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Introduction 1 st day Friederike Ehrhart, PhD Department of Bioinformatics-BiGCaT, Maastricht University, The Netherlands BioSB course: Biological Network Analysis http://tinyurl.com/pl5yreh Amsterdam, 17-18 September 2015

  1. Introduction 1 st day Friederike Ehrhart, PhD Department of Bioinformatics-BiGCaT, Maastricht University, The Netherlands BioSB course: Biological Network Analysis http://tinyurl.com/pl5yreh Amsterdam, 17-18 September 2015 friederike.ehrhart@maastrichtuniversity.nl

  2. Who are we? Friederike Ehrhart, PhD Postdoctoral researcher at BiGCaT Susan Steinbusch-Coort, PhD Assistant Professor at BiGCaT Martina Summer-Kutmon, PhD Postdoctoral researcher at BiGCaT / MaCSBio BioSB 2015 course: Biological Network Analysis, 17 & 18 September 2015 2

  3. Outline of the day Morning session (10:00-12:30) 11:00-11:15 Introduction Friederike Ehrhart, PhD 11:15-11:45 Lecture: Pathway Analysis Susan Steinbusch-Coort, PhD 11:45-12:30 Hands on session: Pathway Analysis I Lunch (12:30-13:30) Afternoon session (13:30-16:30) 13:30-14:00 Hands on session: Pathway Analysis II 14:00-14:30 Lecture: Network Analysis Martina Summer-Kutmon, PhD 14:30-15:00 Coffee Break 15:00-16:30 Hands on session: Network Analysis Quiz and (16:30-17:00) Q&A session BioSB 2015 course: Biological Network Analysis, 17 & 18 September 2015 3

  4. Introduction Pathways & Networks

  5. Data analysis Quantitative measurements Isolated data points Slide adapted from Thomas Kelder BioSB 2015 course: Biological Network Analysis, 17 & 18 September 2015 5

  6. Data analysis Comparative statistics Isolated lists Clustering Isolated groups Gene sets Functional groups Slide adapted from Thomas Kelder BioSB 2015 course: Biological Network Analysis, 17 & 18 September 2015 6

  7. Data analysis Functional organisation Pathways Slide adapted from Thomas Kelder BioSB 2015 course: Biological Network Analysis, 17 & 18 September 2015 7

  8. Data analysis Systems organisation Networks Important link! Slide adapted from Thomas Kelder BioSB 2015 course: Biological Network Analysis, 17 & 18 September 2015 8

  9. Complexity Oltvai, ZN, & Barabasi, AL Life's complexity pyramid. Science (2002) BioSB 2015 course: Biological Network Analysis, 17 & 18 September 2015 9

  10. Network Analysis Broad applications Nodes can mean anything! Biology: Key protein connecting pathways Organization networks: Don’t fire this guy ! Process engineering: Bottleneck Crime networks: Arrest this man! … Slide adapted from Thomas Kelder BioSB 2015 course: Biological Network Analysis, 17 & 18 September 2015 10

  11. Publicly available dataset Human papilloma virus (HPV) Cervical cancer BioSB 2015 course: Biological Network Analysis, 17 & 18 September 2015

  12. Study design To characterize the immune response to HPV-16 L1 vaccination Vaccination PRE Blood collection 1 2 before vaccination 3x intramuscular 50 µg placebo HPV-16 Blood collection after two months. POST Isolation of PBMC (white blood cells) 1) media Treated for 72 hours with: 2) 2.5 µg/ml HPV-16 3) Sf9/baculavirus BioSB 2015 course: Biological Network Analysis, 17 & 18 September 2015

  13. Analysis workflow Study published in BMC Genomics Kutmon M, Evelo CT, Coort SL. (2014) A network biology workflow to study transcriptomics data of the diabetic liver. BMC Genomics. 15:971. doi: 10.1186/1471-2164-15-971. BioSB 2015 course: Biological Network Analysis, 17 & 18 September 2015

  14. Statistical analyzed data ENTREZG_ID logFC Fold Change AveExpr t P.Value adj.P.Val B FC = fold change 5791 0.591922 1.507253064 9.134413 6.510885 6.64E-07 0.005247 5.916612 1318 0.58061 1.49548195 9.192346 5.750084 4.68E-06 0.008414 4.159066 3290 3.083471 8.476516346 7.005056 5.741547 4.79E-06 0.008414 4.138979 logFC: 2 logged fold change 6717 0.715502 1.64205491 9.856558 5.734658 4.87E-06 0.008414 4.122764 Comparing treated PBMCs post 29940 0.777776 1.714485322 8.763883 5.591523 7.08E-06 0.008414 3.784871 51762 0.778194 1.714982218 6.303504 5.542998 8.03E-06 0.008414 3.669908 vaccination with treated PBMCs pre 6653 -1.32238 -2.50078388 7.852464 -5.45257 1.02E-05 0.008414 3.455171 2526 0.480504 1.39523083 4.13608 5.4505 1.02E-05 0.008414 3.450236 vaccination 64174 -1.33343 -2.52001419 4.087996 -5.41868 1.11E-05 0.008414 3.374525 3458 2.035587 4.099895437 4.838017 5.41174 1.13E-05 0.008414 3.357991 8555 -0.25328 -1.191914588 1.886148 -5.38286 1.22E-05 0.008414 3.289179 5718 0.722316 1.649828357 7.102273 5.345311 1.35E-05 0.008414 3.199646 P-value: Significance level when 51182 0.496766 1.411047008 6.764266 5.335507 1.38E-05 0.008414 3.176252 25797 1.43223 2.698635003 7.09996 5.204949 1.95E-05 0.011015 2.864133 comparing post versus pre 3383 1.187166 2.277049286 8.333091 5.161028 2.19E-05 0.011541 2.758916 10797 0.685378 1.608123033 9.321337 5.130084 2.38E-05 0.011739 2.684728 211 1.034332 2.048165777 9.093823 5.058746 2.87E-05 0.013213 2.513529 11188 -0.9035 -1.870593239 8.292531 -5.02405 3.14E-05 0.013213 2.430177 5577 0.809146 1.752173668 3.166374 5.013159 3.24E-05 0.013213 2.404019 23524 -1.31202 -2.482883413 7.223792 -4.97769 3.55E-05 0.013213 2.31877 5690 0.601268 1.517049649 8.845243 4.947878 3.84E-05 0.013213 2.247075 716 1.675489 3.194276422 4.618137 4.92304 4.10E-05 0.013213 2.187326 7453 0.981757 1.97486894 10.75333 4.921188 4.12E-05 0.013213 2.182872 1439 0.755567 1.688294479 9.400976 4.917585 4.16E-05 0.013213 2.174205 1033 0.490903 1.405324249 2.810763 4.902513 4.33E-05 0.013213 2.137939 10213 0.455073 1.370852451 9.417582 4.901325 4.35E-05 0.013213 2.13508 56938 1.096181 2.137880041 3.651963 4.869686 4.73E-05 0.013343 2.058936 BioSB 2015 course: Biological Network Analysis, 17 & 18 September 2015

  15. Data analysis Normalization & Statistical analysis • PBMC’s treated with HPV -16 of vaccinated women after (post) and before (pre) vaccination. • Data quality was checked and the data was normalized. • Performed a (modified) paired t-test in limma. • Compare gene expression in treated PBMCs after vaccination with treated PBMCs before vaccination. BioSB 2015 course: Biological Network Analysis, 17 & 18 September 2015

  16. Questions? Information and material: http://projects.bigcat.unimaas.nl/biosb2015/

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