1
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Golebiewski M, Bader G, Gleeson P, Gorochowski TE, Keating SM, König M, Myers CJ, Nickerson DP, Sommer B, Waltemath D, Schreiber F. Specifications of standards in systems and synthetic biology: status, developments, and tools in 2024. J Integr Bioinform 2024; 21:jib-2024-0015. [PMID: 39026464 DOI: 10.1515/jib-2024-0015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024] Open
Affiliation(s)
- Martin Golebiewski
- 40092 Heidelberg Institute for Theoretical Studies (HITS) , Heidelberg, Germany
| | | | - Padraig Gleeson
- Dept. of Neuroscience, Physiology and Pharmacology, University College London, London, UK
| | | | - Sarah M Keating
- Advanced Research Computing Centre, University College London, London, UK
| | - Matthias König
- 9373 Institute for Biology, Institute for Theoretical Biology, Humboldt-University Berlin , Berlin, Germany
| | - Chris J Myers
- Dept. of Electrical, Computer, and Energy Eng., University of Colorado Boulder, Boulder, USA
| | - David P Nickerson
- 428614 Auckland Bioengineering Institute, University of Auckland , Auckland, New Zealand
| | | | - Dagmar Waltemath
- Medical Informatics Laboratory, University Medicine Greifswald, Greifswald, Germany
| | - Falk Schreiber
- Dept. of Computer and Information Science, 26567 University of Konstanz , Konstanz, Germany
- Faculty of Information Technology, Monash University, Clayton, Australia
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2
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Zhong W, Li Y, Yuan Y, Zhong H, Huang C, Huang J, Lin Y, Huang J. Characterization of Molecular Heterogeneity Associated With Tumor Microenvironment in Clear Cell Renal Cell Carcinoma to Aid Immunotherapy. Front Cell Dev Biol 2021; 9:736540. [PMID: 34631713 PMCID: PMC8495029 DOI: 10.3389/fcell.2021.736540] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 09/03/2021] [Indexed: 12/24/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most common type of kidney cancer and has strong immunogenicity. A systematically investigation of the tumor microenvironment (TME) in ccRCC could contribute to help clinicians develop personalized treatment and facilitate clinical decision-making. In this study, we analyzed the immune-related subtype of ccRCC on the basis of immune-related gene expression data in The Cancer Genome Atlas (TCGA, N = 512) and E-MTAB-1980 (N = 101) dataset, respectively. As a result, two subtypes (C1 and C2) were identified by performing non-negative matrix factorization clustering. Subtype C1 was characterized by increased advance ccRCC cases and immune-related pathways. A higher immune score, stromal score, TMB value, Tumor Immune Dysfunction and Exclusion (TIDE) prediction score, and immune checkpoint genes expression level were also observed in C1. In addition, the C1 subtype might benefit from chemotherapy and immunotherapy. The patients in subtype C2 had more metabolism-related pathways, higher tumor purity, and a better prognosis. Moreover, some small molecular compounds for the treatment of ccRCC were identified between the two subtypes by using the Connectivity Map (CMap) database. Finally, we constructed and validated an immune-related (IR) score to evaluate immune modification individually. A high IR score corresponded to a favorable prognosis compared to a low IR score, while more advanced tumor stage and grade cases were enriched in the low IR score group. The two IR score groups also showed a distinct divergence among immune status, TME, and chemotherapy. The external validation dataset (E-MTAB-1980) and another immunotherapy cohort (IMvigor 210) demonstrated that patients in the high IR score group had a significantly prolonged survival time and clinical benefits compared to the low IR score group. Together, characterization of molecular heterogeneity and IR signature may help develop new insights into the TME of ccRCC and provide new strategies for personalized treatment.
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Affiliation(s)
| | - Yinan Li
- Department of Nephrology, The First Affiliated Hospital of Xiamen University, Xiamen, China
- Department of Clinical Medicine, Fujian Medical University, Fuzhou, China
| | - Yichu Yuan
- Department of Urology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hongbin Zhong
- The Fifth Hospital of Xiamen, Xiamen, China
- Department of Clinical Medicine, Fujian Medical University, Fuzhou, China
| | | | - Jiwei Huang
- Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yao Lin
- Central Laboratory at the Second Affiliated Hospital of Fujian Traditional Chinese Medical University, Collaborative Innovation Center for Rehabilitation Technology, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Jiyi Huang
- The Fifth Hospital of Xiamen, Xiamen, China
- Department of Nephrology, The First Affiliated Hospital of Xiamen University, Xiamen, China
- Department of Clinical Medicine, Fujian Medical University, Fuzhou, China
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3
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Schölzel C, Blesius V, Ernst G, Dominik A. Characteristics of mathematical modeling languages that facilitate model reuse in systems biology: a software engineering perspective. NPJ Syst Biol Appl 2021; 7:27. [PMID: 34083542 PMCID: PMC8175692 DOI: 10.1038/s41540-021-00182-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 04/19/2021] [Indexed: 02/06/2023] Open
Abstract
Reuse of mathematical models becomes increasingly important in systems biology as research moves toward large, multi-scale models composed of heterogeneous subcomponents. Currently, many models are not easily reusable due to inflexible or confusing code, inappropriate languages, or insufficient documentation. Best practice suggestions rarely cover such low-level design aspects. This gap could be filled by software engineering, which addresses those same issues for software reuse. We show that languages can facilitate reusability by being modular, human-readable, hybrid (i.e., supporting multiple formalisms), open, declarative, and by supporting the graphical representation of models. Modelers should not only use such a language, but be aware of the features that make it desirable and know how to apply them effectively. For this reason, we compare existing suitable languages in detail and demonstrate their benefits for a modular model of the human cardiac conduction system written in Modelica.
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Affiliation(s)
- Christopher Schölzel
- Technische Hochschule Mittelhessen - University of Applied Sciences, Giessen, Germany.
| | - Valeria Blesius
- Technische Hochschule Mittelhessen - University of Applied Sciences, Giessen, Germany
| | - Gernot Ernst
- Vestre Viken Hospital Trust, Kongsberg, Norway
- University of Oslo, Oslo, Norway
| | - Andreas Dominik
- Technische Hochschule Mittelhessen - University of Applied Sciences, Giessen, Germany
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4
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Tian S, Yan L, Fu L, Zhang Z, Zhang J, Meng G, Zhang W. A Comprehensive Investigation to Reveal the Relationship Between Plasmacytoid Dendritic Cells and Breast Cancer by Multiomics Data Analysis. Front Cell Dev Biol 2021; 9:640476. [PMID: 33869191 PMCID: PMC8047150 DOI: 10.3389/fcell.2021.640476] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 03/02/2021] [Indexed: 11/13/2022] Open
Abstract
Plasmacytoid dendritic cells (pDC) are an essential immune microenvironment component. They have been reported for crucial roles in linking the adaptive and immune systems. However, the prognostic role of the pDC in breast cancer (BRCA) was controversial. In this work, we collected large sample cohorts and did a comprehensive investigation to reveal the relationship between pDC and BRCA by multiomics data analysis. Elevated pDC levels were correlated with prolonged survival outcomes in BRCA patients. The distinct mutation landscape and lower burden of somatic copy number alterations (SCNA) and lower intratumoral heterogeneity were observed in the high pDC abundance group. Additionally, a more sensitive immune response and chemotherapies response were observed in the high pDC group, which implicates that patients with high pDC abundance can be benefited from the combination of chemotherapy and immunotherapy. In conclusion, the correlation between pDC abundance and BRCA patients' overall survival (OS) was found to be positive. We identified the molecular profiles of BRCA patients with pDC abundance. Our findings may be beneficial in aiding in the development of immunotherapy and elucidating on the precision treatment for BRCA.
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Affiliation(s)
- Saisai Tian
- School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Li Yan
- School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Lu Fu
- School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Zhen Zhang
- School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Jinbo Zhang
- School of Pharmacy, Second Military Medical University, Shanghai, China.,Department of Pharmacy, Tianjin Rehabilitation and Recuperation Center, Joint Logistics Support Force, Tianjin, China
| | - Guofeng Meng
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Weidong Zhang
- School of Pharmacy, Second Military Medical University, Shanghai, China.,Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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5
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Yu DH, Chen C, Liu XP, Yao J, Li S, Ruan XL. Dysregulation of miR-138-5p/RPS6KA1-AP2M1 Is Associated With Poor Prognosis in AML. Front Cell Dev Biol 2021; 9:641629. [PMID: 33732707 PMCID: PMC7959750 DOI: 10.3389/fcell.2021.641629] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 01/28/2021] [Indexed: 12/22/2022] Open
Abstract
Acute myeloid leukemia (AML) is a malignant disease of hematopoietic stem/progenitor cells, and most AML patients are in a severe state. Internal tandem duplication mutations in FLT3 gene (FLT3-ITD) detected in AML stem cells account for 20–30 percent of AML patients. In this study, we attempted to study the impact of the interaction of FLT3-ITD mutation and the CXCL12/CXCR4 axis in AML, and the possible mechanisms caused by the impact by bioinformatics. Gene set variation analysis (GSVA) revealed that the PI3K-Akt-mTOR pathway positively correlated with the status of FLT3-ITD mutation. Multiple survival analyses were performed on TCGA-AML to screen the prognostic-related genes, and RPS6KA1 and AP2M1 are powerful prognostic candidates for overall survival in AML. WGCNA, KEGG/GO analysis, and the functional roles of RPS6KA1 and AP2M1 in AML were clarified by correlation analysis. We found that the expression levels of RPS6KA1 and AP2M1 were significantly associated with chemoresistance of AML, and the CXCL12/CXCR4 axis would regulate RPS6KA1/AP2M1 expression. Besides, miR-138-5p, regulated by the CXCL12/CXCR4 axis, was the common miRNA target of RPS6KA1 and AP2M1. Taken together, the interaction of FLT3-ITD mutation and the CXCL12/CXCR4 axis activated the PI3K-Akt-mTOR pathway, and the increased expression of RPS6KA1 and AP2M1 caused by hsa-miR-138-5p downregulation regulates the multi-resistance gene expression leading to drug indications.
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Affiliation(s)
- Dong-Hu Yu
- Department of Biological Repositories, Human Genetics Resource Preservation Center of Hubei Province, Zhongnan Hospital of Wuhan University, Wuhan, China.,The Second Clinical College, Wuhan University, Wuhan, China
| | - Chen Chen
- Department of Biological Repositories, Human Genetics Resource Preservation Center of Hubei Province, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xiao-Ping Liu
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jie Yao
- Department of Biological Repositories, Human Genetics Resource Preservation Center of Hubei Province, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Sheng Li
- Department of Biological Repositories, Human Genetics Resource Preservation Center of Hubei Province, Zhongnan Hospital of Wuhan University, Wuhan, China.,Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xiao-Lan Ruan
- Department of Hematology, Renmin Hospital of Wuhan University, Wuhan, China
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6
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Touré V, Dräger A, Luna A, Dogrusoz U, Rougny A. The Systems Biology Graphical Notation: Current Status and Applications in Systems Medicine. SYSTEMS MEDICINE 2021. [DOI: 10.1016/b978-0-12-801238-3.11515-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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7
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Du J, Yan X, Mi S, Li Y, Ji H, Hou K, Ma S, Ba Y, Zhou P, Chen L, Xie R, Hu S. Identification of Prognostic Model and Biomarkers for Cancer Stem Cell Characteristics in Glioblastoma by Network Analysis of Multi-Omics Data and Stemness Indices. Front Cell Dev Biol 2020; 8:558961. [PMID: 33195193 PMCID: PMC7604309 DOI: 10.3389/fcell.2020.558961] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 09/22/2020] [Indexed: 12/13/2022] Open
Abstract
The progression of most human cancers mainly involves the gradual accumulation of the loss of differentiated phenotypes and the sequential acquisition of progenitor and stem cell-like features. Glioblastoma multiforme (GBM) stem cells (GSCs), characterized by self-renewal and therapeutic resistance, play vital roles in GBM. However, a comprehensive understanding of GBM stemness remains elusive. Two stemness indices, mRNAsi and EREG-mRNAsi, were employed to comprehensively analyze GBM stemness. We observed that mRNAsi was significantly related to multi-omics parameters (such as mutant status, sample type, transcriptomics, and molecular subtype). Moreover, potential mechanisms and candidate compounds targeting the GBM stemness signature were illuminated. By combining weighted gene co-expression network analysis with differential analysis, we obtained 18 stemness-related genes, 10 of which were significantly related to survival. Moreover, we obtained a prediction model from both two independent cancer databases that was not only an independent clinical outcome predictor but could also accurately predict the clinical parameters of GBM. Survival analysis and experimental data confirmed that the five hub genes (CHI3L2, FSTL3, RPA3, RRM2, and YTHDF2) could be used as markers for poor prognosis of GBM. Mechanistically, the effect of inhibiting the proliferation of GSCs was attributed to the reduction of the ratio of CD133 and the suppression of the invasiveness of GSCs. The results based on an in vivo xenograft model are consistent with the finding that knockdown of the hub gene inhibits the growth of GSCs in vitro. Our approach could be applied to facilitate the development of objective diagnostic and targeted treatment tools to quantify cancer stemness in clinical tumors, and perhaps lead considerable benefits that could predict tumor prognosis, identify new stemness-related targets and targeted therapies, or improve targeted therapy sensitivity. The five genes identified in this study are expected to be the targets of GBM stem cell therapy.
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Affiliation(s)
- Jianyang Du
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Xiuwei Yan
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Shan Mi
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Yuan Li
- Department of Pharmacology (The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, China
| | - Hang Ji
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Kuiyuan Hou
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Shuai Ma
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yixu Ba
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Peng Zhou
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Lei Chen
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China.,Department of Neurosurgery, The First Affiliated Hospital of Harbin, Harbin, China
| | - Rui Xie
- Department of Digestive Internal Medicine, Harbin Medical University Cancer Hospital, Harbin, China
| | - Shaoshan Hu
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
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8
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Shou Y, Yang L, Yang Y, Zhu X, Li F, Xu J. Identification of Signatures of Prognosis Prediction for Melanoma Using a Hypoxia Score. Front Genet 2020; 11:570530. [PMID: 33133157 PMCID: PMC7550673 DOI: 10.3389/fgene.2020.570530] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 09/08/2020] [Indexed: 01/16/2023] Open
Abstract
Melanoma is one of the most aggressive cancers. Hypoxic microenvironment affects multiple cellular pathways and contributes to tumor progression. The purpose of the research was to investigate the association between hypoxia and melanoma, and identify the prognostic value of hypoxia-related genes. Based on the GSVA algorithm, gene expression profile collected from The Cancer Genome Atlas (TCGA) was used for calculating the hypoxia score. The Kaplan–Meier plot suggested that a high hypoxia score was correlated with the inferior survival of melanoma patients. Using differential gene expression analysis and WGCNA, a total of 337 overlapping genes associated with hypoxia were determined. Protein-protein interaction network and functional enrichment analysis were conducted, and Lasso Cox regression was performed to establish the prognostic gene signature. Lasso regression showed that seven genes displayed the best features. A novel seven-gene signature (including ABCA12, PTK6, FERMT1, GSDMC, KRT2, CSTA, and SPRR2F) was constructed for prognosis prediction. The ROC curve inferred good performance in both the TCGA cohort and validation cohorts. Therefore, our study determined the prognostic implication of the hypoxia score in melanoma and showed a novel seven-gene signature to predict prognosis, which may provide insights into the prognosis evaluation and clinical decision making.
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Affiliation(s)
- Yanhong Shou
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Lu Yang
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Yongsheng Yang
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Xiaohua Zhu
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Feng Li
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Jinhua Xu
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China.,Institute of Dermatology, Shanghai, China
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9
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Hoksza D, Gawron P, Ostaszewski M, Hasenauer J, Schneider R. Closing the gap between formats for storing layout information in systems biology. Brief Bioinform 2020; 21:1249-1260. [PMID: 31273380 PMCID: PMC7373180 DOI: 10.1093/bib/bbz067] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 04/23/2019] [Accepted: 05/14/2019] [Indexed: 11/13/2022] Open
Abstract
The understanding of complex biological networks often relies on both a dedicated layout and a topology. Currently, there are three major competing layout-aware systems biology formats, but there are no software tools or software libraries supporting all of them. This complicates the management of molecular network layouts and hinders their reuse and extension. In this paper, we present a high-level overview of the layout formats in systems biology, focusing on their commonalities and differences, review their support in existing software tools, libraries and repositories and finally introduce a new conversion module within the MINERVA platform. The module is available via a REST API and offers, besides the ability to convert between layout-aware systems biology formats, the possibility to export layouts into several graphical formats. The module enables conversion of very large networks with thousands of elements, such as disease maps or metabolic reconstructions, rendering it widely applicable in systems biology.
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Affiliation(s)
- David Hoksza
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6, avenue du Swing L-4367 Belvaux, Luxembourg
- Faculty of Mathematics and Physics, Charles University, Malostranské nám. 25, 118 00 Prague, Czech Republic
| | - Piotr Gawron
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6, avenue du Swing L-4367 Belvaux, Luxembourg
| | - Marek Ostaszewski
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6, avenue du Swing L-4367 Belvaux, Luxembourg
| | - Jan Hasenauer
- Institute of Computational Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
- Department of Mathematics, Technische Universität München, München, Germany
- Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany
| | - Reinhard Schneider
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6, avenue du Swing L-4367 Belvaux, Luxembourg
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10
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Liu HJ, Hu HM, Li GZ, Zhang Y, Wu F, Liu X, Wang KY, Zhang CB, Jiang T. Ferroptosis-Related Gene Signature Predicts Glioma Cell Death and Glioma Patient Progression. Front Cell Dev Biol 2020; 8:538. [PMID: 32733879 PMCID: PMC7363771 DOI: 10.3389/fcell.2020.00538] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 06/08/2020] [Indexed: 01/10/2023] Open
Abstract
Glioma is a fatal brain tumor characterized by rapid proliferation and treatment resistance. Ferroptosis is a newly discovered programmed cell death and plays a crucial role in the occurrence and progression of tumors. In this study, we identified ferroptosis specific markers to reveal the relationship between ferroptosis-related genes and glioma by analyzing whole transcriptome data from Chinese Glioma Genome Atlas, The Cancer Genome Atlas dataset, GSE16011 dataset, and the Repository of Molecular Brain Neoplasia Data dataset. Nineteen ferroptosis-related genes with clinical and pathological features of glioma were identified as highly correlated. Functional assays in glioma cell lines indicated the association of ferroptosis with temozolomide resistance, autophagy, and glioma cell migration. Therefore, the identified ferroptosis-related genes were significantly correlated with glioma progression.
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Affiliation(s)
- Han-Jie Liu
- Beijing Neurosurgical Institute and Beijing Tiantan Hospital of Capital Medical University, Beijing, China
| | - Hui-Min Hu
- Beijing Neurosurgical Institute and Beijing Tiantan Hospital of Capital Medical University, Beijing, China
| | - Guan-Zhang Li
- Beijing Neurosurgical Institute and Beijing Tiantan Hospital of Capital Medical University, Beijing, China
| | - Ying Zhang
- Beijing Neurosurgical Institute and Beijing Tiantan Hospital of Capital Medical University, Beijing, China
| | - Fan Wu
- Beijing Neurosurgical Institute and Beijing Tiantan Hospital of Capital Medical University, Beijing, China
| | - Xiu Liu
- Beijing Neurosurgical Institute and Beijing Tiantan Hospital of Capital Medical University, Beijing, China
| | - Kuan-Yu Wang
- Beijing Neurosurgical Institute and Beijing Tiantan Hospital of Capital Medical University, Beijing, China
| | - Chuan-Bao Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Tao Jiang
- Beijing Neurosurgical Institute and Beijing Tiantan Hospital of Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Center of Brain Tumor, Beijing Institute for Brain Disorders, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China.,Chinese Glioma Genome Atlas Network (CGGA) and Asian Glioma Genome Atlas Network (AGGA), Beijing, China
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11
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Balaur I, Roy L, Mazein A, Karaca SG, Dogrusoz U, Barillot E, Zinovyev A. cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats. Bioinformatics 2020; 36:2620-2622. [DOI: 10.1093/bioinformatics/btz969] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 11/20/2019] [Accepted: 01/01/2020] [Indexed: 12/27/2022] Open
Abstract
Abstract
Motivation
CellDesigner is a well-established biological map editor used in many large-scale scientific efforts. However, the interoperability between the Systems Biology Graphical Notation (SBGN) Markup Language (SBGN-ML) and the CellDesigner’s proprietary Systems Biology Markup Language (SBML) extension formats remains a challenge due to the proprietary extensions used in CellDesigner files.
Results
We introduce a library named cd2sbgnml and an associated web service for bidirectional conversion between CellDesigner’s proprietary SBML extension and SBGN-ML formats. We discuss the functionality of the cd2sbgnml converter, which was successfully used for the translation of comprehensive large-scale diagrams such as the RECON Human Metabolic network and the complete Atlas of Cancer Signalling Network, from the CellDesigner file format into SBGN-ML.
Availability and implementation
The cd2sbgnml conversion library and the web service were developed in Java, and distributed under the GNU Lesser General Public License v3.0. The sources along with a set of examples are available on GitHub (https://github.com/sbgn/cd2sbgnml and https://github.com/sbgn/cd2sbgnml-webservice, respectively).
Supplementary information
Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Irina Balaur
- European Institute for Systems Biology and Medicine, CIRI UMR5308, CNRS-ENS-UCBL-INSERM, Université de Lyon, 69007 Lyon, France
| | - Ludovic Roy
- Institut National de la Santé et de la Recherche Médicale (INSERM), U900, F-75005 Paris, France
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, F-75006 Paris, France
- Institut Curie, PSL Research University, F-75005 Paris, France
| | - Alexander Mazein
- European Institute for Systems Biology and Medicine, CIRI UMR5308, CNRS-ENS-UCBL-INSERM, Université de Lyon, 69007 Lyon, France
- Institute of Cell Biophysics, Russian Academy of Sciences, 3 Institutskaya Street, Moscow Region, Pushchino 142290, Russia
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367 Belvaux, Luxembourg
| | - S Gökberk Karaca
- Computer Engineering Department, Bilkent University, Ankara 06800, Turkey
| | - Ugur Dogrusoz
- Computer Engineering Department, Bilkent University, Ankara 06800, Turkey
| | - Emmanuel Barillot
- Institut National de la Santé et de la Recherche Médicale (INSERM), U900, F-75005 Paris, France
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, F-75006 Paris, France
- Institut Curie, PSL Research University, F-75005 Paris, France
| | - Andrei Zinovyev
- Institut National de la Santé et de la Recherche Médicale (INSERM), U900, F-75005 Paris, France
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, F-75006 Paris, France
- Institut Curie, PSL Research University, F-75005 Paris, France
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12
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Millar AJ, Urquiza U, Freeman PL, Hume A, Plotkin GD, Sorokina O, Zardilis A, Zielinski T. Practical steps to digital organism models, from laboratory model species to 'Crops in silico. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2403-2418. [PMID: 30615184 DOI: 10.1093/jxb/ery435] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 11/28/2018] [Indexed: 05/20/2023]
Abstract
A recent initiative named 'Crops in silico' proposes that multi-scale models 'have the potential to fill in missing mechanistic details and generate new hypotheses to prioritize directed engineering efforts' in plant science, particularly directed to crop species. To that end, the group called for 'a paradigm shift in plant modelling, from largely isolated efforts to a connected community'. 'Wet' (experimental) research has been especially productive in plant science, since the adoption of Arabidopsis thaliana as a laboratory model species allowed the emergence of an Arabidopsis research community. Parts of this community invested in 'dry' (theoretical) research, under the rubric of Systems Biology. Our past research combined concepts from Systems Biology and crop modelling. Here we outline the approaches that seem most relevant to connected, 'digital organism' initiatives. We illustrate the scale of experimental research required, by collecting the kinetic parameter values that are required for a quantitative, dynamic model of a gene regulatory network. By comparison with the Systems Biology Markup Language (SBML) community, we note computational resources and community structures that will help to realize the potential for plant Systems Biology to connect with a broader crop science community.
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Affiliation(s)
- Andrew J Millar
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Uriel Urquiza
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Alastair Hume
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, UK
- EPCC, Bayes Centre, University of Edinburgh, Edinburgh, UK
| | - Gordon D Plotkin
- Laboratory for the Foundations of Computer Science, School of Informatics, University of Edinburgh, Edinburgh, UK
| | - Oxana Sorokina
- Institute for Adaptive and Neural Computation, School of Informatics, University of Edinburgh, Edinburgh, UK
| | - Argyris Zardilis
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Tomasz Zielinski
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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SBGNViz: A Tool for Visualization and Complexity Management of SBGN Process Description Maps. PLoS One 2015; 10:e0128985. [PMID: 26030594 PMCID: PMC4451519 DOI: 10.1371/journal.pone.0128985] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 05/04/2015] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Information about cellular processes and pathways is becoming increasingly available in detailed, computable standard formats such as BioPAX and SBGN. Effective visualization of this information is a key recurring requirement for biological data analysis, especially for -omic data. Biological data analysis is rapidly migrating to web based platforms; thus there is a substantial need for sophisticated web based pathway viewers that support these platforms and other use cases. RESULTS Towards this goal, we developed a web based viewer named SBGNViz for process description maps in SBGN (SBGN-PD). SBGNViz can visualize both BioPAX and SBGN formats. Unique features of SBGNViz include the ability to nest nodes to arbitrary depths to represent molecular complexes and cellular locations, automatic pathway layout, editing and highlighting facilities to enable focus on sub-maps, and the ability to inspect pathway members for detailed information from EntrezGene. SBGNViz can be used within a web browser without any installation and can be readily embedded into web pages. SBGNViz has two editions built with ActionScript and JavaScript. The JavaScript edition, which also works on touch enabled devices, introduces novel methods for managing and reducing complexity of large SBGN-PD maps for more effective analysis. CONCLUSION SBGNViz fills an important gap by making the large and fast-growing corpus of rich pathway information accessible to web based platforms. SBGNViz can be used in a variety of contexts and in multiple scenarios ranging from visualization of the results of a single study in a web page to building data analysis platforms.
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Dräger A, Palsson BØ. Improving collaboration by standardization efforts in systems biology. Front Bioeng Biotechnol 2014; 2:61. [PMID: 25538939 PMCID: PMC4259112 DOI: 10.3389/fbioe.2014.00061] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 11/14/2014] [Indexed: 11/17/2022] Open
Abstract
Collaborative genome-scale reconstruction endeavors of metabolic networks would not be possible without a common, standardized formal representation of these systems. The ability to precisely define biological building blocks together with their dynamic behavior has even been considered a prerequisite for upcoming synthetic biology approaches. Driven by the requirements of such ambitious research goals, standardization itself has become an active field of research on nearly all levels of granularity in biology. In addition to the originally envisaged exchange of computational models and tool interoperability, new standards have been suggested for an unambiguous graphical display of biological phenomena, to annotate, archive, as well as to rank models, and to describe execution and the outcomes of simulation experiments. The spectrum now even covers the interaction of entire neurons in the brain, three-dimensional motions, and the description of pharmacometric studies. Thereby, the mathematical description of systems and approaches for their (repeated) simulation are clearly separated from each other and also from their graphical representation. Minimum information definitions constitute guidelines and common operation protocols in order to ensure reproducibility of findings and a unified knowledge representation. Central database infrastructures have been established that provide the scientific community with persistent links from model annotations to online resources. A rich variety of open-source software tools thrives for all data formats, often supporting a multitude of programing languages. Regular meetings and workshops of developers and users lead to continuous improvement and ongoing development of these standardization efforts. This article gives a brief overview about the current state of the growing number of operation protocols, mark-up languages, graphical descriptions, and fundamental software support with relevance to systems biology.
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Affiliation(s)
- Andreas Dräger
- Systems Biology Research Group, Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- Cognitive Systems, Center for Bioinformatics Tübingen (ZBIT), Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Bernhard Ø. Palsson
- Systems Biology Research Group, Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
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Clancy T, Hovig E. From proteomes to complexomes in the era of systems biology. Proteomics 2014; 14:24-41. [PMID: 24243660 DOI: 10.1002/pmic.201300230] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Revised: 10/22/2013] [Accepted: 11/06/2013] [Indexed: 01/16/2023]
Abstract
Protein complexes carry out almost the entire signaling and functional processes in the cell. The protein complex complement of a cell, and its network of complex-complex interactions, is referred to here as the complexome. Computational methods to predict protein complexes from proteomics data, resulting in network representations of complexomes, have recently being developed. In addition, key advances have been made toward understanding the network and structural organization of complexomes. We review these bioinformatics advances, and their discovery-potential, as well as the merits of integrating proteomics data with emerging methods in systems biology to study protein complex signaling. It is envisioned that improved integration of proteomics and systems biology, incorporating the dynamics of protein complexes in space and time, may lead to more predictive models of cell signaling networks for effective modulation.
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Affiliation(s)
- Trevor Clancy
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
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Babur Ö, Dogrusoz U, Çakır M, Aksoy BA, Schultz N, Sander C, Demir E. Integrating biological pathways and genomic profiles with ChiBE 2. BMC Genomics 2014; 15:642. [PMID: 25086704 PMCID: PMC4131037 DOI: 10.1186/1471-2164-15-642] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 07/24/2014] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Dynamic visual exploration of detailed pathway information can help researchers digest and interpret complex mechanisms and genomic datasets. RESULTS ChiBE is a free, open-source software tool for visualizing, querying, and analyzing human biological pathways in BioPAX format. The recently released version 2 can search for neighborhoods, paths between molecules, and common regulators/targets of molecules, on large integrated cellular networks in the Pathway Commons database as well as in local BioPAX models. Resulting networks can be automatically laid out for visualization using a graphically rich, process-centric notation. Profiling data from the cBioPortal for Cancer Genomics and expression data from the Gene Expression Omnibus can be overlaid on these networks. CONCLUSIONS ChiBE's new capabilities are organized around a genomics-oriented workflow and offer a unique comprehensive pathway analysis solution for genomics researchers. The software is freely available at http://code.google.com/p/chibe.
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Affiliation(s)
- Özgün Babur
- Computational Biology Center, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, Box 460, New York, NY 10065, USA.
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Chaouiya C, Bérenguier D, Keating SM, Naldi A, van Iersel MP, Rodriguez N, Dräger A, Büchel F, Cokelaer T, Kowal B, Wicks B, Gonçalves E, Dorier J, Page M, Monteiro PT, von Kamp A, Xenarios I, de Jong H, Hucka M, Klamt S, Thieffry D, Le Novère N, Saez-Rodriguez J, Helikar T. SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. BMC SYSTEMS BIOLOGY 2013; 7:135. [PMID: 24321545 PMCID: PMC3892043 DOI: 10.1186/1752-0509-7-135] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 11/26/2013] [Indexed: 05/03/2023]
Abstract
BACKGROUND Qualitative frameworks, especially those based on the logical discrete formalism, are increasingly used to model regulatory and signalling networks. A major advantage of these frameworks is that they do not require precise quantitative data, and that they are well-suited for studies of large networks. While numerous groups have developed specific computational tools that provide original methods to analyse qualitative models, a standard format to exchange qualitative models has been missing. RESULTS We present the Systems Biology Markup Language (SBML) Qualitative Models Package ("qual"), an extension of the SBML Level 3 standard designed for computer representation of qualitative models of biological networks. We demonstrate the interoperability of models via SBML qual through the analysis of a specific signalling network by three independent software tools. Furthermore, the collective effort to define the SBML qual format paved the way for the development of LogicalModel, an open-source model library, which will facilitate the adoption of the format as well as the collaborative development of algorithms to analyse qualitative models. CONCLUSIONS SBML qual allows the exchange of qualitative models among a number of complementary software tools. SBML qual has the potential to promote collaborative work on the development of novel computational approaches, as well as on the specification and the analysis of comprehensive qualitative models of regulatory and signalling networks.
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Affiliation(s)
- Claudine Chaouiya
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal
| | - Duncan Bérenguier
- Institut de Mathématiques de Luminy, Campus de Luminy, Case 907, 13288 Marseille Cedex 9, France
| | - Sarah M Keating
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Aurélien Naldi
- Center for Integrative Genomics, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Martijn P van Iersel
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nicolas Rodriguez
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Andreas Dräger
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093-0412, USA
- Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, 72076 Tübingen, Germany
| | - Finja Büchel
- Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, 72076 Tübingen, Germany
| | - Thomas Cokelaer
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Bryan Kowal
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Benjamin Wicks
- College of Information Science and Technology, University of Nebraska at Omaha, Omaha, NE 68182, USA
| | - Emanuel Gonçalves
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Julien Dorier
- Swiss-Prot & Vital-IT group, SIB- Swiss Institute of Bioinformatics, Center for Integrative Genomics, University of Lausanne, Quartier Sorge - Batiment Genopode, CH-1015 Lausanne, Switzerland
| | - Michel Page
- INRIA Grenoble – Rhône-Alpes, 655 avenue de l’Europe, Montbonnot, 38334 Saint-Ismier Cedex, France
- IAE Grenoble, Université Pierre-Mendès-France, Domaine universitaire BP 47, 38040 Grenoble Cedex 9, France
| | - Pedro T Monteiro
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal
- Instituto de Engenharia de Sistemas e Computadores - Investigação e Desenvolvimento (INESC-ID), Rua Alves Redol 9, 1000-029 Lisbon, Portugal
| | - Axel von Kamp
- Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1, D-39106 Magdeburg, Germany
| | - Ioannis Xenarios
- Swiss-Prot & Vital-IT group, SIB- Swiss Institute of Bioinformatics, Center for Integrative Genomics, University of Lausanne, Quartier Sorge - Batiment Genopode, CH-1015 Lausanne, Switzerland
| | - Hidde de Jong
- INRIA Grenoble – Rhône-Alpes, 655 avenue de l’Europe, Montbonnot, 38334 Saint-Ismier Cedex, France
| | - Michael Hucka
- Computing and Mathematical sciences, California Institute of Technology, Pasadena, CA 91125, USA
| | - Steffen Klamt
- Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1, D-39106 Magdeburg, Germany
| | - Denis Thieffry
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS) - UMR CNRS 8197 - INSERM 1024 46 rue d’Ulm, 75230 Paris Cedex 05, France
| | - Nicolas Le Novère
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Julio Saez-Rodriguez
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Tomáš Helikar
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
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Fried JY, van Iersel MP, Aladjem MI, Kohn KW, Luna A. PathVisio-Faceted Search: an exploration tool for multi-dimensional navigation of large pathways. Bioinformatics 2013; 29:1465-6. [PMID: 23547033 DOI: 10.1093/bioinformatics/btt146] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
PURPOSE The PathVisio-Faceted Search plugin helps users explore and understand complex pathways by overlaying experimental data and data from webservices, such as Ensembl BioMart, onto diagrams drawn using formalized notations in PathVisio. The plugin then provides a filtering mechanism, known as a faceted search, to find and highlight diagram nodes (e.g. genes and proteins) of interest based on imported data. The tool additionally provides a flexible scripting mechanism to handle complex queries. AVAILABILITY The PathVisio-Faceted Search plugin is compatible with PathVisio 3.0 and above. PathVisio is compatible with Windows, Mac OS X and Linux. The plugin, documentation, example diagrams and Groovy scripts are available at http://PathVisio.org/wiki/PathVisioFacetedSearchHelp. The plugin is free, open-source and licensed by the Apache 2.0 License.
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Affiliation(s)
- Jake Y Fried
- Computer Engineering, University of Maryland, College Park, MD 20740, USA.
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