to their requirement of a prior threshold for designating genes as differentially expressed genes (DEGs), are categorized as threshold-dependent methods that often suffer from a major criticism on their changing results with different thresholds. RESULTS In the present article, by considering the inherent correlation structure of the GO categories, a continuous measure based on semantic similarity of GO categories is proposed to investigate the functional consistence (or stability) of threshold-dependent methods. The results from several datasets show when simply counting overlapping categories between two groups, the significant category groups selected under different DEG thresholds are seemingly very different. However, based on the semantic similarity measure proposed in this article, the results are rather functionally consistent for a wide range of DEG thresholds. Moreover, we find that the functional consistence of gene lists ranked by SAM metric behaves relatively robust against changing DEG thresholds. AVAILABILITY Source code in R is available on request from the authors.
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Affiliation(s)
- Da Yang
- Department of Bioinformatics, Bio-pharmaceutical Key Laboratory of Heilongjiang Province-Incubator of State Key Laboratory, Harbin Medical University, Harbin 150086, China
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Vêncio RZN, Shmulevich I. ProbCD: enrichment analysis accounting for categorization uncertainty. BMC Bioinformatics 2007; 8:383. [PMID: 17935624 PMCID: PMC2169266 DOI: 10.1186/1471-2105-8-383] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2007] [Accepted: 10/12/2007] [Indexed: 11/10/2022] Open
Abstract
Background As in many other areas of science, systems biology makes extensive use of statistical association and significance estimates in contingency tables, a type of categorical data analysis known in this field as enrichment (also over-representation or enhancement) analysis. In spite of efforts to create probabilistic annotations, especially in the Gene Ontology context, or to deal with uncertainty in high throughput-based datasets, current enrichment methods largely ignore this probabilistic information since they are mainly based on variants of the Fisher Exact Test. Results We developed an open-source R-based software to deal with probabilistic categorical data analysis, ProbCD, that does not require a static contingency table. The contingency table for the enrichment problem is built using the expectation of a Bernoulli Scheme stochastic process given the categorization probabilities. An on-line interface was created to allow usage by non-programmers and is available at: . Conclusion We present an analysis framework and software tools to address the issue of uncertainty in categorical data analysis. In particular, concerning the enrichment analysis, ProbCD can accommodate: (i) the stochastic nature of the high-throughput experimental techniques and (ii) probabilistic gene annotation.
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Affiliation(s)
- Ricardo Z N Vêncio
- Institute for Systems Biology, 1441 North 34th street, Seattle, WA 98103-8904, USA.
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