Digestive Health Center - Bioinformatics Hands On Workshop - 2010:
Title: Functional Enrichment Analysis and Candidate Gene Prioritization
Presenter: Anil Jegga, Assistant Professor, Division of Biomedical Informatics, CCHMC
Description: Topics that will be covered:
- Gene set functional enrichment analyses
- Multi-list gene set analyses for understanding the underlying biological themes
- Candidate gene prioritization or ranking using either functional annotations or network analysis
The workshop will focus on how to use and interpret the results from ToppGene Suite (http://toppgene.cchmc.org) and ToppCluster (http://toppcluster.cchmc.org)
Date: Tuesday May 18, 2010
Time: 10.00 AM - 12:00 Noon
Location: CCHMC Location D2.43
Course Material and Exercises
Download the presentation: Power point OR pdf
Download the handout: pdf
Training Material - Example Files (to download Right Click And Save the file):
Digestive Health Center Bioinformatics Hands On Workshop - 2009:
Title: Know your transcriptome data
Presenter: Anil Jegga, Assistant Professor, Division of Biomedical Informatics, CCHMC
Description: This workshop gives more insight into the analysis of the transcriptome data following the microarray analysis. This workshop mainly aims to give hands on experience to the participants to databases and tools to analyze and interpret the gene expression data sets. Topics covered include gene regulatory network analysis (transcriptional and post-transcriptional) and functional enrichment analysis.
Date: Tuesday September 29, 2009
Time: 9:30 AM - 12:30 PM
Location: CCHMC Location D2.43
Course Material and Exercises
Download the presentation: Power point OR pdf
Download the handout: pdf
Training Material - Example Files (to download Right Click And Save the file):
Additional Exercises
1. Using the following two gene lists, identify conserved and non-conserved common binding sites within the upstream 500 bp (Hint: when downloading the promoter sequences use 500 bp)
Gene List 1:
ADORA1
AGTRAP
CD37
COL3A1
COL4A2
COL6A1
COL6A3
DCN
E2F4
FN1
LOC374395
LOXL1
LRP3
LRP5
LUM
MMP9
NUMA1
PPARBP
PPARD
PPP2R1A
PSG9
PTGDS
PTPRN
ROM1
SNN
SPARC
THBS2
Gene List 2:
APAF1
BAD
BAX
BCL2
BID
BIRC2
BNIP3L
CASP1
CASP2
CHUK
CYCS
DFFA
DFFB
FADD
FAS
MDM2
MYC
NFKB1
NFKBIA
PRF1
RELA
RIPK1
TNF
TNFRSF10B
TP53
TP73
TRAF1
2. What are the enriched diseases for the above two gene lists (use ToppFun disease enrichment feature)? Do any of these genes are known drug targets?
3. How many of these genes interact among themselves?
4. Are there any common miRNA regulators for these genes?
5. How many of these genes have trinucleotide repeats (Hint: Use "intersection" feature in UCSC table browser and intersect with "simple repeats")?
6. Using the gene lists (based on published microarray data; Appendix 1 below), and the applications oPOSSUM, PScan, GenomeTrafac and ConciseScanner:
a. Find the potential common transcription factor binding site clusters that could be responsible for the co-expression.
b. Find additional genome-wide targets for the signature cis-regulatory modules identified (Hint: use the feature ConciseScanner to find genome-wide additional targets for a specific transcription factor).
7. Using gene list 2 from (1) above, find out with which other differentially expressed gene lists do they overlap (use "Coexpression" feature in ToppFun application). Are there any gene expression profile studies where in these genes are down- or up-regulated?
8. Using gene list 1 from (1) above, obtain the mouse orthologs. For the mouse orthologs, download the 3’UTR sequences.
9. How many of the genes in the gene list 2 have a conserved NF-kappaB site (Hint: In oPOSSUM, use "select specific profiles" option and select "NF-kappaB")?
10. For the two above gene lists obtain their gene IDs and RefSeq accession numbers (Hint: use "Gene ID Conversion" feature in DAVID).
11. Use gene lists 2, 4 and 6 from Appendix 1 and identify the enriched pathways, and TFBSs, in the up and down regulated genes (Hint: use ToppCluster).
APPENDIX 1: Co-expressed gene lists
1: Nitric Oxide. 2002 Nov;7(3):165-86.
A DNA microarray study of nitric oxide-induced genes in mouse hepatocytes: implications for hepatic heme oxygenase-1 expression in ischemia/reperfusion.
Zamora R, Vodovotz Y, Aulak KS, Kim PK, Kane JM 3rd, Alarcon L, Stuehr DJ, Billiar TR.
#NAME inos_10_dn
#DESCRIPTION Ten most-downregulated genes following iNOS induction in hepatocytes
#GENES: CD151, EIF5A, EEF2, CD81, PKM2, ACT6
#NAME inos_10_up
#DESCRIPTION Ten most-upregulated genes following iNOS induction in hepatocytes
#GENES: EED, CSRP1, PCNA, HMOX1, MCM2, CDK2, MCM6, GNB1, TUBB1
2: J Nutr. 2004 Apr;134(4):762-70.
Gene expression profiling in human preadipocytes and adipocytes by microarray analysis.
Urs S, Smith C, Campbell B, Saxton AM, Taylor J, Zhang B, Snoddy J, Jones Voy B, Moustaid-Moussa N.
#NAME adip_human_dn
#DESCRIPTION Down-regulated in primary human adipocytes, versus preadipocytes
#GENES: PPARD, CEBPA, MMP2, SNN, SPARC, COL5A1, DCN, COL3A1, LRP3, COL6A3, PSG9, ATRAP, CD37, ROM1, COL4A2, LUM, PPP2R1A, LRP5, LOX, PTPRN, OKL38, IL18BP, THBS4, FN1, THBS1, LOXL1, COL6A1, ADORA1, MMP9, PPARBP, E2F4, PTGDS, THBS2
#NAME adip_human_up
#DESCRIPTION Up-regulated in primary human adipocytes, versus preadipocytes
#GENES: PFKFB3, ABCE1, PLCD1, AGTRL1, CROC4, HSD11B2, AGT, FABP4, DGKG, PTPN21, PTPRZ1, SCD, FABP5, RXRA, SMARCB1, COL1A2, CRYAB, DGAT1, ZNF336, LRP8, CTSG, 3-PAP, APM1, DPT, CAP2, IL22R, SCAP1, USP8, LYPLA1, HPCA, STAT5B, CYB5, E2F5, ALDH6A1, MMP7, LBP, GPD1, GLUL, GPX3, INSR, FXYD1, FACL2, ALDH1A2, MGST1, MAP4K3, MASP1, ECM2, PTPRS, CEBPD, KCNH2, ATP2B2, ACOX3, SPTBN4, TNFAIP2, LIPE, VN, FABP7, UCP4, LPL, ADFP, PPAR- , E2F1, IGFBP2, CHST1, GDF8, ADORA2B, ATP8A2, ATIP1, LIPC, REQ, PLEK, APOB, TAP1, AMT, PLIN, TFCP2, RXRB
3: Science. 2000 Mar 31;287(5462):2486-92.
Mitotic misregulation and human aging.
Ly DH, Lockhart DJ, Lerner RA, Schultz PG.
#NAME middleage_dn
#DESCRIPTION Downregulated in fibroblasts from middle-age individuals, compared to young
#GENES: CCNB, PLK, FOXM1, KIF11, PTGS2, KIF2C, CENPA, CDC20, H2AFX, KIF23, HMGN2, UBE2C, CCNF, CCNA, CENPF, MYB
#NAME middleage_up
#DESCRIPTION Upregulated in fibroblasts from middle-age individuals, compared to young
#GENES: COL15A1, TNFRSF11B, SERPINB2, COL6A2, IL8, FMOD, MMP12, DPT, CST6, COMP, THBS2, PTGS1, CRYBB2, MMP10, PRSS11
4: Oncogene. 2001 Jun 21;20(28):3674-82.
Distinctive gene expression profiles associated with Hepatitis B virus x protein.
Wu CG, Salvay DM, Forgues M, Valerie K, Farnsworth J, Markin RS, Wang XW.
#NAME hbx_dn
#DESCRIPTION Downregulated by expression of Hepatitis HBx protein in hepatocytes
#GENES: CD4, GSTA4, GLG1, WT1, TGFB1, MAP3K1, IL6, APR-3, TP53, CDKN1A, GSTM5, APC, GAS6
#NAME hbx_up
#DESCRIPTION Upregulated by expression of Hepatitis HBx protein in hepatocytes
#GENES: CCNI, DAD1, GSTM4, AP4B1, CDK4, TYMS, TNFRSF6, MYC, CCND3, PDCD2, PTK9, AP4S1, IGF1R, BCL2L1, TUBG1, TUBA4, TUBG2, VCL, IFNGR1, SLC5A1, MFNG, IFNAR2, CASP4, AP4E1, CDKN3
5: Nat Rev Cancer. 2002 Jan;2(1):38-47.
Hypoxia--a key regulatory factor in tumour growth.
Harris AL.
#NAME hypoxia_review
#DESCRIPTION Genes known to be induced by hypoxia
#GENES: EDN1, PFKP, MMP13, HSF, AK3, BIK, TGM2, P4HA, TEK, CDKN1B, SLC2A3, TF, CCNG2, CD99, SAT, FTL, PFKL, BNIP3, TH, RP1, STC1, HIF2A, PDGFB, VIM, IL8, LDHA, SPP1, CA9, PTGS2, PRPS1, BHLHB2, HK1, IGFBP2, TGFB1, APEX1, TFRC, ALDOA, CCL2, CA12, IL6, SLC2A1, ANGPT2, ACAT, L1CAM, TAGLN, HMOX1, FLT1, ANXA, TGFB3, PGF, IGF2, VEGF, IGFBP1, DDIT3, FOS, LRP8, ENPEP, HK2, G22P1, NOS, ADRA, HIF1A, TGFA, ENO1, PKM2, FGF3, HDAC, CDKN1A, ITGA, BNIP3L, ADM, XRCC5, EDN2, MIF, NFKB1, SERPINE, TXN, IGFBP3, COL5A1, F3, JUN, GAPD, PLAUR, TFF3, EPO, CP, HGF, PGK1
6: Science. 1999 Aug 27;285(5432):1390-3.
Gene expression profile of aging and its retardation by caloric restriction.
Lee CK, Klopp RG, Weindruch R, Prolla TA.
#NAME aged_mouse_muscle_dn
#DESCRIPTION Downregulated in the gastrocnemius muscle of aged adult mice (30-month) vs. young adult (5-month)
#GENES: IL6ST, CALM3, SIN3A, GFER, USP4, ABCB4, COL1A2, PRKCSH, PTPRR, POLA2, PLA2G7, HNRPD, COL1A1, PPP1R2, PRSS15, CLTB, FDFT1, PMP22, PSMB8, MYH2, TST, BMP8B, ADAM28, SRPR, PSMC3, CDC2L2, PPP3CC, S100A10, RAI2, NR2F1, PHOX2A, WNT4
#NAME aged_mouse_muscle_up
#DESCRIPTION Upregulated in the gastrocnemius muscle of aged adult mice (30-month) vs. young adult (5-month)
#GENES: GDF9, ARF5, MFAP5, HSPA6, HSPB1, ETV4, TFAP2B, ISLR, GADD45A, CKMT2, USP53, ATF3, ACTR1B, PBEF1, RAB1A, DCTN1, STARD7, DDX5, TM4SF3, U2AF2, SOX17, RAB21, AP3S2, CDC42, PLAGL1, AMY2B, PRSS11, ZFP90, POU3F2, HINT1, TGFB1I1, TGIF, ARHGDIB
Suggestions and comments: Anil Jegga
This page was last updated on May 18, 2010