Transcript Pathway Analysis - University of Pittsburgh

Pathway Informatics
4th December, 2013
Ansuman Chattopadhyay, PhD
Head, Molecular Biology Information Services
Health Sciences Library System
University of Pittsburgh
[email protected]
Biological Pathway Map
http://www.hsls.pitt.edu/molbio
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
Gene list to pathways
Gene List
Biological Interaction Network
B -factor, properdin
A P E X nuclease (m ultifunctional D N A repair enzym e) 1
A D P -ribosyltransferase (N A D +; poly (A D P -ribose) polym erase)
proliferating cell nuclear antigen
heterogeneous nuclear ribonucleoprotein A 1
fm s-related tyrosine k inase 1 (vascular endothelial grow th factor/vascular perm eability factor receptor)
three prim e repair exonuclease 2
ligase I, D N A , A T P -dependent
flap structure-specific endonuclease 1
cyclin A 2
cyclin-dependent k inase inhibitor 1A (P 21)
check point k inase 1 hom olog (S . pom be)
replication protein A 1, 70k D a
W erner syndrom e
exonuclease 1
uracil-D N A glycosylase 2
Biological Table
Nam e
IL 6
T im e 0 T im e 1 5 m in s T im e 1 h r T im e 5 h r
3 5 .4 5 %
3 6 .4 6 %
9 5 .3 4 %
1 3 .9 1 %
PDG FRA
3 2 .4 2 %
4 5 .4 3 %
3 0 .9 9 %
5 6 .6 2 %
DCN
ZFP36L1
2 1 .4 2 %
4 8 .1 7 %
1 .2 9 %
4 7 .5 6 %
3 3 .1 3 %
8 4 .3 1 %
4 1 .4 0 %
6 .7 2 %
DEGS
GNB2
4 6 .4 1 %
4 2 .3 7 %
9 0 .3 0 %
9 8 .2 5 %
5 2 .1 4 %
2 5 .2 8 %
3 1 .6 1 %
5 3 .2 6 %
A TR N
9 3 .4 2 %
7 5 .9 0 %
1 .5 6 %
8 2 .6 1 %
PDK4
8 8 .1 8 %
3 8 .0 3 %
9 5 .9 5 %
5 .7 8 %
MAPK1
2 0 .8 8 %
6 4 .9 9 %
4 3 .1 8 %
5 2 .7 7 %
TH B S 1
9 9 .6 1 %
5 4 .3 5 %
8 5 .2 8 %
8 5 .6 9 %
9 .3 5 %
4 4 .8 1 %
6 9 .0 3 %
6 4 .8 8 %
D IA P H 2
S ep 6
5 4 .1 6 %
3 0 .1 2 %
3 4 .4 7 %
4 8 .8 3 %
6 3 .2 6 %
2 8 .5 7 %
3 3 .4 6 %
7 6 .2 8 %
BFAR
1 0 .1 8 %
7 .6 5 %
6 0 .3 0 %
4 2 .6 6 %
CCRK
7 9 .0 3 %
1 9 .5 4 %
9 6 .1 5 %
8 8 .7 9 %
M T1 E
4 9 .0 7 %
2 3 .6 0 %
9 3 .1 3 %
1 5 .8 3 %
CD68
http://www.hsls.pitt.edu/molbio
Topics

Databases

Biological Pathway Maps

Protein-Protein Interaction

High-throughput gene
expression (Microarray)
Database
http://www.hsls.pitt.edu/molbio
Topics

Software

Create a gene list: Geo2R, NextBio

Pathway Analysis : NIH DAVID, Ingenuity
Metacore,
http://www.hsls.pitt.edu/molbio
IPA,
Pathway Databases
http://www.hsls.pitt.edu/molbio
Biological Pathways

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Metabolic
Signaling
http://www.hsls.pitt.edu/molbio
Biological Pathway Databases

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KEGG
Ingenuity IPA
GeneGo Metacore
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Millipore Pathways (Metacore)
Sigma Your Favorite Genes (IPA)
Life Technologies GeneAssist
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Pathway Commons
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
http://www.hsls.pitt.edu/molbio
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
PPI Databases
http://www.hsls.pitt.edu/molbio
What proteins interact with my favorite protein?
http://www.hsls.pitt.edu/molbio
PPI Databases

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BioGRID
STRING
http://www.hsls.pitt.edu/molbio
- Retrieve interacting partners of a protein of
your interest
-What proteins interact with human EGFR?
Resources
BioGrid:
http://thebiogrid.org/
STRING: http://string-db.org/
Link to the video tutorial:
http://media.hsls.pitt.edu/media/molbiovideos/ppi.swf
BioGrid
http://www.hsls.pitt.edu/molbio
BioGrid Search Result Page
http://www.hsls.pitt.edu/molbio
STRING - Known and Predicted ProteinProtein 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
STRING
http://www.hsls.pitt.edu/molbio
Gene Lists
http://www.hsls.pitt.edu/molbio
Gene Lists

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Microarrays
Protein arrays
CHIP-chip
SNP arrays
RNA Seq
Literature Search
http://www.hsls.pitt.edu/molbio
Gene Expression Databases
NCBI
• Gene Expression Omnibus
(GEO)
EBI
• ArrayExpress
http://www.hsls.pitt.edu/molbio
Gene Expression Database
http://www.hsls.pitt.edu/molbio
Use of GEO Data

http://goo.gl/yD2hR
http://www.hsls.pitt.edu/molbio
Generate a gene list
http://www.hsls.pitt.edu/molbio
Pathway Analysis
Control
Treated
A549 cell
+
Ethanol (25mmol/L) 48 hr
A549 cell
+
Resveratrol (25mmol/L) 48 hr
http://www.hsls.pitt.edu/molbio
Retrieve Gene Expression data


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NCBI GEO
EBI ArrayExpress
NextBio Research
http://www.hsls.pitt.edu/molbio
Gene Expression Database
http://www.hsls.pitt.edu/molbio
Searching GEO
http://www.hsls.pitt.edu/molbio
Searching GEO
http://www.hsls.pitt.edu/molbio
Searching GEO
http://www.hsls.pitt.edu/molbio
GEO2R
http://www.hsls.pitt.edu/molbio
GEO2R – Experiment to Gene List
http://www.hsls.pitt.edu/molbio
GEO2R – Experiment to Gene List
http://www.hsls.pitt.edu/molbio
GEO2R – Experiment to Gene List
http://www.hsls.pitt.edu/molbio
http://www.hsls.pitt.edu/molbio
NextBio Registration
https://www.nextbio.com/b/register/register.nb
http://www.hsls.pitt.edu/molbio
NextBio
http://www.hsls.pitt.edu/molbio
NextBio
http://www.hsls.pitt.edu/molbio
NextBio
http://www.hsls.pitt.edu/molbio
NextBio Search
http://www.hsls.pitt.edu/molbio
NextBio GeneList
http://www.hsls.pitt.edu/molbio
Gene Expression Atlas
http://www.ebi.ac.uk/gxa/
http://www.hsls.pitt.edu/molbio
Array Express
http://www.hsls.pitt.edu/guides/genetics
Literature to GeneList
GEO
Geo2R
NextBio
Gene List
http://www.hsls.pitt.edu/molbio
Gene Lists to Biology
http://www.hsls.pitt.edu/molbio
Suggested Reading
http://www.ploscollections.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002820
http://www.hsls.pitt.edu/molbio
GO Consortium
http://www.hsls.pitt.edu/molbio
GO Annotation
 Cellular
Component
 Biological
Process
 Molecular
Function
http://www.hsls.pitt.edu/molbio
Levels of abstraction
Gene Ontology (GO)
Khatri, P. et al. Bioinformatics 2005 21:3587-3595; doi:10.1093/bioinformatics/bti565
Copyright restrictions may apply.
Evolution history of GO-based functional analysis software
Development of gene ontology based tools
Khatri, P. et al. Bioinformatics 2005 21:3587-3595; doi:10.1093/bioinformatics/bti565
Copyright restrictions may apply.
http://www.hsls.pitt.edu/molbio
Gene list to Biology
Biological List
B -fa c to r, p ro p e rd in
A P E X n u c le a s e (m u ltifu n c tio n a l D N A re p a ir e n zym e ) 1
A D P -rib o s yltra n s fe ra s e (N A D + ; p o ly (A D P -rib o s e ) p o lym e ra s e )
p ro life ra tin g c e ll n u c le a r a n tig e n
h e te ro g e n e o u s n u c le a r rib o n u c le o p ro te in A 1
fm s -re la te d tyro s in e k in a s e 1 (va s c u la r e n d o th e lia l g ro w th fa c to r/va s c u la r p e rm e a b ility fa c to r re c e p to r)
th re e p rim e re p a ir e x o n u c le a s e 2
lig a s e I, D N A , A T P -d e p e n d e n t
fla p s tru c tu re -s p e c ific e n d o n u c le a s e 1
c yc lin A 2
c yc lin -d e p e n d e n t k in a s e in h ib ito r 1 A (P 2 1 )
c h e c k p o in t k in a s e 1 h o m o lo g (S . p o m b e )
re p lic a tio n p ro te in A 1 , 7 0 k D a
W e rn e r s yn d ro m e
e x o n u c le a s e 1
u ra c il-D N A g lyc o s yla s e 2
Functions
Pathways
Biological Table
Nam e
IL 6
T im e 0 T im e 1 5 m in s T im e 1 h r T im e 5 h r
3 5 .4 5 %
3 6 .4 6 %
9 5 .3 4 %
1 3 .9 1 %
PDG FRA
3 2 .4 2 %
4 5 .4 3 %
3 0 .9 9 %
5 6 .6 2 %
DCN
ZFP36L1
2 1 .4 2 %
4 8 .1 7 %
1 .2 9 %
4 7 .5 6 %
3 3 .1 3 %
8 4 .3 1 %
4 1 .4 0 %
6 .7 2 %
DEGS
GNB2
4 6 .4 1 %
4 2 .3 7 %
9 0 .3 0 %
9 8 .2 5 %
5 2 .1 4 %
2 5 .2 8 %
3 1 .6 1 %
5 3 .2 6 %
A TR N
9 3 .4 2 %
7 5 .9 0 %
1 .5 6 %
8 2 .6 1 %
PDK4
8 8 .1 8 %
3 8 .0 3 %
9 5 .9 5 %
5 .7 8 %
MAPK1
2 0 .8 8 %
6 4 .9 9 %
4 3 .1 8 %
5 2 .7 7 %
TH B S 1
9 9 .6 1 %
5 4 .3 5 %
8 5 .2 8 %
8 5 .6 9 %
9 .3 5 %
4 4 .8 1 %
6 9 .0 3 %
6 4 .8 8 %
D IA P H 2
S ep 6
5 4 .1 6 %
3 0 .1 2 %
3 4 .4 7 %
4 8 .8 3 %
6 3 .2 6 %
2 8 .5 7 %
3 3 .4 6 %
7 6 .2 8 %
BFAR
1 0 .1 8 %
7 .6 5 %
6 0 .3 0 %
4 2 .6 6 %
CCRK
7 9 .0 3 %
1 9 .5 4 %
9 6 .1 5 %
8 8 .7 9 %
M T1 E
4 9 .0 7 %
2 3 .6 0 %
9 3 .1 3 %
1 5 .8 3 %
CD68
Interaction Networks
http://www.hsls.pitt.edu/molbio
Discovery Step: Pathway Analysis
Ingenuity
IPA
DAVID
Gene List
Metacore
http://www.hsls.pitt.edu/molbio
Pathway Analysis Software
NLP Driven
PathwayArchitect
PathwayStudio
Human Curated
Ingenuity IPA
GeneGO’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/molbio
DAVID Bioinformatics Resources
http://www.hsls.pitt.edu/molbio
DAVID Tools

Functional Annotation

Clustering


Chart – Term centric
Table – Gene centric
http://www.hsls.pitt.edu/molbio
DAVID
http://www.nature.com/nprot/journal/v4/n1/fig_tab/nprot.2008.211_T1.html
http://www.hsls.pitt.edu/guides/genetics
NIH DAVID
http://www.hsls.pitt.edu/molbio
Ingenuity IPA
http://www.hsls.pitt.edu/molbio
IPA
IPA
IPA
IPA Function
IPA Function
IPA Pathways
IPA Pathway
IPS Upstream Regulator
IPA Mechanistic Network
IPA Networks
IPA Networks
IPA
GeneGo: Metacore
http://www.hsls.pitt.edu/guides/genetics
Pathway Analysis: GeneGo Metacore
http://www.hsls.pitt.edu/guides/genetics
Metacore: Analyze Network (receptors)
C-Myc
p53
Metacore: Transcription Regulation
http://www.hsls.pitt.edu/guides/genetics
Cytoscape
http://www.hsls.pitt.edu/molbio
Hands-on Exercise

Use NIH DAVID to uncover enriched
pathways associated with the “gene list – 1”
http://www.hsls.pitt.edu/molbio
Thank you!
Any questions?
Ansuman Chattopadhyay
[email protected]
http://www.hsls.pitt.edu/molbio