Supported byProminent international speakers from             h"p://workshop.eisbm.eu1
EISBM 2012                                      WikiBioPath                        new perspectives in biological data ana...
Core expertise                                                            Analysis & high level                           ...
Core expertise : application fields                            Analysis & interpretation                             & Dat...
Challenge                                                Bio-statistical                                                  ...
Knowledge integration                                          Bio-statistical                                            ...
expression Experimental           Data Analysis             Experimental data           •    MicroArray (Illumina, RNG/MRC...
expression Experimental           Data Analysis        • PreProcessing & Quality Control           •    Hybridization issu...
expression Experimental           Data Analysis    Statistical Analysis • Gene level:   • expression level modelization   ...
expression Experimental           Data Analysis       Statistical Analysis, Knowledge integration    • Geneset level:     ...
expression Experimental           Data Analysis       Population structuration    • Structuring genes (hidden state models...
expression Experimental           Data Analysis       Population structuration    • Structuring genesets, knowledge integr...
Interpretation of Data             Analysis Results             Why interpretation:           • Data analysis: Crucial ste...
Interpretation of Data             Analysis Results        WikiBioPath (in short):        Web App with online specific tool...
Web Portals/Apps, Applications                                                             Wikispublic/external + private/...
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ALTRABio presents WikiBioPath: new perspectives in biological data analysis

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Presentation made during the EISBM workshop, 13-15 June 2012 by Laurent Buffat (ALTRABio).

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ALTRABio presents WikiBioPath: new perspectives in biological data analysis

  1. 1. Supported byProminent international speakers from h"p://workshop.eisbm.eu1
  2. 2. EISBM 2012 WikiBioPath new perspectives in biological data analysis laurent Buffat, MD, PhD Simon de Bernard, X, PhDmercredi 13 juin 2012 1
  3. 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 analysismercredi 13 juin 2012 2
  4. 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 Optimizationmercredi 13 juin 2012 3
  5. 5. Challenge Bio-statistical Interpretation Experimental Data analysis Discovery Data Warehouses ? Scientific litterature Private / Publicmercredi 13 juin 2012 4
  6. 6. Knowledge integration Bio-statistical Interpretation Data generation analysis Discovery Data Warehouses Knowledge integration Scientific litterature WikiBioPathPrivate / Publicmercredi 13 juin 2012 5
  7. 7. expression Experimental Data Analysis Experimental data • MicroArray (Illumina, RNG/MRC, Agilent, Affymetrix, etc.) • High Throughput Sequencing • SNPs • Copy Number • GenoTypingmercredi 13 juin 2012 6
  8. 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. 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 Bmercredi 13 juin 2012 8
  10. 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 Bmercredi 13 juin 2012 9
  11. 11. expression Experimental Data Analysis Population structuration • Structuring genes (hidden state models) Distance from closest class New classes Known Discriminative powermercredi 13 juin 2012 10
  12. 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 Samplesmercredi 13 juin 2012 11
  13. 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 waymercredi 13 juin 2012 12
  14. 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 testersmercredi 13 juin 2012 13
  15. 15. Web Portals/Apps, Applications Wikispublic/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 Warehousespublic/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

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