Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information...

78
Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of Pittsburgh [email protected]

Transcript of Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information...

Page 1: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

Pathway Informatics6th July, 2015

Ansuman Chattopadhyay, PhDHead, Molecular Biology Information ServicesHealth Sciences Library SystemUniversity of [email protected]

mailto:[email protected]
Page 2: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

Biological Pathway Map

http://www.hsls.pitt.edu/molbio

http://www.hsls.pitt.edu/molbio/
http://www.hsls.pitt.edu/molbio/
Page 3: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

Pathway Informatics

L i s t o f G e n e s

Protein-Protein Interaction Database

P a t h w a y M a p

http://www.hsls.pitt.edu/molbio

http://www.hsls.pitt.edu/molbio/
http://www.hsls.pitt.edu/molbio/
Page 4: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

Biological Interaction Network

Name Time 0 Time 15 mins Time 1 hr Time 5 hrIL6 35.45% 36.46% 95.34% 13.91%PDGFRA 32.42% 45.43% 30.99% 56.62%DCN 21.42% 1.29% 33.13% 41.40%ZFP36L1 48.17% 47.56% 84.31% 6.72%DEGS 46.41% 90.30% 52.14% 31.61%GNB2 42.37% 98.25% 25.28% 53.26%ATRN 93.42% 75.90% 1.56% 82.61%PDK4 88.18% 38.03% 95.95% 5.78%MAPK1 20.88% 64.99% 43.18% 52.77%THBS1 99.61% 54.35% 85.28% 85.69%CD68 9.35% 44.81% 69.03% 64.88%DIAPH2 54.16% 34.47% 63.26% 33.46%Sep6 30.12% 48.83% 28.57% 76.28%BFAR 10.18% 7.65% 60.30% 42.66%CCRK 79.03% 19.54% 96.15% 88.79%MT1E 49.07% 23.60% 93.13% 15.83%

Biological Table

B-factor, properdinAPEX nuclease (multifunctional DNA repair enzyme) 1ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)proliferating cell nuclear antigenheterogeneous nuclear ribonucleoprotein A1fms-related tyrosine kinase 1 (vascular endothelial growth factor/vascular permeability factor receptor)three prime repair exonuclease 2ligase I, DNA, ATP-dependentflap structure-specific endonuclease 1cyclin A2cyclin-dependent kinase inhibitor 1A (P21)checkpoint kinase 1 homolog (S. pombe)replication protein A1, 70kDaWerner syndromeexonuclease 1uracil-DNA glycosylase 2

Gene List

Gene list to pathways

http://www.hsls.pitt.edu/molbio

http://www.hsls.pitt.edu/molbio/
http://www.hsls.pitt.edu/molbio/
Page 5: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

Topics

D a t a b a s e s

B i o l o g i c a l P a t h w a y M a p s

P r o t e i n - P r o t e i n I n t e r a c t i o n

H i g h - t h r o u g h p u t g e n e e x p r e s s i o n ( M i c r o a r r a y ) D a t a b a s e

http://www.hsls.pitt.edu/molbio

http://www.hsls.pitt.edu/molbio/
http://www.hsls.pitt.edu/molbio/
Page 6: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

Topics

Software

Create a gene list: Geo2R, NextBio

Pathway Analysis : NIH DAVID, Ingenuity IPA, Metacore,

http://www.hsls.pitt.edu/molbio

http://www.hsls.pitt.edu/molbio/
http://www.hsls.pitt.edu/molbio/
Page 7: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

Pathway Databases

http://www.hsls.pitt.edu/molbio

http://www.hsls.pitt.edu/molbio/
http://www.hsls.pitt.edu/molbio/
Page 8: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

Biological Pathways

Metabolic Signaling

http://www.hsls.pitt.edu/molbio

http://www.hsls.pitt.edu/molbio/
http://www.hsls.pitt.edu/molbio/
Page 9: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

Biological Pathway Databases KEGG Ingenuity IPA GeneGo Metacore

Millipore Pathways (Metacore) Sigma Your Favorite Genes (IPA) Life Technologies GeneAssist

Pathway Commons

http://www.hsls.pitt.edu/molbio

http://www.millipore.com/pathways/pw/pathways
http://www.millipore.com/pathways/pw/pathways
http://www.millipore.com/pathways/pw/pathways
http://www.millipore.com/pathways/pw/pathways
http://www.sigmaaldrich.com/life-science.html
http://www5.appliedbiosystems.com/tools/pathway/
http://www5.appliedbiosystems.com/tools/pathway/
http://www.pathwaycommons.org/about/
http://www.hsls.pitt.edu/molbio/
http://www.hsls.pitt.edu/molbio/
Page 10: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

Databases-Pathways

NCBI Biosystems KEGG http://www.ncbi.nlm.nih.gov/biosystems

Pathway Commons: http://www.pathwaycommons.org/pc/

YFG – Sigma Aldrich: Your Favorite Gene

Millipore Pathways: http://www.millipore.com/pathways/pw/pathways

Applied BioSystems: http://www5.appliedbiosystems.com/tools/pathway/

http://www.hsls.pitt.edu/molbio

http://www.ncbi.nlm.nih.gov/biosystems
http://www.pathwaycommons.org/pc/
http://www.sigmaaldrich.com/life-science/your-favorite-gene-search.html
http://www.millipore.com/pathways/pw/pathways
http://www5.appliedbiosystems.com/tools/pathway/
http://www5.appliedbiosystems.com/tools/pathway/
http://www.hsls.pitt.edu/molbio/
http://www.hsls.pitt.edu/molbio/
Page 11: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

PPI Databases

http://www.hsls.pitt.edu/molbio

http://www.hsls.pitt.edu/molbio/
http://www.hsls.pitt.edu/molbio/
Page 12: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

What proteins interact with my favorite protein?

http://www.hsls.pitt.edu/molbio

http://www.hsls.pitt.edu/molbio/
http://www.hsls.pitt.edu/molbio/
Page 13: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

PPI Databases

BioGRID STRING

http://www.hsls.pitt.edu/molbio

http://www.hsls.pitt.edu/molbio/
http://www.hsls.pitt.edu/molbio/
Page 14: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

Link to the video tutorial:http://media.hsls.pitt.edu/media/molbiovideos/ppi.swf

Resources

BioGrid: http://thebiogrid.org/

STRING: http://string-db.org/

- Retrieve interacting partners of a protein of your interest

-What proteins interact with human EGFR?

-

http://media.hsls.pitt.edu/media/molbiovideos/ppi.swf
http://thebiogrid.org/
http://string-db.org/
Page 15: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

BioGrid

http://www.hsls.pitt.edu/molbio

http://www.hsls.pitt.edu/molbio/
http://www.hsls.pitt.edu/molbio/
Page 16: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

BioGrid Search Result Page

http://www.hsls.pitt.edu/molbio

http://www.hsls.pitt.edu/molbio/
http://www.hsls.pitt.edu/molbio/
Page 17: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

STRING - Known and Predicted Protein-Protein Interactions

An ultimate resource for finding both predicted and experimental verified PPI

Not limited to human, mouse and rat

Developed at CPR, EMBL, SIB, KU, TUD and UZH

http://www.hsls.pitt.edu/molbio

http://www.cpr.ku.dk/
http://www.embl.org/
http://www.isb-sib.ch/
http://healthsciences.ku.dk/
http://www.biotec.tu-dresden.de/
http://www.uzh.ch/
http://www.hsls.pitt.edu/molbio/
http://www.hsls.pitt.edu/molbio/
Page 18: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

STRING

http://www.hsls.pitt.edu/molbio

http://www.hsls.pitt.edu/molbio/
http://www.hsls.pitt.edu/molbio/
Page 19: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

Gene Lists

http://www.hsls.pitt.edu/molbio

http://www.hsls.pitt.edu/molbio/
http://www.hsls.pitt.edu/molbio/
Page 20: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

Gene Lists

Microarrays Protein arrays CHIP-chip SNP arrays RNA Seq Literature Search

http://www.hsls.pitt.edu/molbio

http://www.hsls.pitt.edu/molbio/
http://www.hsls.pitt.edu/molbio/
Page 21: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

Gene Expression Databases

NCBI• Gene Expression Omnibus (GEO)

EBI• ArrayExpress

http://www.hsls.pitt.edu/molbio

http://www.hsls.pitt.edu/molbio/
http://www.hsls.pitt.edu/molbio/
Page 22: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

Gene Expression Database

http://www.hsls.pitt.edu/molbio

http://www.hsls.pitt.edu/molbio/
http://www.hsls.pitt.edu/molbio/
Page 23: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

Use of GEO Data

http://goo.gl/yD2hR

http://www.hsls.pitt.edu/molbio

http://goo.gl/yD2hR
http://www.hsls.pitt.edu/molbio/
http://www.hsls.pitt.edu/molbio/
Page 24: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

Generate a gene list

http://www.hsls.pitt.edu/molbio

http://www.hsls.pitt.edu/molbio/
http://www.hsls.pitt.edu/molbio/
Page 25: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

Pathway Analysis

Control A549 cell

+

Ethanol (25mmol/L) 48 hr

TreatedA549 cell

+

Resveratrol (25mmol/L) 48 hr

http://www.hsls.pitt.edu/molbio

http://www.hsls.pitt.edu/molbio/
http://www.hsls.pitt.edu/molbio/
Page 26: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

Retrieve Gene Expression data

NCBI GEO EBI ArrayExpress NextBio Research

http://www.hsls.pitt.edu/molbio

http://www.hsls.pitt.edu/molbio/
http://www.hsls.pitt.edu/molbio/
Page 27: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

Gene Expression Database

http://www.hsls.pitt.edu/molbio

http://www.hsls.pitt.edu/molbio/
http://www.hsls.pitt.edu/molbio/
Page 28: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

Searching GEO

http://www.hsls.pitt.edu/molbio

http://www.hsls.pitt.edu/molbio/
http://www.hsls.pitt.edu/molbio/
Page 29: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

Searching GEO

http://www.hsls.pitt.edu/molbio

http://www.hsls.pitt.edu/molbio/
http://www.hsls.pitt.edu/molbio/
Page 30: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

Searching GEO

http://www.hsls.pitt.edu/molbio

http://www.hsls.pitt.edu/molbio/
http://www.hsls.pitt.edu/molbio/
Page 31: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

GEO2R

http://www.hsls.pitt.edu/molbio

http://www.hsls.pitt.edu/molbio/
http://www.hsls.pitt.edu/molbio/
Page 32: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

GEO2R – Experiment to Gene List

http://www.hsls.pitt.edu/molbio

http://www.hsls.pitt.edu/molbio/
http://www.hsls.pitt.edu/molbio/
Page 33: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

GEO2R – Experiment to Gene List

http://www.hsls.pitt.edu/molbio

http://www.hsls.pitt.edu/molbio/
http://www.hsls.pitt.edu/molbio/
Page 34: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

GEO2R – Experiment to Gene List

http://www.hsls.pitt.edu/molbio

http://www.hsls.pitt.edu/molbio/
http://www.hsls.pitt.edu/molbio/
Page 35: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

http://www.hsls.pitt.edu/molbio

http://www.hsls.pitt.edu/molbio/
http://www.hsls.pitt.edu/molbio/
Page 36: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

NextBio Registration

https://www.nextbio.com/b/register/register.nb

http://www.hsls.pitt.edu/molbio

https://www.nextbio.com/b/register/register.nb
http://www.hsls.pitt.edu/molbio/
http://www.hsls.pitt.edu/molbio/
Page 37: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

NextBio

http://www.hsls.pitt.edu/molbio

http://www.hsls.pitt.edu/molbio/
http://www.hsls.pitt.edu/molbio/
Page 38: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

NextBio

http://www.hsls.pitt.edu/molbio

http://www.hsls.pitt.edu/molbio/
http://www.hsls.pitt.edu/molbio/
Page 39: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

NextBio

http://www.hsls.pitt.edu/molbio

http://www.hsls.pitt.edu/molbio/
http://www.hsls.pitt.edu/molbio/
Page 40: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

NextBio Search

http://www.hsls.pitt.edu/molbio

http://www.hsls.pitt.edu/molbio/
http://www.hsls.pitt.edu/molbio/
Page 41: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

NextBio GeneList

http://www.hsls.pitt.edu/molbio

http://www.hsls.pitt.edu/molbio/
http://www.hsls.pitt.edu/molbio/
Page 42: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

Gene Expression Atlas

http://www.ebi.ac.uk/gxa/

http://www.hsls.pitt.edu/molbio

http://www.ebi.ac.uk/gxa/
http://www.hsls.pitt.edu/molbio/
http://www.hsls.pitt.edu/molbio/
Page 43: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

Array Express

http://www.hsls.pitt.edu/guides/genetics

http://www.hsls.pitt.edu/guides/genetics
Page 44: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

Literature to GeneList

GEO

Geo2R NextBio

Gene List

http://www.hsls.pitt.edu/molbio

http://www.hsls.pitt.edu/molbio/
http://www.hsls.pitt.edu/molbio/
Page 45: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

Gene Lists to Biology

http://www.hsls.pitt.edu/molbio

http://www.hsls.pitt.edu/molbio/
http://www.hsls.pitt.edu/molbio/
Page 46: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

Suggested Reading

http://www.ploscollections.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002820

http://www.hsls.pitt.edu/molbio

http://www.ploscollections.org/article/info:doi/10.1371/journal.pcbi.1002820
http://www.hsls.pitt.edu/molbio/
http://www.hsls.pitt.edu/molbio/
Page 47: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

GO Consortium

http://www.hsls.pitt.edu/molbio

http://www.hsls.pitt.edu/molbio/
http://www.hsls.pitt.edu/molbio/
Page 48: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

GO Annotation

Cellular Component

Biological Process

Molecular Function

http://www.hsls.pitt.edu/molbio

http://www.hsls.pitt.edu/molbio/
http://www.hsls.pitt.edu/molbio/
Page 49: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

Copyright restrictions may apply.

Khatri, P. et al. Bioinformatics 2005 21:3587-3595; doi:10.1093/bioinformatics/bti565

Levels of abstraction

Gene Ontology (GO)

Page 50: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

Copyright restrictions may apply.

Khatri, P. et al. Bioinformatics 2005 21:3587-3595; doi:10.1093/bioinformatics/bti565

Evolution history of GO-based functional analysis software

Development of gene ontology based tools

Page 51: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

http://www.hsls.pitt.edu/molbio

http://www.hsls.pitt.edu/molbio/
http://www.hsls.pitt.edu/molbio/
Page 52: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

Name Time 0 Time 15 mins Time 1 hr Time 5 hrIL6 35.45% 36.46% 95.34% 13.91%PDGFRA 32.42% 45.43% 30.99% 56.62%DCN 21.42% 1.29% 33.13% 41.40%ZFP36L1 48.17% 47.56% 84.31% 6.72%DEGS 46.41% 90.30% 52.14% 31.61%GNB2 42.37% 98.25% 25.28% 53.26%ATRN 93.42% 75.90% 1.56% 82.61%PDK4 88.18% 38.03% 95.95% 5.78%MAPK1 20.88% 64.99% 43.18% 52.77%THBS1 99.61% 54.35% 85.28% 85.69%CD68 9.35% 44.81% 69.03% 64.88%DIAPH2 54.16% 34.47% 63.26% 33.46%Sep6 30.12% 48.83% 28.57% 76.28%BFAR 10.18% 7.65% 60.30% 42.66%CCRK 79.03% 19.54% 96.15% 88.79%MT1E 49.07% 23.60% 93.13% 15.83%

Biological Table

B-factor, properdinAPEX nuclease (multifunctional DNA repair enzyme) 1ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)proliferating cell nuclear antigenheterogeneous nuclear ribonucleoprotein A1fms-related tyrosine kinase 1 (vascular endothelial growth factor/vascular permeability factor receptor)three prime repair exonuclease 2ligase I, DNA, ATP-dependentflap structure-specific endonuclease 1cyclin A2cyclin-dependent kinase inhibitor 1A (P21)checkpoint kinase 1 homolog (S. pombe)replication protein A1, 70kDaWerner syndromeexonuclease 1uracil-DNA glycosylase 2

Biological List

Gene list to Biology

Functions

Pathways

Interaction Networks

http://www.hsls.pitt.edu/molbio

http://www.hsls.pitt.edu/molbio/
http://www.hsls.pitt.edu/molbio/
Page 53: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

Discovery Step: Pathway Analysis

Ingenuity IPA

DAVID

MetacoreGene List

http://www.hsls.pitt.edu/molbio

http://www.hsls.pitt.edu/molbio/
http://www.hsls.pitt.edu/molbio/
Page 54: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

Pathway Analysis Software

NLP DrivenPathwayArchitectPathwayStudio

Human CuratedIngenuity IPAGeneGO’s MetacoreBiobase Explain

“ Axin binds beta-catenin, GSK-3beta and APC.”

Extracted Facts:Axin - beta-catenin interaction: BindingAxin - GSK-3beta interaction: BindingAxin - APC interaction: Binding

http://www.hsls.pitt.edu/molbio

http://www.hsls.pitt.edu/molbio/
http://www.hsls.pitt.edu/molbio/
Page 55: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

DAVID Bioinformatics Resources 

http://www.hsls.pitt.edu/molbio

http://www.hsls.pitt.edu/molbio/
http://www.hsls.pitt.edu/molbio/
Page 56: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

DAVID Tools

Functional Annotation Clustering

Chart – Term centric Table – Gene centric

http://www.hsls.pitt.edu/molbio

http://www.hsls.pitt.edu/molbio/
http://www.hsls.pitt.edu/molbio/
Page 57: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

DAVID

http://www.nature.com/nprot/journal/v4/n1/fig_tab/nprot.2008.211_T1.html

http://www.hsls.pitt.edu/guides/genetics

http://www.nature.com/nprot/journal/v4/n1/fig_tab/nprot.2008.211_T1.html
http://www.hsls.pitt.edu/guides/genetics
Page 58: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

NIH DAVID

http://www.hsls.pitt.edu/molbio

http://www.hsls.pitt.edu/molbio/
http://www.hsls.pitt.edu/molbio/
Page 59: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

Ingenuity IPA

http://www.hsls.pitt.edu/molbio

http://www.hsls.pitt.edu/molbio/
http://www.hsls.pitt.edu/molbio/
Page 60: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

IPA

Page 61: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

IPA

Page 62: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

IPA

Page 63: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

IPA Function

Page 64: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

IPA Function

Page 65: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

IPA Pathways

Page 66: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

IPA Pathway

Page 67: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

IPS Upstream Regulator

Page 68: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

IPA Mechanistic Network

Page 69: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

IPA Networks

Page 70: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

IPA Networks

Page 71: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

IPA

Page 72: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

GeneGo: Metacore

http://www.hsls.pitt.edu/guides/genetics

http://www.hsls.pitt.edu/guides/genetics
Page 73: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

Pathway Analysis: GeneGo Metacore

http://www.hsls.pitt.edu/guides/genetics

http://www.hsls.pitt.edu/guides/genetics
Page 74: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

Metacore: Analyze Network (receptors)

p53C-Myc

Page 75: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

Metacore: Transcription Regulation

http://www.hsls.pitt.edu/guides/genetics

http://www.hsls.pitt.edu/guides/genetics
Page 76: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

Cytoscape

http://www.hsls.pitt.edu/molbio

http://www.hsls.pitt.edu/molbio/
http://www.hsls.pitt.edu/molbio/
Page 77: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

Hands-on Exercise

Use NIH DAVID to uncover enriched pathways associated with the “gene list – 1”

http://www.hsls.pitt.edu/molbio

http://www.hsls.pitt.edu/molbio/
http://www.hsls.pitt.edu/molbio/
Page 78: Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

Thank you!Any questions?

Ansuman [email protected]

http://www.hsls.pitt.edu/molbio

mailto:[email protected]
http://www.hsls.pitt.edu/molbio
http://www.hsls.pitt.edu/molbio

Online Resources for Psychiatric Genetics 19 th March, 2009 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library.

Online Resources for Psychiatric Genetics 19 th March, 2009 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library.

AC2012-3221 ... INVESTIGATIONOFPROPORTIONALANDNON-PROPORTIONAL LOADINGS USING MOHR’S CIRCLE Prof. Somnath Chattopadhyay, Georgia Southern University Somnath Chattopadhyay is in the

AC2012-3221 ... INVESTIGATIONOFPROPORTIONALANDNON-PROPORTIONAL LOADINGS USING MOHR’S CIRCLE Prof. Somnath Chattopadhyay, Georgia Southern University Somnath Chattopadhyay is in the

Chattopadhyay Review Class Theory and History Capitalism and Communism in the USSR Chattopadhyay Historical Materialism 2006/1

Chattopadhyay Review Class Theory and History Capitalism and Communism in the USSR Chattopadhyay Historical Materialism 2006/1

ASHOK K. LAHIRI SAUMEN CHATTOPADHYAY ANURADHA BHASIN

ASHOK K. LAHIRI SAUMEN CHATTOPADHYAY ANURADHA BHASIN

Bankimchandra Chattopadhyay (1838-94)(2)

Bankimchandra Chattopadhyay (1838-94)(2)

*Irene Borillo Llorca *Rajarshi Chattopadhyay *Benjamin Mellman ...

*Irene Borillo Llorca *Rajarshi Chattopadhyay *Benjamin Mellman ...

Regulation of Gene Expression 13 February, 2013 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System.

Regulation of Gene Expression 13 February, 2013 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System.

Paresh Chattopadhyay Passage to Socialism:The Dialectic of

Paresh Chattopadhyay Passage to Socialism:The Dialectic of

Introduction to CLC Main Workbench 20 June, 2012 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System.

Introduction to CLC Main Workbench 20 June, 2012 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System.

Durgeshnandini by Bankimchandra Chattopadhyay

Durgeshnandini by Bankimchandra Chattopadhyay

Biology in Silico : Online Tools for “Omics” ANSUMAN CHATTOPADHYAY, PHD HEAD, MOLECULAR BIOLOGY INFORMATION SERVICE HEALTH SCIENCES LIBRARY SYSTEM UNIVERSITY.

Biology in Silico : Online Tools for “Omics” ANSUMAN CHATTOPADHYAY, PHD HEAD, MOLECULAR BIOLOGY INFORMATION SERVICE HEALTH SCIENCES LIBRARY SYSTEM UNIVERSITY.

Paresh Chattopadhyay Economic Content of Socialism in ... Chattopadhyay... · Paresh Chattopadhyay Economic Content of Socialism in Lenin Is It the Same as in Marx? Economic and Political

Paresh Chattopadhyay Economic Content of Socialism in ... Chattopadhyay... · Paresh Chattopadhyay Economic Content of Socialism in Lenin Is It the Same as in Marx? Economic and Political

Reaching the Masses: multimedia biomedical instruction @ the point of need Carrie Iwema, PhD, MLS Information Specialist in Molecular Biology Ansuman Chattopadhyay,

Reaching the Masses: multimedia biomedical instruction @ the point of need Carrie Iwema, PhD, MLS Information Specialist in Molecular Biology Ansuman Chattopadhyay,

Prof. Saibal Chattopadhyay IIM Calcutta

Prof. Saibal Chattopadhyay IIM Calcutta

Bluebeauty by ananyo chattopadhyay

Bluebeauty by ananyo chattopadhyay

Going Against Goliath 23 rd May 2010 Katrina Kurtz, MLIS Carrie Iwema, PhD, MLS Ansuman Chattopadhyay, PhD Health Sciences Library System University of.

Going Against Goliath 23 rd May 2010 Katrina Kurtz, MLIS Carrie Iwema, PhD, MLS Ansuman Chattopadhyay, PhD Health Sciences Library System University of.

Locating Gene/Protein Information September 26, 2013 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System.

Locating Gene/Protein Information September 26, 2013 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System.

Sudip Kumar Chattopadhyay - iiests.ac.in

Sudip Kumar Chattopadhyay - iiests.ac.in

Genes, Proteins and Literature Searching Ansuman Chattopadhyay, PhD Molecular Biology Information Services Health Sciences Library System University of.

Genes, Proteins and Literature Searching Ansuman Chattopadhyay, PhD Molecular Biology Information Services Health Sciences Library System University of.

Tanmay Chattopadhyay, Shradha Shivani, Mahesh Krishnan

Tanmay Chattopadhyay, Shradha Shivani, Mahesh Krishnan