ALTRABio presents WikiBioPath: new perspectives in biological data analysis
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The document discusses WikiBioPath, a company that provides integrative data analysis of bio-molecular data through statistical analysis and interpretation of results in the context of biological knowledge. It offers expertise in transcriptomics, proteomics and genomics data from samples to help identify biomarkers, optimize drug compounds, and support personalized medicine. Key services discussed include pre-processing and quality control of experimental data, statistical analysis at the gene and gene set level, identifying population structures, and integrating results with knowledge from literature and databases.
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ALTRABio presents WikiBioPath: new perspectives in biological data analysis
- 1. Supported by Prominent international speakers from h"p://workshop.eisbm.eu1
- 2. EISBM 2012 WikiBioPath new perspectives in biological data analysis laurent Buffat, MD, PhD Simon de Bernard, X, PhD mercredi 13 juin 2012 1
- 3. Core expertise Analysis & high level interpretation of bio-molecular data : • Transcriptomics • Proteomics • Genomics Pharmaco-genomics Functional Genomics Samples Data Bio-statistical Interpretation generation analysis Reports For research & industry in WikiBioPath the Life Sciences Integrative data analysis mercredi 13 juin 2012 2
- 4. Core expertise : application fields Analysis & interpretation & Data mIning of bio- molecular data Molecules repositionning - new Biomarker discovery market applications Pharmaco-genomics Pathway studies, Functional Genomics Toxicity studies Patient class Identification / support to personalized medecine Drug compound Optimization mercredi 13 juin 2012 3
- 5. Challenge Bio-statistical Interpretation Experimental Data analysis Discovery Data Warehouses ? Scientific litterature Private / Public mercredi 13 juin 2012 4
- 6. Knowledge integration Bio-statistical Interpretation Data generation analysis Discovery Data Warehouses Knowledge integration Scientific litterature WikiBioPath Private / Public mercredi 13 juin 2012 5
- 7. expression Experimental Data Analysis Experimental data • MicroArray (Illumina, RNG/MRC, Agilent, Affymetrix, etc.) • High Throughput Sequencing • SNPs • Copy Number • GenoTyping mercredi 13 juin 2012 6
- 8. expression Experimental Data Analysis • PreProcessing & Quality Control • Hybridization issues solving • Background corrections • Probeset summarization • RNA degradation correction • identification of annotations errors • Correction of systematic bias • etc. mercredi 13 juin 2012 7
- 9. expression Experimental Data Analysis Statistical Analysis • Gene level: • expression level modelization − KRT75 − RNASE7 − UPP1 − LCN2 − C4orf19 − SPRR2G − SPRR2A − KRT17 − ODC1 − RPTN − HMGCS2 − DHRS9 & visualization (linear models, − C14orf34 − SPRR3 − TCHH − MMP3 − MMP10 − S100A12 − S100A7 − CCAR1 − TAF1D − TSPAN5 − LEPROT − DNAJC1 − SECISBP2 − ANKRD11 − SFRS18 − PVRL4 − SMC3 − MALAT1 − TAOK1 − HIST1H4C − USO1 contrasts, multitesting correction) − M6PR − TOP1 − LOC100131261 − EPRS − FABP4 − KRT9 − CHST2 − SYNM − SPRR4 − PI3 − SPINK6 − IGFL1 − IFIT3 − IFIT1 − IFIH1 • statistical expression level − MX1 − XAF1 − IFI44 − IFITM1 − DDX60 − HLA−B − ISG15 − IFITM3 − IFI27 − IFI6 − PRSS23 − YARS − PCK2 − ASNS − AARS − XBP1 − TARS − MARS − HERPUD1 − CHAC1 − TUBE1 − PSPH comparison − SLC7A11 − SERPINE2 − BCHE − CADM1 − CBS − SHMT2 − MOCOS − PSAT1 − RCN1 − ASS1 − NUPR1 − EIF4EBP1 − PHGDH − ECM2 − STC2 − S100P − CH25H − PHLDA1 − SLC7A5 − ANKRD30BL − S100A7A − TCN1 • etc. − KCTD11 − ADM − PPP1R3C − ANGPTL4 − C7orf68 − PFKFB3 − ANKRD37 − NDRG1 − FUT11 − SERPINE1 − MT1X − PFKFB4 − PPFIA4 − PGF − LRMP − IER3 − P4HA1 − CA9 − EGLN3 − DDIT4 − FOS − ALDOC − IGFBP3 − NDUFA4L2 − PFKP − PTTG1 − CLCA4 − SLC6A8 − ZNF395 − MKNK2 − HOXC6 − HMGB2 − NUAK1 − TYRP1 − C15orf59 − SLC46A2 − SLC1A6 − ALOX12 − SLC16A10 − TMEM99 − SLC45A4 − GAN − ACPP − CA6 − RARRES1 − FAM83D − C1orf105 − HSD11B1 − SERPINB12 − TNNC1 − PTGS1 − TPX2 − SLC40A1 − INHBB − KRT77 − CRNN − CASP14 − SERPINB4 PBS A PBS A PBS A PBS A PBS A PBS B PBS B PBS B PBS B PBS B None B None B None B None B None B None B T1 A T1 A T1 A T1 A T1 A T1 A T1 B T1 B T1 B T1 B T1 B T1 B T2 A T2 A T2 A T2 A T2 A T2 B T2 B T2 B T2 B T2 B T2 B T3 A T3 A T3 A T3 A T3 A T3 B T3 B T3 B T3 B T3 B T3 B mercredi 13 juin 2012 8
- 10. expression Experimental Data Analysis Statistical Analysis, Knowledge integration • Geneset level: • geneset based analyses / correlation identification • parametric analysis of geneset enrichment p−values < 1e−04 Broad:NAGASHIMA_EGF_SIGNALING < 1e−04 Broad:JIANG_HYPOXIA_NORMAL < 1e−04 Broad:MENSE_HYPOXIA < 1e−04 Broad:ZHOU_INFLAMMATORY_RESPONSE_LIVE < 1e−04 Broad:ZHOU_INFLAMMATORY_RESPONSE_LPS < 1e−04 ... 0.00022 Broad:LEONARD_HYPOXIA 0.00025 CTD:Carbaryl 0.00032 CTD:Amiloride 0.00038 CTD:Kainic Acid 0.00050 positive regulation of response to stimulus (GO:0048584) 0.00082 CTD:Buthionine Sulfoximine 0.00085 Broad:BIOCARTA_TOLL_PATHWAY 0.00085 serine family amino acid metabolic process (GO:0009069) 0.00088 Broad:GOLDRATH_IMMUNE_MEMORY 0.00097 Broad:SCIAN_INVERSED_TARGETS_OF_TP53_AND_TP73 0.00112 neutral amino acid transport (GO:0015804) 0.00133 CTD:allylpyrocatechol 0.00160 CTD:temozolomide 0.00178 CTD:2,4−dinitrotoluene 0.00183 L2L:hypoxia_reg 0.00198 Broad:GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_RED 0.00252 CTD:Paraquat 0.00258 One carbon pool by folate (KEGG:00670) 0.00265 L2L:calres_mouse 0.00267 Broad:SABATES_COLORECTAL_ADENOMA_SIZE 0.00275 Broad:BREDEMEYER_RAG_SIGNALING_VIA_ATM_NOT_VIA_NFKB 0.00300 CTD:butylbenzyl phthalate 0.00300 CTD:Cocaine 0.00300 Broad:ST_GAQ_PATHWAY 0.00308 Broad:SCHLOSSER_MYC_TARGETS_AND_SERUM_RESPONSE 0.00323 CTD:Diclofenac 0.00340 secretion (GO:0046903) 0.00352 positive regulation of endothelial cell migration (GO:0010595) 0.00358 ... 0.00385 Broad:GENTILE_UV_RESPONSE_CLUSTER_D6 0.00390 nucleoside catabolic process (GO:0009164) 0.00395 L2L:hdaci_colon_cursul 0.00405 CTD:2−nitrotoluene 0.00405 CTD:Platelet Activating Factor 0.00417 CTD:Allopurinol 0.00455 CTD:2,4−diaminotoluene 0.00477 CTD:Pam(3)CSK(4) peptide 0.00480 secretion by cell (GO:0032940) 0.00505 protein amino acid O−linked glycosylation (GO:0006493) 0.00513 CTD:bis(maltolato)oxovanadium(IV) 0.00522 CTD:Apigenin 0.00565 L2L:stress_genotoxic_specific 0.00568 CTD:4−(4−fluorophenyl)−2−(4−hydroxyphenyl)−5−(4−pyridyl)imidazole 0.00568 Broad:ST_GA13_PATHWAY PBS A PBS A PBS A PBS A PBS A PBS B PBS B PBS B PBS B PBS B None B None B None B None B None B None B T1 A T1 A T1 A T1 A T1 A T1 A T1 B T1 B T1 B T1 B T1 B T1 B T2 A T2 A T2 A T2 A T2 A T2 B T2 B T2 B T2 B T2 B T2 B T3 A T3 A T3 A T3 A T3 A T3 B T3 B T3 B T3 B T3 B T3 B mercredi 13 juin 2012 9
- 11. expression Experimental Data Analysis Population structuration • Structuring genes (hidden state models) Distance from closest class New classes Known Discriminative power mercredi 13 juin 2012 10
- 12. expression Experimental Data Analysis Population structuration • Structuring genesets, knowledge integration • geneset based analyses / correlation identification • parametric analysis of geneset enrichment Pvalues Concepts Genes GeneSets Samples mercredi 13 juin 2012 11
- 13. Interpretation of Data Analysis Results Why interpretation: • Data analysis: Crucial step • but need to contextualize results within the context of biological knowledge to turn data into really actionable results Interpretation challenges: Integrative Data Analysis • Gathering heterogeneous Knowledge and Data resources • Present Knowledge & Data in a manageable way mercredi 13 juin 2012 12
- 14. Interpretation of Data Analysis Results WikiBioPath (in short): Web App with online specific tools for • storing/managing Knowledge & Data (K&D) • enriching/curating K&D • querying/exploring/visualizing / mining K&D Allows heterogeneous K&D integration into the interpretation process Will be available as Free & Open Source We are currently looking for collaborations / beta testers mercredi 13 juin 2012 13
- 15. Web Portals/Apps, Applications Wikis public/external + private/internal public/external + private/internal External AND/OR External & WikiBioPath’s private Web Portals/ dedicated specialized Apps, Applications Wikis (Genes, Proteins, (NCBI, Kegg, ... ) Diseases, ... ) WBP’s linking & “bridging” WBP’s specialized functionalities for functionalities knowledge storing/querying/managing/... WikiBioPath Core Web based interface & online Tools for Data & Knowledge storing, managing, querying, visualizing, mining and more... Text Mining based Search WBP’s specialized functionalities for Engine & Explorer data storing/querying/managing/... Textual Data (Unstructured data repositories) Data Warehouses public/external + private/internal public/external + private/internal Bibliographical Databases Experimental Data & with low structured Experimental Data Analyses textual data Data Warehouses (Medline, own text (Micro Array Exp. Data, Micro collection ...) Array Analyses Results ...) mercredi 13 juin 2012 14