6 th July 2015 Ansuman Chattopadhyay PhD Head Molecular Biology Information Services Health Sciences Library System University of Pittsburgh ansumanpittedu Biological Pathway Map ID: 545648
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Pathway Informatics6th July, 2015
Ansuman Chattopadhyay, PhDHead, Molecular Biology Information ServicesHealth Sciences Library SystemUniversity of Pittsburghansuman@pitt.eduSlide2
Biological Pathway Map
http://www.hsls.pitt.edu/molbioSlide3
Pathway Informatics
http://www.hsls.pitt.edu/molbioSlide4
Biological Interaction Network
Biological Table
Gene List
Gene list to pathways
http://
www.hsls.pitt.edu/molbioSlide5
TopicsDatabasesBiological Pathway MapsProtein-Protein InteractionHigh-throughput gene expression (Microarray) Database
http://www.hsls.pitt.edu/molbioSlide6
TopicsSoftwareCreate a gene list: Geo2R, NextBioPathway Analysis : NIH DAVID, Ingenuity IPA
, Metacore, http://www.hsls.pitt.edu/molbioSlide7
Pathway Databases
http://www.hsls.pitt.edu/molbioSlide8
Biological PathwaysMetabolicSignaling
http://www.hsls.pitt.edu/molbioSlide9
Biological Pathway DatabasesKEGGIngenuity IPAGeneGo MetacoreMillipore Pathways (Metacore)Sigma Your Favorite Genes (IPA)
Life Technologies GeneAssistPathway Commons
http://
www.hsls.pitt.edu/molbioSlide10
Databases-PathwaysNCBI BiosystemsKEGGhttp://www.ncbi.nlm.nih.gov/biosystemsPathway Commons: http://www.pathwaycommons.org/pc/YFG – Sigma Aldrich: Your Favorite Gene
Millipore Pathways: http://www.millipore.com/pathways/pw/pathwaysApplied BioSystems: http://www5.appliedbiosystems.com/tools/pathway/
http://www.hsls.pitt.edu/molbioSlide11
PPI Databases
http://www.hsls.pitt.edu/molbioSlide12
What proteins interact with my favorite protein?
http://www.hsls.pitt.edu/molbioSlide13
PPI DatabasesBioGRIDSTRING
http://www.hsls.pitt.edu/molbioSlide14
Link to the video tutorial:
http://media.hsls.pitt.edu/media/molbiovideos/ppi.swf ResourcesBioGrid: http://thebiogrid.org/STRING: http://string-db.org/
Retrieve interacting partners of a protein of your interest -
What proteins interact with human EGFR?
-Slide15
BioGridhttp://
www.hsls.pitt.edu/molbioSlide16
BioGrid Search Result Page
http://www.hsls.pitt.edu/molbioSlide17
STRING - Known and Predicted Protein-Protein InteractionsAn ultimate resource for finding both predicted and experimental verified PPINot limited to human, mouse and ratDeveloped at CPR, EMBL,
SIB, KU, TUD and UZHhttp://www.hsls.pitt.edu/molbioSlide18
STRINGhttp://
www.hsls.pitt.edu/molbioSlide19
Gene Lists
http://www.hsls.pitt.edu/molbioSlide20
Gene ListsMicroarraysProtein arraysCHIP-chipSNP arraysRNA SeqLiterature Search
http://www.hsls.pitt.edu/molbioSlide21
Gene Expression Databases
http://www.hsls.pitt.edu/molbioSlide22
Gene Expression Database
http://www.hsls.pitt.edu/molbioSlide23
Use of GEO Datahttp://goo.gl/yD2hR
http://www.hsls.pitt.edu/molbioSlide24
Generate a gene listhttp://
www.hsls.pitt.edu/molbioSlide25
Pathway Analysis
http://www.hsls.pitt.edu/molbioSlide26
Retrieve Gene Expression dataNCBI GEOEBI ArrayExpressNextBio Research
http://www.hsls.pitt.edu/molbioSlide27
Gene Expression Database
http://www.hsls.pitt.edu/molbioSlide28
Searching GEO
http://www.hsls.pitt.edu/molbioSlide29
Searching GEO
http://www.hsls.pitt.edu/molbioSlide30
Searching GEO
http://www.hsls.pitt.edu/molbioSlide31
GEO2R
http://www.hsls.pitt.edu/molbioSlide32
GEO2R – Experiment to Gene List
http://www.hsls.pitt.edu/molbioSlide33
GEO2R – Experiment to Gene List
http://www.hsls.pitt.edu/molbioSlide34
GEO2R – Experiment to Gene List
http://www.hsls.pitt.edu/molbioSlide35
http://
www.hsls.pitt.edu/molbioSlide36
NextBio Registrationhttps://www.nextbio.com/b/register/register.nb
http://www.hsls.pitt.edu/molbioSlide37
NextBio
http://www.hsls.pitt.edu/molbioSlide38
NextBio
http://www.hsls.pitt.edu/molbioSlide39
NextBio
http://www.hsls.pitt.edu/molbioSlide40
NextBio Search
http://www.hsls.pitt.edu/molbioSlide41
NextBio GeneList
http://www.hsls.pitt.edu/molbioSlide42
Gene Expression Atlashttp://www.ebi.ac.uk/gxa/
http://www.hsls.pitt.edu/molbioSlide43
Array Expresshttp://www.hsls.pitt.edu/guides/geneticsSlide44
Literature to GeneList
http://www.hsls.pitt.edu/molbioSlide45
Gene Lists to Biology
http://www.hsls.pitt.edu/molbioSlide46
Suggested Reading
http://www.ploscollections.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002820http://www.hsls.pitt.edu/molbioSlide47
GO Consortium
http://
www.hsls.pitt.edu/molbioSlide48
GO AnnotationCellular ComponentBiological ProcessMolecular Function
http://www.hsls.pitt.edu/molbioSlide49
Copyright restrictions may apply.
Khatri, P. et al. Bioinformatics 2005 21:3587-3595; doi:10.1093/bioinformatics/bti565Levels of abstractionGene Ontology (GO)Slide50
Copyright restrictions may apply.
Khatri, P. et al. Bioinformatics 2005 21:3587-3595; doi:10.1093/bioinformatics/bti565Evolution history of GO-based functional analysis softwareDevelopment of gene ontology based toolsSlide51
http://
www.hsls.pitt.edu/molbioSlide52
Biological Table
Biological ListGene list to BiologyFunctions
Pathways
Interaction Networks
http://
www.hsls.pitt.edu/molbioSlide53
Discovery Step: Pathway Analysis
Gene Listhttp://www.hsls.pitt.edu/molbioSlide54
Pathway Analysis SoftwareNLP DrivenPathwayArchitect
PathwayStudioHuman CuratedIngenuity IPAGeneGO’s
Metacore
Biobase
Explain
“
Axin
binds
beta-catenin
,
GSK-3beta
and
APC
.”
Extracted Facts:
Axin
- beta-catenin interaction: Binding
Axin
- GSK-3beta interaction: Binding
Axin
- APC interaction: Binding
http://
www.hsls.pitt.edu/molbioSlide55
DAVID Bioinformatics Resources
http://www.hsls.pitt.edu/molbioSlide56
DAVID ToolsFunctional AnnotationClustering Chart – Term centricTable – Gene centric
http://www.hsls.pitt.edu/molbioSlide57
DAVIDhttp://www.nature.com/nprot/journal/v4/n1/fig_tab/nprot.2008.211_T1.html
http://www.hsls.pitt.edu/guides/geneticsSlide58
NIH DAVID
http://www.hsls.pitt.edu/molbioSlide59
Ingenuity IPAhttp://
www.hsls.pitt.edu/molbioSlide60
IPASlide61
IPASlide62
IPASlide63
IPA FunctionSlide64
IPA FunctionSlide65
IPA PathwaysSlide66
IPA PathwaySlide67
IPS Upstream RegulatorSlide68
IPA Mechanistic NetworkSlide69
IPA NetworksSlide70
IPA NetworksSlide71
IPASlide72
GeneGo: Metacore
http://www.hsls.pitt.edu/guides/geneticsSlide73
Pathway Analysis: GeneGo Metacore
http://www.hsls.pitt.edu/guides/geneticsSlide74
Metacore: Analyze Network (receptors)p53C-MycSlide75
Metacore: Transcription Regulation
http://www.hsls.pitt.edu/guides/geneticsSlide76
Cytoscape
http://www.hsls.pitt.edu/molbioSlide77
Hands-on ExerciseUse NIH DAVID to uncover enriched pathways associated with the “gene list – 1”http://
www.hsls.pitt.edu/molbioSlide78
Thank you!Any questions? Ansuman Chattopadhyay
ansuman@pitt.edu http://www.hsls.pitt.edu/molbio