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Wang M, Li F, Wu H, Liu Q, Li S. PredPromoter-MF(2L): A Novel Approach of Promoter Prediction Based on Multi-source Feature Fusion and Deep Forest. Interdiscip Sci 2022; 14:697-711. [PMID: 35488998 DOI: 10.1007/s12539-022-00520-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 04/05/2022] [Accepted: 04/05/2022] [Indexed: 12/12/2022]
Abstract
Promoters short DNA sequences play vital roles in initiating gene transcription. However, it remains a challenge to identify promoters using conventional experiment techniques in a high-throughput manner. To this end, several computational predictors based on machine learning models have been developed, while their performance is unsatisfactory. In this study, we proposed a novel two-layer predictor, called PredPromoter-MF(2L), based on multi-source feature fusion and ensemble learning. PredPromoter-MF(2L) was developed based on various deep features learned by a pre-trained deep learning network model and sequence-derived features. Feature selection based on XGBoost was applied to reduce fused features dimensions, and a cascade deep forest model was trained on the selected feature subset for promoter prediction. The results both fivefold cross-validation and independent test demonstrated that PredPromoter-MF(2L) outperformed state-of-the-art methods.
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Affiliation(s)
- Miao Wang
- College of Information Engineering, Northwest A&F University, Yangling, 712100, Shanxi, China
| | - Fuyi Li
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, 792 Elizabeth Street, Melbourne, VIC, 3000, Australia
| | - Hao Wu
- School of Software, Shandong University, Jinan, 250100, Shandong, China
| | - Quanzhong Liu
- College of Information Engineering, Northwest A&F University, Yangling, 712100, Shanxi, China.
| | - Shuqin Li
- College of Information Engineering, Northwest A&F University, Yangling, 712100, Shanxi, China.
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Wang C, Liao S, Wang Y, Hu X, Xu J. Computational Identification of Guillain-Barré Syndrome-Related Genes by an mRNA Gene Expression Profile and a Protein–Protein Interaction Network. Front Mol Neurosci 2022; 15:850209. [PMID: 35370550 PMCID: PMC8968047 DOI: 10.3389/fnmol.2022.850209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 02/24/2022] [Indexed: 11/22/2022] Open
Abstract
Background In the present study, we used a computational method to identify Guillain–Barré syndrome (GBS) related genes based on (i) a gene expression profile, and (ii) the shortest path analysis in a protein–protein interaction (PPI) network. Materials and Methods mRNA Microarray analyses were performed on the peripheral blood mononuclear cells (PBMCs) of four GBS patients and four age- and gender-matched healthy controls. Results Totally 30 GBS-related genes were screened out, in which 20 were retrieved from PPI analysis of upregulated expressed genes and 23 were from downregulated expressed genes (13 overlap genes). Gene ontology (GO) enrichment and KEGG enrichment analysis were performed, respectively. Results showed that there were some overlap GO terms and KEGG pathway terms in both upregulated and downregulated analysis, including positive regulation of macromolecule metabolic process, intracellular signaling cascade, cell surface receptor linked signal transduction, intracellular non-membrane-bounded organelle, non-membrane-bounded organelle, plasma membrane, ErbB signaling pathway, focal adhesion, neurotrophin signaling pathway and Wnt signaling pathway, which indicated these terms may play a critical role during GBS process. Discussion These results provided basic information about the genetic and molecular pathogenesis of GBS disease, which may improve the development of effective genetic strategies for GBS treatment in the future.
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Affiliation(s)
- Chunyang Wang
- Department of Neurology, Tianjin Medical University General Hospital, Tianjin, China
| | - Shiwei Liao
- Tianjin Key Laboratory of Cerebral Vascular and Neurodegenerative Diseases, Department of Neurorehabilitation and Neurology, Tianjin Huanhu Hospital, Tianjin Neurosurgical Institute, Tianjin, China
| | - Yiyi Wang
- Department of Neurology, Tianjin Haihe Hospital, Tianjin, China
| | - Xiaowei Hu
- Department of Neurology, Tianjin Medical University General Hospital, Tianjin, China
| | - Jing Xu
- Department of Neurology, Tianjin Medical University General Hospital, Tianjin, China
- *Correspondence: Jing Xu,
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Muhie S, Gautam A, Chakraborty N, Hoke A, Meyerhoff J, Hammamieh R, Jett M. Molecular indicators of stress-induced neuroinflammation in a mouse model simulating features of post-traumatic stress disorder. Transl Psychiatry 2017; 7:e1135. [PMID: 28534873 PMCID: PMC5534959 DOI: 10.1038/tp.2017.91] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 03/08/2017] [Indexed: 12/26/2022] Open
Abstract
A social-stress mouse model was used to simulate features of post-traumatic stress disorder (PTSD). The model involved exposure of an intruder (male C57BL/6) mouse to a resident aggressor (male SJL) mouse for 5 or 10 consecutive days. Transcriptome changes in brain regions (hippocampus, amygdala, medial prefrontal cortex and hemibrain), blood and spleen as well as epigenome changes in the hemibrain were assayed after 1- and 10-day intervals following the 5-day trauma or after 1- and 42-day intervals following the 10-day trauma. Analyses of differentially expressed genes (common among brain, blood and spleen) and differentially methylated promoter regions revealed that neurogenesis and synaptic plasticity pathways were activated during the early responses but were inhibited after the later post-trauma intervals. However, inflammatory pathways were activated throughout the observation periods, except in the amygdala in which they were inhibited only at the later post-trauma intervals. Phenotypically, inhibition of neurogenesis was corroborated by impaired Y-maze behavioral responses. Sustained neuroinflammation appears to drive the development and maintenance of behavioral manifestations of PTSD, potentially via its inhibitory effect on neurogenesis and synaptic plasticity. By contrast, peripheral inflammation seems to be directly responsible for tissue damage underpinning somatic comorbid pathologies. Identification of overlapping, differentially regulated genes and pathways between blood and brain suggests that blood could be a useful and accessible brain surrogate specimen for clinical translation.
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Affiliation(s)
- S Muhie
- The Geneva Foundation, Frederick, MD, USA,Advanced Academics Programs, Krieger School of Arts & Sciences, Johns Hopkins University, Baltimore, MD, USA
| | - A Gautam
- Integrative Systems Biology, US Army Center for Environmental Health Research, Frederick, MD, USA
| | | | - A Hoke
- The Geneva Foundation, Frederick, MD, USA
| | | | - R Hammamieh
- Integrative Systems Biology, US Army Center for Environmental Health Research, Frederick, MD, USA
| | - M Jett
- Integrative Systems Biology, US Army Center for Environmental Health Research, Frederick, MD, USA,Integrative Systems Biology, US Army Center for Environmental Health Research, 568 Doughten Drive, Fort Detrick, Frederick, MD 21702-5010, USA. E-mail:
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Mitra R, Edmonds MD, Sun J, Zhao M, Yu H, Eischen CM, Zhao Z. Reproducible combinatorial regulatory networks elucidate novel oncogenic microRNAs in non-small cell lung cancer. RNA (NEW YORK, N.Y.) 2014; 20:1356-68. [PMID: 25024357 PMCID: PMC4138319 DOI: 10.1261/rna.042754.113] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2013] [Accepted: 05/01/2014] [Indexed: 06/03/2023]
Abstract
While previous studies reported aberrant expression of microRNAs (miRNAs) in non-small cell lung cancer (NSCLC), little is known about which miRNAs play central roles in NSCLC's pathogenesis and its regulatory mechanisms. To address this issue, we presented a robust computational framework that integrated matched miRNA and mRNA expression profiles in NSCLC using feed-forward loops. The network consists of miRNAs, transcription factors (TFs), and their common predicted target genes. To discern the biological meaning of their associations, we introduced the direction of regulation. A network edge validation strategy using three independent NSCLC expression profiling data sets pinpointed reproducible biological regulations. Reproducible regulation, which may reflect the true molecular interaction, has not been applied to miRNA-TF co-regulatory network analyses in cancer or other diseases yet. We revealed eight hub miRNAs that connected to a higher proportion of targets validated by independent data sets. Network analyses showed that these miRNAs might have strong oncogenic characteristics. Furthermore, we identified a novel miRNA-TF co-regulatory module that potentially suppresses the tumor suppressor activity of the TGF-β pathway by targeting a core pathway molecule (TGFBR2). Follow-up experiments showed two miRNAs (miR-9-5p and miR-130b-3p) in this module had increased expression while their target gene TGFBR2 had decreased expression in a cohort of human NSCLC. Moreover, we demonstrated these two miRNAs directly bind to the 3' untranslated region of TGFBR2. This study enhanced our understanding of miRNA-TF co-regulatory mechanisms in NSCLC. The combined bioinformatics and validation approach we described can be applied to study other types of diseases.
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Affiliation(s)
- Ramkrishna Mitra
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Mick D Edmonds
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Jingchun Sun
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Min Zhao
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Hui Yu
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Christine M Eischen
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Zhongming Zhao
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA Department of Psychiatry, Vanderbilt University School of Medicine, Nashville, Tennessee 37212, USA Center for Quantitative Sciences, Vanderbilt University, Nashville, Tennessee 37232, USA
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Li L, Lian B, Li C, Li W, Li J, Zhang Y, He X, Li Y, Xie L. Integrative analysis of transcriptional regulatory network and copy number variation in intrahepatic cholangiocarcinoma. PLoS One 2014; 9:e98653. [PMID: 24897108 PMCID: PMC4045758 DOI: 10.1371/journal.pone.0098653] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2014] [Accepted: 05/06/2014] [Indexed: 01/02/2023] Open
Abstract
Background Transcriptional regulatory network (TRN) is used to study conditional regulatory relationships between transcriptional factors and genes. However few studies have tried to integrate genomic variation information such as copy number variation (CNV) with TRN to find causal disturbances in a network. Intrahepatic cholangiocarcinoma (ICC) is the second most common hepatic carcinoma with high malignancy and poor prognosis. Research about ICC is relatively limited comparing to hepatocellular carcinoma, and there are no approved gene therapeutic targets yet. Method We first constructed TRN of ICC (ICC-TRN) using forward-and-reverse combined engineering method, and then integrated copy number variation information with ICC-TRN to select CNV-related modules and constructed CNV-ICC-TRN. We also integrated CNV-ICC-TRN with KEGG signaling pathways to investigate how CNV genes disturb signaling pathways. At last, unsupervised clustering method was applied to classify samples into distinct classes. Result We obtained CNV-ICC-TRN containing 33 modules which were enriched in ICC-related signaling pathways. Integrated analysis of the regulatory network and signaling pathways illustrated that CNV might interrupt signaling through locating on either genomic sites of nodes or regulators of nodes in a signaling pathway. In the end, expression profiles of nodes in CNV-ICC-TRN were used to cluster the ICC patients into two robust groups with distinct biological function features. Conclusion Our work represents a primary effort to construct TRN in ICC, also a primary effort to try to identify key transcriptional modules based on their involvement of genetic variations shown by gene copy number variations (CNV). This kind of approach may bring the traditional studies of TRN based only on expression data one step further to genetic disturbance. Such kind of approach can easily be extended to other disease samples with appropriate data.
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Affiliation(s)
- Ling Li
- School of Life Sciences and Technology, Tongji University, Shanghai, P.R.China
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, P.R.China
| | - Baofeng Lian
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, P.R.China
- School of Life Sciences and Technology, Shanghai Jiaotong University, Shanghai, P.R.China
| | - Chao Li
- Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P.R.China
| | - Wei Li
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, P.R.China
| | - Jing Li
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, P.R.China
| | - Yuannv Zhang
- Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P.R.China
| | - Xianghuo He
- Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P.R.China
| | - Yixue Li
- School of Life Sciences and Technology, Tongji University, Shanghai, P.R.China
- School of Life Sciences and Technology, Shanghai Jiaotong University, Shanghai, P.R.China
- Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P.R.China
- * E-mail: (LX); (YL)
| | - Lu Xie
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, P.R.China
- * E-mail: (LX); (YL)
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Yang J, Yu H, Liu BH, Zhao Z, Liu L, Ma LX, Li YX, Li YY. DCGL v2.0: an R package for unveiling differential regulation from differential co-expression. PLoS One 2013; 8:e79729. [PMID: 24278165 PMCID: PMC3835854 DOI: 10.1371/journal.pone.0079729] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2013] [Accepted: 10/03/2013] [Indexed: 12/25/2022] Open
Abstract
Motivation Differential co-expression analysis (DCEA) has emerged in recent years as a novel, systematic investigation into gene expression data. While most DCEA studies or tools focus on the co-expression relationships among genes, some are developing a potentially more promising research domain, differential regulation analysis (DRA). In our previously proposed R package DCGL v1.0, we provided functions to facilitate basic differential co-expression analyses; however, the output from DCGL v1.0 could not be translated into differential regulation mechanisms in a straightforward manner. Results To advance from DCEA to DRA, we upgraded the DCGL package from v1.0 to v2.0. A new module named “Differential Regulation Analysis” (DRA) was designed, which consists of three major functions: DRsort, DRplot, and DRrank. DRsort selects differentially regulated genes (DRGs) and differentially regulated links (DRLs) according to the transcription factor (TF)-to-target information. DRrank prioritizes the TFs in terms of their potential relevance to the phenotype of interest. DRplot graphically visualizes differentially co-expressed links (DCLs) and/or TF-to-target links in a network context. In addition to these new modules, we streamlined the codes from v1.0. The evaluation results proved that our differential regulation analysis is able to capture the regulators relevant to the biological subject. Conclusions With ample functions to facilitate differential regulation analysis, DCGL v2.0 was upgraded from a DCEA tool to a DRA tool, which may unveil the underlying differential regulation from the observed differential co-expression. DCGL v2.0 can be applied to a wide range of gene expression data in order to systematically identify novel regulators that have not yet been documented as critical. Availability DCGL v2.0 package is available at http://cran.r-project.org/web/packages/DCGL/index.html or at our project home page http://lifecenter.sgst.cn/main/en/dcgl.jsp.
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Affiliation(s)
- Jing Yang
- School of Biotechnology, East China University of Science and Technology, Shanghai, P. R. China
- Bioinformatics Center, Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P. R. China
| | - Hui Yu
- Shanghai Center for Bioinformation Technology, Shanghai Industrial Technology Institute, Shanghai, P. R. China
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Bao-Hong Liu
- Shanghai Center for Bioinformation Technology, Shanghai Industrial Technology Institute, Shanghai, P. R. China
| | - Zhongming Zhao
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- Departments of Psychiatry, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Lei Liu
- Bioinformatics Center, Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P. R. China
| | - Liang-Xiao Ma
- Shanghai Center for Bioinformation Technology, Shanghai Industrial Technology Institute, Shanghai, P. R. China
| | - Yi-Xue Li
- School of Biotechnology, East China University of Science and Technology, Shanghai, P. R. China
- Shanghai Center for Bioinformation Technology, Shanghai Industrial Technology Institute, Shanghai, P. R. China
- * E-mail: (YYL); (YXL)
| | - Yuan-Yuan Li
- Shanghai Center for Bioinformation Technology, Shanghai Industrial Technology Institute, Shanghai, P. R. China
- * E-mail: (YYL); (YXL)
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Naeem H, Zimmer R, Tavakkolkhah P, Küffner R. Rigorous assessment of gene set enrichment tests. ACTA ACUST UNITED AC 2012; 28:1480-6. [PMID: 22492315 DOI: 10.1093/bioinformatics/bts164] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
MOTIVATION Several statistical tests are available to detect the enrichment of differential expression in gene sets. Such tests were originally proposed for analyzing gene sets associated with biological processes. The objective evaluation of tests on real measurements has not been possible as it is difficult to decide a priori, which processes will be affected in given experiments. RESULTS We present a first large study to rigorously assess and compare the performance of gene set enrichment tests on real expression measurements. Gene sets are defined based on the targets of given regulators such as transcription factors (TFs) and microRNAs (miRNAs). In contrast to processes, TFs and miRNAs are amenable to direct perturbations, e.g. regulator over-expression or deletion. We assess the ability of 14 different statistical tests to predict the perturbations from expression measurements in Escherichia coli, Saccharomyces cerevisiae and human. We also analyze how performance depends on the quality and comprehensiveness of the regulator targets via a permutation approach. We find that ANOVA and Wilcoxons test consistently perform better than for instance Kolmogorov-Smirnov and hypergeometric tests. For scenarios where the optimal test is not known, we suggest to combine all evaluated tests into an unweighted consensus, which also performs well in our assessment. Our results provide a guide for the selection of existing tests as well as a basis for the development and assessment of novel tests.
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Affiliation(s)
- Haroon Naeem
- Department of Informatics, Ludwig-Maximilians Universität, Amalienstrasse 17, Munich, Germany
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Identification of colorectal cancer related genes with mRMR and shortest path in protein-protein interaction network. PLoS One 2012; 7:e33393. [PMID: 22496748 PMCID: PMC3319543 DOI: 10.1371/journal.pone.0033393] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Accepted: 02/13/2012] [Indexed: 11/19/2022] Open
Abstract
One of the most important and challenging problems in biomedicine and genomics is how to identify the disease genes. In this study, we developed a computational method to identify colorectal cancer-related genes based on (i) the gene expression profiles, and (ii) the shortest path analysis of functional protein association networks. The former has been used to select differentially expressed genes as disease genes for quite a long time, while the latter has been widely used to study the mechanism of diseases. With the existing protein-protein interaction data from STRING (Search Tool for the Retrieval of Interacting Genes), a weighted functional protein association network was constructed. By means of the mRMR (Maximum Relevance Minimum Redundancy) approach, six genes were identified that can distinguish the colorectal tumors and normal adjacent colonic tissues from their gene expression profiles. Meanwhile, according to the shortest path approach, we further found an additional 35 genes, of which some have been reported to be relevant to colorectal cancer and some are very likely to be relevant to it. Interestingly, the genes we identified from both the gene expression profiles and the functional protein association network have more cancer genes than the genes identified from the gene expression profiles alone. Besides, these genes also had greater functional similarity with the reported colorectal cancer genes than the genes identified from the gene expression profiles alone. All these indicate that our method as presented in this paper is quite promising. The method may become a useful tool, or at least plays a complementary role to the existing method, for identifying colorectal cancer genes. It has not escaped our notice that the method can be applied to identify the genes of other diseases as well.
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Huang CL, Lamb J, Chindelevitch L, Kostrowicki J, Guinney J, DeLisi C, Ziemek D. Correlation set analysis: detecting active regulators in disease populations using prior causal knowledge. BMC Bioinformatics 2012; 13:46. [PMID: 22443377 PMCID: PMC3382432 DOI: 10.1186/1471-2105-13-46] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Accepted: 03/23/2012] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Identification of active causal regulators is a crucial problem in understanding mechanism of diseases or finding drug targets. Methods that infer causal regulators directly from primary data have been proposed and successfully validated in some cases. These methods necessarily require very large sample sizes or a mix of different data types. Recent studies have shown that prior biological knowledge can successfully boost a method's ability to find regulators. RESULTS We present a simple data-driven method, Correlation Set Analysis (CSA), for comprehensively detecting active regulators in disease populations by integrating co-expression analysis and a specific type of literature-derived causal relationships. Instead of investigating the co-expression level between regulators and their regulatees, we focus on coherence of regulatees of a regulator. Using simulated datasets we show that our method performs very well at recovering even weak regulatory relationships with a low false discovery rate. Using three separate real biological datasets we were able to recover well known and as yet undescribed, active regulators for each disease population. The results are represented as a rank-ordered list of regulators, and reveals both single and higher-order regulatory relationships. CONCLUSIONS CSA is an intuitive data-driven way of selecting directed perturbation experiments that are relevant to a disease population of interest and represent a starting point for further investigation. Our findings demonstrate that combining co-expression analysis on regulatee sets with a literature-derived network can successfully identify causal regulators and help develop possible hypothesis to explain disease progression.
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Affiliation(s)
- Chia-Ling Huang
- Bioinformatics Graduate Program, and Department of Biomedical Engineering, Boston University, 44 Cummington Street, Boston, MA 02215, USA
| | - John Lamb
- Oncology Research Unit, Worldwide Research & Development, Pfizer, 10646 Science center Drive, San Diego, CA 92121, USA
| | - Leonid Chindelevitch
- Computational Sciences Center of Emphasis, Worldwide Research & Development, Pfizer, 35 Cambridgepark Drive, Cambridge, MA 02140, USA
| | - Jarek Kostrowicki
- Oncology Research Unit, Worldwide Research & Development, Pfizer, 10646 Science center Drive, San Diego, CA 92121, USA
| | - Justin Guinney
- Sage Bionetworks, 1100 Fairview Ave North, Seattle, WA 98109, USA
| | - Charles DeLisi
- Bioinformatics Graduate Program, and Department of Biomedical Engineering, Boston University, 44 Cummington Street, Boston, MA 02215, USA
| | - Daniel Ziemek
- Computational Sciences Center of Emphasis, Worldwide Research & Development, Pfizer, 35 Cambridgepark Drive, Cambridge, MA 02140, USA
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MIRTFnet: analysis of miRNA regulated transcription factors. PLoS One 2011; 6:e22519. [PMID: 21857930 PMCID: PMC3157336 DOI: 10.1371/journal.pone.0022519] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Accepted: 06/27/2011] [Indexed: 01/02/2023] Open
Abstract
Background Several expression datasets of miRNA transfection experiments are available to analyze the regulatory mechanisms downstream of miRNA effects. The miRNA induced regulatory effects can be propagated via transcription factors (TFs). We propose the method MIRTFnet to identify miRNA controlled TFs as active regulators if their downstream target genes are differentially expressed. Methodology/Principal Findings MIRTFnet enables the determination of active transcription factors (TFs) and is sensitive enough to exploit the small expression changes induced by the activity of miRNAs. For this purpose, different statistical tests were evaluated and compared. Based on the identified TFs, databases, computational predictions and the literature we construct regulatory models downstream of miRNA actions. Transfecting miRNAs are connected to active regulators via a network of miRNA-TF, miRNA-kinase-TF as well as TF-TF relationships. Based on 43 transfection experiments involving 17 cancer relevant miRNAs we show that MIRTFnet detects active regulators reliably. Conclusions/Significance The consensus of the individual regulatory models shows that the examined miRNAs induce activity changes in a common core of transcription factors involved in cancer related processes such as proliferation or apoptosis.
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