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Ashrafuzzaman M. Artificial Intelligence, Machine Learning and Deep Learning in Ion Channel Bioinformatics. MEMBRANES 2021; 11:membranes11090672. [PMID: 34564489 PMCID: PMC8467682 DOI: 10.3390/membranes11090672] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 08/20/2021] [Accepted: 08/30/2021] [Indexed: 11/28/2022]
Abstract
Ion channels are linked to important cellular processes. For more than half a century, we have been learning various structural and functional aspects of ion channels using biological, physiological, biochemical, and biophysical principles and techniques. In recent days, bioinformaticians and biophysicists having the necessary expertise and interests in computer science techniques including versatile algorithms have started covering a multitude of physiological aspects including especially evolution, mutations, and genomics of functional channels and channel subunits. In these focused research areas, the use of artificial intelligence (AI), machine learning (ML), and deep learning (DL) algorithms and associated models have been found very popular. With the help of available articles and information, this review provide an introduction to this novel research trend. Ion channel understanding is usually made considering the structural and functional perspectives, gating mechanisms, transport properties, channel protein mutations, etc. Focused research on ion channels and related findings over many decades accumulated huge data which may be utilized in a specialized scientific manner to fast conclude pinpointed aspects of channels. AI, ML, and DL techniques and models may appear as helping tools. This review aims at explaining the ways we may use the bioinformatics techniques and thus draw a few lines across the avenue to let the ion channel features appear clearer.
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Affiliation(s)
- Md Ashrafuzzaman
- Department of Biochemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
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2
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Supplitt S, Karpinski P, Sasiadek M, Laczmanska I. Current Achievements and Applications of Transcriptomics in Personalized Cancer Medicine. Int J Mol Sci 2021; 22:1422. [PMID: 33572595 PMCID: PMC7866970 DOI: 10.3390/ijms22031422] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/19/2021] [Accepted: 01/21/2021] [Indexed: 12/12/2022] Open
Abstract
Over the last decades, transcriptome profiling emerged as one of the most powerful approaches in oncology, providing prognostic and predictive utility for cancer management. The development of novel technologies, such as revolutionary next-generation sequencing, enables the identification of cancer biomarkers, gene signatures, and their aberrant expression affecting oncogenesis, as well as the discovery of molecular targets for anticancer therapies. Transcriptomics contribute to a change in the holistic understanding of cancer, from histopathological and organic to molecular classifications, opening a more personalized perspective for tumor diagnostics and therapy. The further advancement on transcriptome profiling may allow standardization and cost reduction of its analysis, which will be the next step for transcriptomics to become a canon of contemporary cancer medicine.
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Affiliation(s)
- Stanislaw Supplitt
- Department of Genetics, Wroclaw Medical University, Marcinkowskiego 1, 50-368 Wroclaw, Poland; (P.K.); (M.S.); (I.L.)
| | - Pawel Karpinski
- Department of Genetics, Wroclaw Medical University, Marcinkowskiego 1, 50-368 Wroclaw, Poland; (P.K.); (M.S.); (I.L.)
- Laboratory of Genomics and Bioinformatics, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Weigla 12, 53-114 Wroclaw, Poland
| | - Maria Sasiadek
- Department of Genetics, Wroclaw Medical University, Marcinkowskiego 1, 50-368 Wroclaw, Poland; (P.K.); (M.S.); (I.L.)
| | - Izabela Laczmanska
- Department of Genetics, Wroclaw Medical University, Marcinkowskiego 1, 50-368 Wroclaw, Poland; (P.K.); (M.S.); (I.L.)
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3
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Poortahmasebi V, Alavian SM, Nasiri-Toosi M, Norouzi M, Hosseini M, Jazayeri SM. Transcriptome analysis of peripheral blood mononuclear cells from chronic hepatitis B and hepatocellular carcinoma patients: a network-based attitude. Future Virol 2017. [DOI: 10.2217/fvl-2017-0087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aim: The aim of the study was constructing a protein–protein interaction network for chronic hepatitis B (CHB) and hepatocellular carcinoma (HCC) patients. Materials & methods: Comprehensive gene expression profile of peripheral blood mononuclear cells of CHB and HCC were obtained from Gene Expression Omnibus/NCBI database. Differentially expressed genes (DEGs) of samples were analyzed using GEO2R web application. Results: The majority of DEGs in both CHB and HCC has been enriched in immune system responses. However, there was a significant disparity between the enrichment of these genes (especially genes associated with Toll-like receptor-and-TNF) in CHB-HCC compared with normal-CHB. Conclusion: The transcriptome properties of peripheral blood mononuclear cells are changed in patients with HBV-HCC. The immune response genes are the most deregulated genes in HCC patients. [Formula: see text]
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Affiliation(s)
- Vahdat Poortahmasebi
- Hepatitis B Molecular Laboratory, Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
- Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
| | - Seyed Moayed Alavian
- Baqiyatallah Research Center for Gastroenterology & Liver Diseases, Baqiyatallah University of Medical Sciences, Tehran, Iran
- Middle East Liver Diseases (MELD) Center, Tehran, Iran
| | - Mohsen Nasiri-Toosi
- Liver Transplantation Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Mehdi Norouzi
- Hepatitis B Molecular Laboratory, Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
- Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
| | - Mostafa Hosseini
- Liver Transplantation Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Seyed Mohammad Jazayeri
- Hepatitis B Molecular Laboratory, Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
- Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
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4
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Sandoval-Bórquez A, Polakovicova I, Carrasco-Véliz N, Lobos-González L, Riquelme I, Carrasco-Avino G, Bizama C, Norero E, Owen GI, Roa JC, Corvalán AH. MicroRNA-335-5p is a potential suppressor of metastasis and invasion in gastric cancer. Clin Epigenetics 2017; 9:114. [PMID: 29075357 PMCID: PMC5645854 DOI: 10.1186/s13148-017-0413-8] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 10/02/2017] [Indexed: 12/13/2022] Open
Abstract
Background Multiple aberrant microRNA expression has been reported in gastric cancer. Among them, microRNA-335-5p (miR-335), a microRNA regulated by DNA methylation, has been reported to possess both tumor suppressor and tumor promoter activities. Results Herein, we show that miR-335 levels are reduced in gastric cancer and significantly associate with lymph node metastasis, depth of tumor invasion, and ultimately poor patient survival in a cohort of Amerindian/Hispanic patients. In two gastric cancer cell lines AGS and, Hs 746T the exogenous miR-335 decreases migration, invasion, viability, and anchorage-independent cell growth capacities. Performing a PCR array on cells transfected with miR-335, 19 (30.6%) out of 62 genes involved in metastasis and tumor invasion showed decreased transcription levels. Network enrichment analysis narrowed these genes to nine (PLAUR, CDH11, COL4A2, CTGF, CTSK, MMP7, PDGFA, TIMP1, and TIMP2). Elevated levels of PLAUR, a validated target gene, and CDH11 were confirmed in tumors with low expression of miR-335. The 3′UTR of CDH11 was identified to be directly targeted by miR-335. Downregulation of miR-335 was also demonstrated in plasma samples from gastric cancer patients and inversely correlated with DNA methylation of promoter region (Z = 1.96, p = 0.029). DNA methylation, evaluated by methylation-specific PCR assay, was found in plasma from 23 (56.1%) out of 41 gastric cancer patients but in only 9 (30%) out of 30 healthy donors (p = 0.029, Pearson’s correlation). Taken in consideration, our results of the association with depth of invasion, lymph node metastasis, and poor prognosis together with functional assays on cell migration, invasion, and tumorigenicity are in accordance with the downregulation of miR-335 in gastric cancer. Conclusions Comprehensive evaluation of metastasis and invasion pathway identified a subset of associated genes and confirmed PLAUR and CDH11, both targets of miR-335, to be overexpressed in gastric cancer tissues. DNA methylation of miR-335 may be a promissory strategy for non-invasive approach to gastric cancer. Electronic supplementary material The online version of this article (10.1186/s13148-017-0413-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alejandra Sandoval-Bórquez
- Advanced Center for Chronic Diseases (ACCDiS), Pontificia Universidad Católica de Chile, Santiago, Chile.,Laboratory of Molecular Pathology, Department of Pathology, School of Medicine, BIOREN-CEGIN, and Graduate Program in Applied Cell and Molecular Biology, Universidad de La Frontera, Temuco, Chile.,Center UC for Investigational in Oncology (CITO), Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Iva Polakovicova
- Advanced Center for Chronic Diseases (ACCDiS), Pontificia Universidad Católica de Chile, Santiago, Chile.,Center UC for Investigational in Oncology (CITO), Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Nicolás Carrasco-Véliz
- Advanced Center for Chronic Diseases (ACCDiS), Pontificia Universidad Católica de Chile, Santiago, Chile.,Center UC for Investigational in Oncology (CITO), Pontificia Universidad Católica de Chile, Santiago, Chile.,Instituto de Química, Faculty of Science, Pontificia Universidad Católica de Valparaíso, Valparaiso, Chile
| | - Lorena Lobos-González
- Advanced Center for Chronic Diseases (ACCDiS), Universidad de Chile, Santiago, Chile.,Fundación Ciencia y Vida, Parque Biotecnológico, Santiago, Chile
| | - Ismael Riquelme
- Laboratory of Molecular Pathology, Department of Pathology, School of Medicine, BIOREN-CEGIN, and Graduate Program in Applied Cell and Molecular Biology, Universidad de La Frontera, Temuco, Chile
| | - Gonzalo Carrasco-Avino
- Advanced Center for Chronic Diseases (ACCDiS), Pontificia Universidad Católica de Chile, Santiago, Chile.,Department of Pathology, Faculty of Medicine, Hospital Clínico Universidad de Chile, Santiago, Chile
| | - Carolina Bizama
- Center UC for Investigational in Oncology (CITO), Pontificia Universidad Católica de Chile, Santiago, Chile.,Department of Pathology, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Enrique Norero
- Esophagogastric Surgery Unit, Hospital Dr. Sótero del Río, Santiago, Chile.,Digestive Surgery Department, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Gareth I Owen
- Advanced Center for Chronic Diseases (ACCDiS), Pontificia Universidad Católica de Chile, Santiago, Chile.,Center UC for Investigational in Oncology (CITO), Pontificia Universidad Católica de Chile, Santiago, Chile.,Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Juan C Roa
- Advanced Center for Chronic Diseases (ACCDiS), Pontificia Universidad Católica de Chile, Santiago, Chile.,Laboratory of Molecular Pathology, Department of Pathology, School of Medicine, BIOREN-CEGIN, and Graduate Program in Applied Cell and Molecular Biology, Universidad de La Frontera, Temuco, Chile.,Center UC for Investigational in Oncology (CITO), Pontificia Universidad Católica de Chile, Santiago, Chile.,Department of Pathology, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alejandro H Corvalán
- Advanced Center for Chronic Diseases (ACCDiS), Pontificia Universidad Católica de Chile, Santiago, Chile.,Center UC for Investigational in Oncology (CITO), Pontificia Universidad Católica de Chile, Santiago, Chile.,Department of Hematology-Oncology, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
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5
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Jagga Z, Gupta D. Machine learning for biomarker identification in cancer research - developments toward its clinical application. Per Med 2015; 12:371-387. [PMID: 29771660 DOI: 10.2217/pme.15.5] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The patterns identified from the systematically collected molecular profiles of patient tumor samples, along with clinical metadata, can assist personalized treatments for effective management of cancer patients with similar molecular subtypes. There is an unmet need to develop computational algorithms for cancer diagnosis, prognosis and therapeutics that can identify complex patterns and help in classifications based on plethora of emerging cancer research outcomes in public domain. Machine learning, a branch of artificial intelligence, holds a great potential for pattern recognition in cryptic cancer datasets, as evident from recent literature survey. In this review, we focus on the current status of machine learning applications in cancer research, highlighting trends and analyzing major achievements, roadblocks and challenges toward its implementation in clinics.
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Affiliation(s)
- Zeenia Jagga
- Bioinformatics Laboratory, Structural & Computational Biology Group, International Centre for Genetic Engineering & Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Dinesh Gupta
- Bioinformatics Laboratory, Structural & Computational Biology Group, International Centre for Genetic Engineering & Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi 110 067, India
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Feichtinger J, McFarlane RJ, Larcombe LD. CancerEST: a web-based tool for automatic meta-analysis of public EST data. Database (Oxford) 2014; 2014:bau024. [PMID: 24715218 PMCID: PMC3978373 DOI: 10.1093/database/bau024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Revised: 02/26/2014] [Accepted: 02/27/2014] [Indexed: 11/23/2022]
Abstract
The identification of cancer-restricted biomarkers is fundamental to the development of novel cancer therapies and diagnostic tools. The construction of comprehensive profiles to define tissue- and cancer-specific gene expression has been central to this. To this end, the exploitation of the current wealth of 'omic'-scale databases can be facilitated by automated approaches, allowing researchers to directly address specific biological questions. Here we present CancerEST, a user-friendly and intuitive web-based tool for the automated identification of candidate cancer markers/targets, for examining tissue specificity as well as for integrated expression profiling. CancerEST operates by means of constructing and meta-analyzing expressed sequence tag (EST) profiles of user-supplied gene sets across an EST database supporting 36 tissue types. Using a validation data set from the literature, we show the functionality and utility of CancerEST. DATABASE URL: http://www.cancerest.org.uk.
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Affiliation(s)
- Julia Feichtinger
- North West Cancer Research Institute, Bangor University, Bangor, Gwynedd LL57 2UW, UK, Institute for Genomics and Bioinformatics, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria, Core Facility Bioinformatics, Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria, NISCHR Cancer Genetics Biomedical Research Unit, Bangor University, Bangor, Gwynedd LL57 2UW, UK, Liverpool Cancer Research UK Centre, University of Liverpool, Liverpool, Merseyside L3 9TA, UK and Applied Mathematics and Computing Group, Cranfield University, Cranfield, Bedfordshire MK43 0AL, UK
| | - Ramsay J. McFarlane
- North West Cancer Research Institute, Bangor University, Bangor, Gwynedd LL57 2UW, UK, Institute for Genomics and Bioinformatics, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria, Core Facility Bioinformatics, Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria, NISCHR Cancer Genetics Biomedical Research Unit, Bangor University, Bangor, Gwynedd LL57 2UW, UK, Liverpool Cancer Research UK Centre, University of Liverpool, Liverpool, Merseyside L3 9TA, UK and Applied Mathematics and Computing Group, Cranfield University, Cranfield, Bedfordshire MK43 0AL, UK
| | - Lee D. Larcombe
- North West Cancer Research Institute, Bangor University, Bangor, Gwynedd LL57 2UW, UK, Institute for Genomics and Bioinformatics, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria, Core Facility Bioinformatics, Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria, NISCHR Cancer Genetics Biomedical Research Unit, Bangor University, Bangor, Gwynedd LL57 2UW, UK, Liverpool Cancer Research UK Centre, University of Liverpool, Liverpool, Merseyside L3 9TA, UK and Applied Mathematics and Computing Group, Cranfield University, Cranfield, Bedfordshire MK43 0AL, UK
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7
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Whittle CA, Johannesson H. Evolutionary dynamics of sex-biased genes in a hermaphrodite fungus. Mol Biol Evol 2013; 30:2435-46. [PMID: 23966547 DOI: 10.1093/molbev/mst143] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Differential gene expression is believed to largely explain sexually dichotomous phenotypes. This phenomenon is especially significant in hermaphrodites, in which male and female sexual tissues have identical genotypes. Sex differences in transcription have been linked to molecular evolution: genes with higher expression in male compared with female sexual tissues (i.e., male-biased genes) have been associated with rapid gene divergence in various animals and plants, implying that selective differences exist among the sexual structures. In the present investigation, we examined expressed sequence tags, microarrays, and gene sequence data from the hermaphroditic fungus Neurospora crassa and confirmed selective differences of genes with disparate expression among male versus female sexual structures in this organism. The results held across various genotypes and stages of sexual development. Furthermore, our data showed that N. crassa comprises a rare example of an organism where female-biased genes evolve rapidly; they exhibited faster evolution at the protein level and reduced optimal codon usage compared with male-biased genes, sexually unbiased genes, and vegetative genes. Female-biased genes also had a greater portion of sites that experienced positive selection and showed stronger signals of selective sweeps than male-biased genes, suggesting that the rapid evolution is at least partly driven by adaptive evolution. Distinctive aspects of the reproductive biology of N. crassa which might explain the rapid evolution of female-biased genes are discussed, particularly the propensity for female-female competition during mating, as well as the multifunctional nature of male structures. The present findings open new opportunities to test hypotheses about sex-biased gene expression and molecular evolution.
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Affiliation(s)
- Carrie A Whittle
- Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden
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Zhao D, Wu J, Zhou Y, Gong W, Xiao J, Yu J. WikiCell: a unified resource platform for human transcriptomics research. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2012; 16:357-62. [PMID: 22702248 PMCID: PMC3369277 DOI: 10.1089/omi.2011.0139] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Here we present a database, WikiCell, as a portal for a unified view of the human transcriptome. At present, WikiCell consists of Expressed Sequenced Tags (ESTs), and users can access, curate, and submit database data by interactive mode, and also can browse, query, upload, and download sequences. Researchers can utilize the transcriptome model based on a human taxonomy graph. The sequences in each model are sorted by attributes such as physiological and pathological samples. The Genbank EST data format are conserved. Gene information is provided, including housekeeping genes, taxonomy location, and gene ontology (GO) description. We believe that WikiCell provides a useful resource for defining expression pattern and tissue differentiation based on human taxonomy mode. It can be accessed at http://www.wikicell.org/.
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Affiliation(s)
- Dongyu Zhao
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- Graduate School of Chinese Academy of Sciences, Beijing, China
| | - Jiayan Wu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Yuanyuan Zhou
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- Graduate School of Chinese Academy of Sciences, Beijing, China
| | - Wei Gong
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- Graduate School of Chinese Academy of Sciences, Beijing, China
| | - Jingfa Xiao
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Jun Yu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
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10
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Yao C, Zhang M, Zou J, Li H, Wang D, Zhu J, Guo Z. Functional modules with disease discrimination abilities for various cancers. SCIENCE CHINA-LIFE SCIENCES 2011; 54:189-93. [PMID: 21318490 DOI: 10.1007/s11427-010-4129-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2009] [Accepted: 09/22/2009] [Indexed: 12/13/2022]
Abstract
Selecting differentially expressed genes (DEGs) is one of the most important tasks in microarray applications for studying multi-factor diseases including cancers. However, the small samples typically used in current microarray studies may only partially reflect the widely altered gene expressions in complex diseases, which would introduce low reproducibility of gene lists selected by statistical methods. Here, by analyzing seven cancer datasets, we showed that, in each cancer, a wide range of functional modules have altered gene expressions and thus have high disease classification abilities. The results also showed that seven modules are shared across diverse cancers, suggesting hints about the common mechanisms of cancers. Therefore, instead of relying on a few individual genes whose selection is hardly reproducible in current microarray experiments, we may use functional modules as functional signatures to study core mechanisms of cancers and build robust diagnostic classifiers.
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Affiliation(s)
- Chen Yao
- Bioinformatics Centre, School of Life Science, University of Electronic Science and Technology of China, Chengdu 610054, China
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11
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Hsu CC, Chiang CW, Cheng HC, Chang WT, Chou CY, Tsai HW, Lee CT, Wu ZH, Lee TY, Chao A, Chow NH, Ho CL. Identifying LRRC16B as an oncofetal gene with transforming enhancing capability using a combined bioinformatics and experimental approach. Oncogene 2010; 30:654-67. [PMID: 21102520 DOI: 10.1038/onc.2010.451] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Oncofetal genes are expressed in embryos or fetuses, are downregulated or undetectable in adult tissues, and then re-expressed in tumors. Known oncofetal genes, such as AFP, GCB, FGF18, IMP-1 and SOX1, often have important clinical applications or pivotal biological functions. To find new oncofetal-like genes, we used the public information of expressed sequence tags to systematically analyze gene expression patterns and identified a novel oncofetal-like gene, LRRC16B. It increased the proliferation, anchorage-independent growth and tumorigenesis of transformed cells in xenografts, possibly through its effects on cyclin B1 protein levels. These findings exemplify the feasibility of using bioinformatics to find new oncofetal-like genes and suggest that more genes with important functional roles will be uncovered in the candidate gene list.
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Affiliation(s)
- C-C Hsu
- Institute of Basic Medical Science, College of Medicine, National Cheng Kung University, Tainan, Taiwan
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Abstract
Cancer has currently overtaken heart disease as the major cause of mortality in the United States. The Human Genome Project, advances in informatics, miniaturization of sample collection, and increased knowledge of cell signaling pathways has revolutionized the study of disease. Genomics, proteomics, and metabolomics are currently being used to develop molecular signatures for disease diagnosis, prognosis, and therapeutic efficacy. Tumor-associated antigens discovered by these methods are being used to develop passive (humoral) as well as active immunotherapy strategies to stimulate the immune system. Development and validation of biomarkers on a parallel track with therapeutics can speed development times by accurate screening of patient populations and substituting surrogate markers that correlate well with clinical outcomes.
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Affiliation(s)
- Uriel M Malyankar
- Biomarkers, Division of Translational Medicine, MannKind Corporation, Valencia, California 91355, USA.
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13
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Yang Y, Adelstein SJ, Kassis AI. Target discovery from data mining approaches. Drug Discov Today 2009; 14:147-54. [PMID: 19135549 DOI: 10.1016/j.drudis.2008.12.005] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2008] [Revised: 11/27/2008] [Accepted: 12/08/2008] [Indexed: 11/18/2022]
Abstract
Data mining of available biomedical data and information has greatly boosted target discovery in the 'omics' era. Target discovery is the key step in the biomarker and drug discovery pipeline to diagnose and fight human diseases. In biomedical science, the 'target' is a broad concept ranging from molecular entities (such as genes, proteins and miRNAs) to biological phenomena (such as molecular functions, pathways and phenotypes). Within the context of biomedical science, data mining refers to a bioinformatics approach that combines biological concepts with computer tools or statistical methods that are mainly used to discover, select and prioritize targets. In response to the huge demand of data mining for target discovery in the 'omics' era, this review explicates various data mining approaches and their applications to target discovery with emphasis on text and microarray data analysis. Two emerging data mining approaches, chemogenomic data mining and proteomic data mining, are briefly introduced. Also discussed are the limitations of various data mining approaches found in the level of database integration, the quality of data annotation, sample heterogeneity and the performance of analytical and mining tools. Tentative strategies of integrating different data sources for target discovery, such as integrated text mining with high-throughput data analysis and integrated mining with pathway databases, are introduced.
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Affiliation(s)
- Yongliang Yang
- Harvard Medical School, Harvard University, Department of Radiology, Armenise Building, Room D2-137, 200 Longwood Avenue, Boston, MA 02115, USA.
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Integrative genomic data mining for discovery of potential blood-borne biomarkers for early diagnosis of cancer. PLoS One 2008; 3:e3661. [PMID: 18987750 PMCID: PMC2575235 DOI: 10.1371/journal.pone.0003661] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2008] [Accepted: 10/16/2008] [Indexed: 11/19/2022] Open
Abstract
Background With the arrival of the postgenomic era, there is increasing interest in the discovery of biomarkers for the accurate diagnosis, prognosis, and early detection of cancer. Blood-borne cancer markers are favored by clinicians, because blood samples can be obtained and analyzed with relative ease. We have used a combined mining strategy based on an integrated cancer microarray platform, Oncomine, and the biomarker module of the Ingenuity Pathways Analysis (IPA) program to identify potential blood-based markers for six common human cancer types. Methodology/Principal Findings In the Oncomine platform, the genes overexpressed in cancer tissues relative to their corresponding normal tissues were filtered by Gene Ontology keywords, with the extracellular environment stipulated and a corrected Q value (false discovery rate) cut-off implemented. The identified genes were imported to the IPA biomarker module to separate out those genes encoding putative secreted or cell-surface proteins as blood-borne (blood/serum/plasma) cancer markers. The filtered potential indicators were ranked and prioritized according to normalized absolute Student t values. The retrieval of numerous marker genes that are already clinically useful or under active investigation confirmed the effectiveness of our mining strategy. To identify the biomarkers that are unique for each cancer type, the upregulated marker genes that are in common between each two tumor types across the six human tumors were also analyzed by the IPA biomarker comparison function. Conclusion/Significance The upregulated marker genes shared among the six cancer types may serve as a molecular tool to complement histopathologic examination, and the combination of the commonly upregulated and unique biomarkers may serve as differentiating markers for a specific cancer. This approach will be increasingly useful to discover diagnostic signatures as the mass of microarray data continues to grow in the ‘omics’ era.
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15
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Dreses-Werringloer U, Lambert JC, Vingtdeux V, Zhao H, Vais H, Siebert A, Jain A, Koppel J, Rovelet-Lecrux A, Hannequin D, Pasquier F, Galimberti D, Scarpini E, Mann D, Lendon C, Campion D, Amouyel P, Davies P, Foskett JK, Campagne F, Marambaud P. A polymorphism in CALHM1 influences Ca2+ homeostasis, Abeta levels, and Alzheimer's disease risk. Cell 2008; 133:1149-61. [PMID: 18585350 DOI: 10.1016/j.cell.2008.05.048] [Citation(s) in RCA: 252] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2008] [Revised: 04/30/2008] [Accepted: 05/22/2008] [Indexed: 12/31/2022]
Abstract
Alzheimer's disease (AD) is a genetically heterogeneous disorder characterized by early hippocampal atrophy and cerebral amyloid-beta (Abeta) peptide deposition. Using TissueInfo to screen for genes preferentially expressed in the hippocampus and located in AD linkage regions, we identified a gene on 10q24.33 that we call CALHM1. We show that CALHM1 encodes a multipass transmembrane glycoprotein that controls cytosolic Ca(2+) concentrations and Abeta levels. CALHM1 homomultimerizes, shares strong sequence similarities with the selectivity filter of the NMDA receptor, and generates a large Ca(2+) conductance across the plasma membrane. Importantly, we determined that the CALHM1 P86L polymorphism (rs2986017) is significantly associated with AD in independent case-control studies of 3404 participants (allele-specific OR = 1.44, p = 2 x 10(-10)). We further found that the P86L polymorphism increases Abeta levels by interfering with CALHM1-mediated Ca(2+) permeability. We propose that CALHM1 encodes an essential component of a previously uncharacterized cerebral Ca(2+) channel that controls Abeta levels and susceptibility to late-onset AD.
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Affiliation(s)
- Ute Dreses-Werringloer
- Litwin-Zucker Research Center for the Study of Alzheimer's Disease, The Feinstein Institute for Medical Research, North Shore-LIJ, Manhasset, NY 11030, USA
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Aguilar D, Skrabanek L, Gross SS, Oliva B, Campagne F. Beyond tissueInfo: functional prediction using tissue expression profile similarity searches. Nucleic Acids Res 2008; 36:3728-37. [PMID: 18483083 PMCID: PMC2441795 DOI: 10.1093/nar/gkn233] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We present and validate tissue expression profile similarity searches (TEPSS), a computational approach to identify transcripts that share similar tissue expression profiles to one or more transcripts in a group of interest. We evaluated TEPSS for its ability to discriminate between pairs of transcripts coding for interacting proteins and non-interacting pairs. We found that ordering protein-protein pairs by TEPSS score produces sets significantly enriched in reported pairs of interacting proteins [interacting versus non-interacting pairs, Odds-ratio (OR) = 157.57, 95% confidence interval (CI) (36.81-375.51) at 1% coverage, employing a large dataset of about 50 000 human protein interactions]. When used with multiple transcripts as input, we find that TEPSS can predict non-obvious members of the cytosolic ribosome. We used TEPSS to predict S-nitrosylation (SNO) protein targets from a set of brain proteins that undergo SNO upon exposure to physiological levels of S-nitrosoglutathione in vitro. While some of the top TEPSS predictions have been validated independently, several of the strongest SNO TEPSS predictions await experimental validation. Our data indicate that TEPSS is an effective and flexible approach to functional prediction. Since the approach does not use sequence similarity, we expect that TEPSS will be useful for various gene discovery applications. TEPSS programs and data are distributed at http://icb.med.cornell.edu/crt/tepss/index.xml.
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Affiliation(s)
- Daniel Aguilar
- HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Medical College of Cornell University, 1305 York Ave, New York, NY 10021, USA
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Klee EW. Data Mining for Biomarker Development: A Review of Tissue Specificity Analysis. Clin Lab Med 2008; 28:127-43, viii. [DOI: 10.1016/j.cll.2007.10.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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