Publisher’s Note:Abstraction for Data Integration:Fusing Mammalian Molecular, Cellular and Phenotype Big Datasets for Better Knowledge Extraction

Overview

Journal Comput Biol Chem

Publisher Elsevier

Date 2015 Jun 24

PMID 26101093

Citations 3

Authors

Andrew D Rouillard

Zichen Wang

Avi Maayan

Affiliations

Soon will be listed here.

Citing Articles

Unsupervised Learning and Multipartite Network Models: A Promising Approach for Understanding Traditional Medicine.

Jafari M, Wang Y, Amiryousefi A, Tang J Front Pharmacol. 2020; 11:1319.

PMID: 32982738 PMC: 7479204. DOI: 10.3389/fphar.2020.01319.

Machine Learning and Integrative Analysis of Biomedical Big Data.

Mirza B, Wang W, Wang J, Choi H, Chung N, Ping P Genes (Basel). 2019; 10(2).

PMID: 30696086 PMC: 6410075. DOI: 10.3390/genes10020087.

The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins.

Rouillard A, Gundersen G, Fernandez N, Wang Z, Monteiro C, McDermott M Database (Oxford). 2016; 2016.

PMID: 27374120 PMC: 4930834. DOI: 10.1093/database/baw100.

References

Chen E, Tan C, Kou Y, Duan Q, Wang Z, Meirelles G . Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinformatics. 2013; 14:128. PMC: 3637064. DOI: 10.1186/1471-2105-14-128. View

Vastrik I, DEustachio P, Schmidt E, Joshi-Tope G, Gopinath G, Croft D . Reactome: a knowledge base of biologic pathways and processes. Genome Biol. 2007; 8(3):R39. PMC: 1868929. DOI: 10.1186/gb-2007-8-3-r39. View

He X, Fuller C, Song Y, Meng Q, Zhang B, Yang X . Sherlock: detecting gene-disease associations by matching patterns of expression QTL and GWAS. Am J Hum Genet. 2013; 92(5):667-80. PMC: 3644637. DOI: 10.1016/j.ajhg.2013.03.022. View

Ciofani M, Madar A, Galan C, Sellars M, Mace K, Pauli F . A validated regulatory network for Th17 cell specification. Cell. 2012; 151(2):289-303. PMC: 3503487. DOI: 10.1016/j.cell.2012.09.016. View

Moore T, Cohen M, Furberg C . Serious adverse drug events reported to the Food and Drug Administration, 1998-2005. Arch Intern Med. 2007; 167(16):1752-9. DOI: 10.1001/archinte.167.16.1752. View

Fung D, Li S, Goel A, Hong S, Wilkins M . Visualization of the interactome: what are we looking at?. Proteomics. 2012; 12(10):1669-86. DOI: 10.1002/pmic.201100454. View

Persico M, Ceol A, Gavrila C, Hoffmann R, Florio A, Cesareni G . HomoMINT: an inferred human network based on orthology mapping of protein interactions discovered in model organisms. BMC Bioinformatics. 2005; 6 Suppl 4:S21. PMC: 1866386. DOI: 10.1186/1471-2105-6-S4-S21. View

Haibe-Kains B, El-Hachem N, Birkbak N, Jin A, Beck A, Aerts H . Inconsistency in large pharmacogenomic studies. Nature. 2013; 504(7480):389-93. PMC: 4237165. DOI: 10.1038/nature12831. View

Bernstein B, Stamatoyannopoulos J, Costello J, Ren B, Milosavljevic A, Meissner A . The NIH Roadmap Epigenomics Mapping Consortium. Nat Biotechnol. 2010; 28(10):1045-8. PMC: 3607281. DOI: 10.1038/nbt1010-1045. View

10.

Helbling Chadwick L . The NIH Roadmap Epigenomics Program data resource. Epigenomics. 2012; 4(3):317-24. PMC: 3381455. DOI: 10.2217/epi.12.18. View

11.

Wilhelm M, Schlegl J, Hahne H, Gholami A, Lieberenz M, Savitski M . Mass-spectrometry-based draft of the human proteome. Nature. 2014; 509(7502):582-7. DOI: 10.1038/nature13319. View

12.

Barretina J, Caponigro G, Stransky N, Venkatesan K, Margolin A, Kim S . The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature. 2012; 483(7391):603-7. PMC: 3320027. DOI: 10.1038/nature11003. View

13.

Harpaz R, DuMouchel W, LePendu P, Bauer-Mehren A, Ryan P, Shah N . Performance of pharmacovigilance signal-detection algorithms for the FDA adverse event reporting system. Clin Pharmacol Ther. 2013; 93(6):539-46. PMC: 3857139. DOI: 10.1038/clpt.2013.24. View

14.

Kuhn M, Szklarczyk D, Franceschini A, von Mering C, Jensen L, Bork P . STITCH 3: zooming in on protein-chemical interactions. Nucleic Acids Res. 2011; 40(Database issue):D876-80. PMC: 3245073. DOI: 10.1093/nar/gkr1011. View

15.

Li M, Wang P, Liu X, Lim E, Wang Z, Yeager M . GWASdb: a database for human genetic variants identified by genome-wide association studies. Nucleic Acids Res. 2011; 40(Database issue):D1047-54. PMC: 3245026. DOI: 10.1093/nar/gkr1182. View

16.

Cheung H, Cowley G, Weir B, Boehm J, Rusin S, Scott J . Systematic investigation of genetic vulnerabilities across cancer cell lines reveals lineage-specific dependencies in ovarian cancer. Proc Natl Acad Sci U S A. 2011; 108(30):12372-7. PMC: 3145679. DOI: 10.1073/pnas.1109363108. View

17.

Croft D, Mundo A, Haw R, Milacic M, Weiser J, Wu G . The Reactome pathway knowledgebase. Nucleic Acids Res. 2013; 42(Database issue):D472-7. PMC: 3965010. DOI: 10.1093/nar/gkt1102. View

18.

Greshock J, Bachman K, Degenhardt Y, Jing J, Wen Y, Eastman S . Molecular target class is predictive of in vitro response profile. Cancer Res. 2010; 70(9):3677-86. DOI: 10.1158/0008-5472.CAN-09-3788. View

19.

Kilpinen H, Waszak S, Gschwind A, Raghav S, Witwicki R, Orioli A . Coordinated effects of sequence variation on DNA binding, chromatin structure, and transcription. Science. 2013; 342(6159):744-7. PMC: 5502466. DOI: 10.1126/science.1242463. View

20.

Karp P, Riley M, Paley S . The MetaCyc Database. Nucleic Acids Res. 2001; 30(1):59-61. PMC: 99148. DOI: 10.1093/nar/30.1.59. View