Download Presentation - Anil Jegga - Cincinnati Children`s Hospital Medical

Making Sense Out of
Transcriptome
Integrative Bioinformatic Approaches
Anil Jegga, D.V.M., M.S.
Division of Biomedical Informatics
Cincinnati Children’s Hospital Medical Center
Department of Pediatrics
University of Cincinnati College of Medicine
Email: [email protected]
Homepage: http://anil.cchmc.org
Acknowledgements
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Jing Chen*
Siva Gowrisankar
Vivek Kaimal
Amit Sinha*
Mrunal Deshmukh
Nishanth Vepachedu
Divya Sardana
• Scott Tabar
• Eric Bardes
• Bruce Aronow
Expression Profile - Gene Lists
Annotation Databases
Gene Ontology, Pathways
DNA Repair
XRCC1
Angiogenesis
OGG1
HIF1A
ERCC1
ANGPT1
MPG…..
VEGF
KLF5….
Genome-wide Promoters
Putative Regulatory
Signatures
E2F
RB1
PDX1
MCM4 GLUT2 p53
FOS
PAX4 CDKN1A
SIVA….. PDX1 CTSD
IAPP…. CASP
DDB2….
Gene lists associated with similar
function/process/pathway
Enrichment Analysis
P53
E2F
CTSD
CASP
DDB2….
RB1
MCM4
FOS…
DNA Repair
Expected
Observed
XRCC1
OGG1
ERCC1
MPG….
Random
Distribution
Angiogenesis
HIF1A
ANGPT1
VEGF…..
Significant
Enrichment
I have a list of co-expressed mRNAs (Transcriptome)….
Now what?
1. Identify putative shared
regulatory elements
2. Identify the underlying
biological theme
• Known transcription
• Gene Ontology
factor binding sites
• Pathways
(TFBS)
• Phenotype/Disease
• Conserved
Association
• Non-conserved
• Protein Domains
• Unknown TFBS or
• Protein Interactions
Novel motifs
• Expression in other
• Conserved
tissues/experiments
Give a man a fish and you feed him for a day.
• Non-conserved
Teach a man to fish and you feed him for a lifetime
• MicroRNAs
Gene Regulatory Networks (GRNs)
Biological question: Are co-expressed
genes co-regulated?
Do they share cis-elements or TFBSs?
Are there any significant common
motifs within the promoter regions?
http://genometrafac.cchmc.org
You need to have a login account;
contact [email protected]
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DiRE: http://dire.dcode.org
http://www.cisreg.ca/oPOSSUM/
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Golden Path:
http://genome.ucsc.edu
Genome Browser Gateway choices:
1. Select Clade
2. Select genome/species: You can search only one species at a time
3. Assembly: the official backbone DNA sequence
4. Position: location in the genome to examine or search term (gene symbol,
accession number, etc.)
5. Image width: how many pixels in display window; 5000 max
6. Configure: make fonts bigger + other options
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1. Paste the gene symbols
2. Remember it is case-sensitive:
• Human: all upper case (e.g. XRCC1)
• Mouse: lower case (first letter upper case.
E.g. Xrcc1)
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1. Select “refFlat”
under “table”
2. Ensure that
“region” is
“genome”
3. Click on “paste list”
Describe your track
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Enter number of bp you want
to analyze/download
Select the output format as
“custom track”
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1. Select “Variation and
Repeats” under
“Group”
2. Click on “create”
under “intersection”
Change the “group” to
“Custom Tracks” and
select the appropriate
“track” and “table”
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Try GTF output too
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Genome Browser view that lists all
the SNPs lying within the upstream
1 kb (the region we queried) region
of one of the genes analyzed.
One drawback with this output is it
doesn’t tell you which SNPs are in
the upstream region of which gene.
However, since the positions of
SNPs are included, you can compare
them with the gene coordinates
and figure it out .
Functional Networks
Biological question: Are co-expressed
genes functionally similar?
Do they share same GO terms or
pathways?
Are there any significant enriched
terms within a group of gene list?
http://david.abcc.ncifcrf.gov/
http://www.pantherdb.org/
You can compare
multiple lists!
ToppGene – General Schema
http://toppgene.cchmc.org
TOPPGene - Data Sources
1. Gene Ontology: GO and NCBI Entrez Gene
2. Mouse Phenotype: MGI (used for the first time for
human disease gene prioritization)
3. Pathways: KEGG, BioCarta, BioCyc, Reactome,
GenMAPP, MSigDB
4. Domains: UniProt (Pfam, Interpro,etc.)
5. Interactions: NCBI Entrez Gene (Biogrid, Reactome,
BIND, HPRD, etc.)
6. Pubmed IDs: NCBI Entrez Gene
7. Expression: GEO
8. Cytoband: MSigDB
9. Cis-Elements: MSigDB
10. miRNA Targets: MSigDB
http://www.fatigo.org
http://vortex.cs.wayne.edu/projects.htm
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My NCBI: Can create/store queries; Set mail options
to receive new articles on your chosen
queries/subjects
PubMed Limits: Useful to refine your queries and
get more appropriate results
Preview/Index: You can customize (intersect, etc.)
your previous queries