Functional annotation of genetic variants- 2015:
- Description: This lecture is delivered as part of the "Advanced Fundamentals of Human Genetics" course (see details below) and will focus on computational approaches for functional enrichment of genes and gene lists and disease candidate gene prioritization. This 1-hour lecture mainly aims to give an overview of databases and servers/tools which can assist in functional interpreation of variants.
- Course Title: Advanced Fundamentals of Human Genetics
- Course Number: MG 8011
- Course Directors: Drs. Lisa Martin, Ge Zhang and Bill Nichols
- Lecture/Topic Title: Functional annotation of genetic variant
- Presenter: Anil Jegga, Associate Professor, Division of Biomedical Informatics, CCHMC
- Date: September 14, 2015 Time: 11:00 AM - 12:00 Noon
- Location: Cincinnati Childrens Hospital and Medical Center
- Download the presentation: pdf
Gene Regulatory Networks - 2012:
Description: This lecture is delivered as part of the "Advanced Molecular Genetics I: Gene Regulation" course (see details below) and will focus on computational approaches to understand gene regulatory networks in higher eukaryotes. This 2-day lecture mainly aims to give an overview of databases and servers/tools which can assist in analyzing and interpreting the gene regulatory networks.
Course Title: Advanced Molecular Genetics I: Gene Regulation
Course Number: 26 MG 710-001
Course Director: Iain Cartwright
Lecture/Topic Title: Comparative Genomics and Gene Regulatory Networks
Presenter: Anil Jegga, Assistant Professor, Division of Biomedical Informatics, CCHMC
Date: February 23 through February 24, 2012
Time: 10:00 AM - 11:00 AM
Location: University of Cincinnati College of Medicine
Download the presentation:
- Session 1 - Feb 23, 2012: Power point OR pdf
- Session 2 - Feb 24, 2012: Power point OR pdf
Gene Regulatory Networks - 2011:
Description: This lecture is delivered as part of the "Advanced Molecular Genetics I: Gene Regulation" course (see details below) and will focus on computational approaches to understand gene regulatory networks in higher eukaryotes. This 2-day lecture mainly aims to give an overview of databases and servers/tools which can assist in analyzing and interpreting the gene regulatory networks.
Course Title: Advanced Molecular Genetics I: Gene Regulation
Course Number: 26 MG 710-001
Course Director: Iain Cartwright
Lecture/Topic Title: Comparative Genomics and Gene Regulatory Networks
Presenter: Anil Jegga, Assistant Professor, Division of Biomedical Informatics, CCHMC
Date: February 23 through February 24, 2011
Time: 10:00 AM - 11:00 AM
Location: Room E602 MSB, University of Cincinnati College of Medicine
Gene Regulatory Networks - 2010:
Description: This lecture is delivered as part of the "Advanced Molecular Genetics I: Gene Regulation" course (see details below) and will focus on computational approaches to understand gene regulatory networks in higher eukaryotes. This 3-day lecture mainly aims to give hands on experience to the participants to databases and tools to analyze and interpret the gene regulatory networks. Topics covered include an overview of comparative genomics, gene regulatory network analysis (transcriptional and post-transcriptional) and functional enrichment analysis.
Course Title: Advanced Molecular Genetics I: Gene Regulation
Course Number: 26 MG 710-001
Course Director: Iain Cartwright
Lecture/Topic Title: Comparative Genomics and Gene Regulatory Networks
Presenter: Anil Jegga, Assistant Professor, Division of Biomedical Informatics, CCHMC
Date: January 20 through January 22, 2010
Time: 10:00 AM - 10:50 AM
Location: Room E602 MSB, University of Cincinnati College of Medicine
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. Using each of the known regulatory sequences given below, identify:
- What species do they belong to?
- What genes do they belong to or what is the nearest neighboring gene(s)?
- How conserved are these regions evolutionarily?
- What is the cis-element composition of these regions?
- Identify reported SNPs in these regions?
>Example-1 GAATTCTTAGGCAAATGGATGGAAATATAACTCTTAGGGAATNGGGAATTTTAATTAAAGGTAAAGGGTT AGTGGGGAGATGGCTCAGTGGCGAAAGTGCTTGGCATGCATGATGCCTTGGGTTTGATCCCTGGGACCCA CATAAAAAGCCAGGCATGGCAGCATATATGGATTAATCCCTGTGCTGGGAAGGTGGAGACAGGCTCTCTG GGGCTTGCTGGCCAGCCAGTGTTTCTCTGAATCAGTGGGCTTCAGATTCAGTGAGAGACTGTCTCAAAAT TCAGGTGGAGAGGATAAGAGAAAGCTAACTGATGTTGATCGCCGACCTGAAAATGCACACACATGAACTA AGGGAAAGCAGTAATAAAGTGACTTGAGTGCCCGCTCTGACNACCCAGGAGAACTAACTCAGAGACAACC TGTCAGGCCATCTGAATTTCAATCTTCAAATATGGAGGACAATTCAAAATATAGTTTATTAAAATAGGTT TATATATATTTTGCCTGCATTTATTTATATGTGTACCATACGTGTGTCTGGTGACCATGAGTTCAGAAGT GGGAAGGCATTGAAGCCCGAGTAACTGGAATTACATGCAGTTGAAAAGCCACCATGTGGGTAAACTGAAA TGGGTCTTCTAAAAGAGCAATAAATATTCTTAACTGCTGAGCAATCTCCCTAGCCCGGATTCTATTTTAT ACATGGTCTTATCTCTACATGGTTTACAAATGAATAGTTTTAATATTTAAATACCTTTATTTAACCTCAA TTTTCCACTCAAGATGTGTCATTGGATCCAGACTTCATTTACCAATAGTGGGAAAAAAGGGTAACTAAAT CTACGGATGAAATCATAAAATGTTGTTTGCTTGNATACCATTTATTATTTTTAAAACTGTTTTCAAATCA TTNTTGATTTTGAAACTTGTTTTGAAAAACACTTTTAAGTTAGAAATGAGACAAAATTTTGTGAGAAATT GTTTCCACAATATGAAAGTACTGAAAACCAGTTATGGTAGTGCTTTTCTGTAATCCCAGCCCGGGGGAGT TGGGGCAGAACGGTCACCATGGGTTTCAGGCAAATCTGAGATACATAGTGAGATTATGTCTCAAAACCAC CAAAAATCAGCCAAGCAACAAAACAGAAAGAACAACCTTGGGAAGTTCAAGAAACAGTAAAATCTTGTAA CTACTAATAGGGAACCAGTGAGTGATACTTGGTAATTAGGAGATATGAAGTGGCATTTTAGGAAACATGA ATATTGNAAACAATGAATCTAGCTTCCAAGTTCACAGTGAAACTTCTACAACAGTATTTGTAATGGCTGA AAGTATTACCCGCCCATTCCTTTATTAAAAAGTTGAATAATACGGGAATAATGCTATTAAGACTTAGGCA AAGTAGATTGTGGGAGAGCACTTCCACAGCATGTGTGAGGCCCTAGATTGATTCCTGTGTCATTAACAAA ACANACAAAAAATTGAAATAAATACAGAGGGAGGGGAGAGGGAGACCATAATTACATGCAGGGATAGCTG AAGTCCTGAGCCACAAATCGAAGGATGTTCCCCAGCATATGGAGTAGTCTTCATGTTCTCCCAGGGACAG TCAGCACTATGTTCACCTCAGGATCATCAAGATGAGGTAAACTGTCAAGTATGATTTCAGTCATAGGGAG GTCTGCTTGGGATCATCAGTATTATGCAATCACGATAGATAGTTTATACAGCACCAAACTGCCACTTGGG AAATCTTGAACTCAAACAAAAGCTCAGNNATTATTACTGTCAAAAGGTACACNTTAGACAAAATTNGGTT GGCAGTAAGAAAGATGNGTCAAAGAGGAAAAAAAACCCATCTAATTTGTATAATCAAAATAACAAATATT TTGTCGTTGGTAACTACTTTTAAGTTTCAGCAAAGTTATATGCTATTATCTCTATTATCATTATACTTAA AAATATTATCACTGATAATACTTAAAATGTTTCTATACAGCAATGTATTTGTAGAGACACAACTTAGAAT CACATATACTTTCTTACTCAAAATCTTTATTTTCAACATGATTCAGAGTAAAGAATCTTTTATATATAGG AATAAGTAGTAACATTGAAAACATTGGACCATTTTATGTTTTTCCTTTAGCTAAATAGTCAAAAAAAAAC TTTAAAAGAGAAGACTTAGTTTTCTGGAAATATTTAAACATGCTAAAATCATGTCAGTCTGATGACTTTT ACAGAAAATAAAAGCATGAACTTAAAATATAAACTGATGTAACGAATCCCAGAAATTCCTCAGATATCTT GTAAGCACTGGAACAATGTATACTTATAAATGATACAACACATTATTCTATTAGCAAACATAAACTTTAC TATCTTTAAATCAGCCCCCACCCATACTCTCAAAAGGAATGTCGTCGAGCGTCAGTGCCTGAAGTGATAC GCTCTGACAAATCTAACAGCTCTCTCTGTGTCATTCCTAATGCACTTGTCACTCAGCATTATCCATCCTC ATTAATGACAATGGGAAAGTTTATCTTGGGAACACGTTTTAAATCATCTACTCTTTACAATGGGACCATG AAATCTCTTACAAAACATGAGGCGGGAACTACTCTGACAACAAAACCCCTTCCTGGCAGCTTTATTCTTA ATTCCTGTTCAAGGAGTAATCTGTTTATTATAAAATCATACAGAACAATATATTAAACAGAATTTGAAAC AAGAATAGCTAGTGTGATTTTCAAGCTTACAAGTATTTTTACAACATTTTTATTAAGCTGAAAACACTGT TGAGCCTTTTTGTGTGGTTTCATGCAATCATTTTTTTTTCTATTCTACATTATATCAACCTTTGAAAAGG GGTTTTGCTTTGCCCAATTTTAAAATAAACTAATGACCTAGCTCTTATATATATTAAAATGCAATAATTT GCATTACCTTAAAAGCAATTACTTAGAACCAAATNTATCCTATTAAAAAGGCTGAAAAAGTGCTGAAAAC TCAAGTTACCTAGTNTACNTTAAAATTANCT
>Example-2 CCCACCTCTCCTCTGCTCCTTTGTCGGAATCACAAAACCCTAAAGGTTGTCTCACTTGGGAAGGCAGCAG ATAGGTACATTTCCGTAGCCCAGAAATGCCACTTTTATGGCCCTGTTTGTCTCCCTGCTCTAGGTTCTGA ATGGGGCTGAACAAAACAGCAGTGCAGAGCTGGCTAGACGTCTGGGCTTAATTGTTTTATGGTTTAAATA AGGTGGACACTCTTTCCTTTGAAATCGGATTATAGGAATGTTTTGTCTATGGCCCACGGAGATCAGGATC TTTCTGGCTGAGAGGGAGAGGTGAAGAGCATTCAAGGAATGGGCTACAAACTGGGGAGTGGGGGCAGCCT GGAACAGTCAGAGTCCTACTCTGAAGTCTTGCAGGCAGCAGCGGAAATAAACTGTGCATCAGGATAAGGG GGCCTGGGAGTTTAGGGTACGTGCCAGGAGCAGAGGTCCTGGGAGCTTCGGATAGAGTGGTGCATCCGCG TGCGCAAAGGGTTTTCTAGACTAGAAAAACGCCTGAGTGGAGGAGATTCTGGCCATTCCTTTGCAATGTT TCTTTATTCCTGAAGGGAGGGTAACAAAAGAGGACAGTGTGGAACCCTTCTCAAGGTTTATTTCAAGAAT TTAGAGAACTAAAGAACAGAGGCAACTACCTTCCGGGAATCCCTCTCCTTTGGAGCTGTTTAGAGGCTTC TTTCTCCCAACTTGCCTTCGGCTCAGCCTGGGATCTCTGCTGGCTTTTCTCCAACCAGTTTGCATTGGAA CAAGTGAACGCGAGGTGGCGCTGTTGCTCAATGTTAGAGGC
>Example-3 AGATCTCACCTAAGAAGGCATCATGTGACACCCCCCCCTTCTGTGGGCTCCTGGGAACCCCAGGACCCAG CTCCAAAAGCCTCCGTTTGCATGTCCCCTAAGATTCCCTGGCTTGGACGTTGGAGCTACAAGCCCCTGCT TCACATCCCCCCTTCGGATGTTCCAGCTGCCTTTATCTCCCTGTGGTAACAGAGCAAATATACTCAGGCC CTGGAGCAGGGCACATGCAGGCTGTTGACTCTTGAGCAAAGTCTTCCCTCCGGAGGGCGCAGCACAGGCT GCTGGACATGTGTGGAGAGGCCAATGGCCTCTTGCATAACCCAGGAGGCCTCCTGCCCACCCCGGGGCCT TTTCAGGGTTAGGGGTGAGACAAATTGCAAACTCATGCCCAGTTAATTTTTTAAAGCAAGACCAACAGGC TCAGCAATGATTAGCAGACAGGTAAGTTCATCTTAATCACACTGAGGACAGGGAGGGAGGAAGAGGCTAC TGGAGGCCCCAGGGATGGGGCCCAGTTATCAGTTAACCACACAAATGTTTCTTTCTAAAACCGCTGGCCT TCAGCCCCCAACACTCTCATCTTCCTCTCTGAGATTCTGTGGTCAATGAGCAAGCTAGTGGCCAACAGCC ATTGAGTGAAGCGACATGTAGCCATCCACAGTCTGTGGGATAGAAAAGCGACAGGATCC
>Example-4 GGTACCTTTTTCCCAGCAGATAGAGCTACATCTGTTGGGTTTGTAATGTAATTTGTAATTACTGCCCTTC ATGTGGTCCAATGCCTTGAACCATCTTTAATTAAAAGCATAATTAAGGGAAGATCTAAAGGAAGACAATT ACCAGATGGTCTTTTTTTTTTTTTTTTTTAGAAGCGGTTCGTTGCTCGGAGGGCGCAGCCCGGTCCGCTT CGGACTCGGCTTAAGGGCCGGAGGGGTCGGAGAGGGAGGGGGGGGGGGGTCCGAGCCAGGGCTCGGG
>Example-5 AGGCTTTAATGACGGGAGATCTTTCCGCTCATTGCCCTTTCAAATACAATTGTAGATCGAACTCAGCCTT GTCACGTTGAGGAGCGGTGCGTCCCTAACATCCAGGACGTGCCTGTCGGCTCTCGGCGGATTGCATCCCA TCACCCCCGGGGAATGCAGC
>Example-6 AACAATTGAGAAAGTGAAACGAAGACAAAATGTGACCCACCCTTCAAACAGTTCACACCCTGAAAAATAA GAGCAACAAATAGATAACGTAAACTTGAAAGAGCATGGCTAGATGCAGGATATGCTGGCATGTACGTGGT TAACTGAAAGAGTTTATGGGAAGCTCAGACAGCTGGGAACTCCTGATTAAGGAGAGGCTGAAGGGCAGAA CAGAAGCCATGTGAACAGCTGCTAAAAGGGCTAGAAGATTTCCTCTGGATTAGGTGTCCCCAGCCCATCC CTAATGGGCCATTTCAGCACGCATCAAGTGTTATCAAGGGGTTC
>Example-7 AGACACCAGGAGATGACCTTGGCCTCTAGCCCTGTTTCTTTTCTTGGACCCTCTCCATTCCTTCACGCTG TTATAACTGAACTTGTAGGTCCTGCCCGTCATTTATCACTGACTTTGGCTCCCAACTTGCAGACTTCCCC CACCCTGTTCCTTCTGTAATCCTCCCAATGACATCACTAACCACGCAGATGGTGACCTGGCTGTACTCTG ACCTCTGAGTGGCTGGTTGTGATAGCGCATG
>Example-8 TATGAACTTGTTTACAGGGCTTCATGGCTCAGAACCTACCCAGAGAATTTTCTGTTCTACATCCCCAACC AAGCCAAGGTGTTGGGGTTCAAATTTGAGCCCCAGCTGTTAGCCCTCTGCAAAGAAAAAAAAAAAAAAAA AAGAACAAAGGGCCTAGATTTCCCTTCTGAGCCCCACCCTAAGATGAAGCCTCTTCTTTCAAGGGAGTGG GGTTGGGGTGGAGGCGGATCCTGTCAGCTTTGCTCTCTCTGTGGCTGGCAGTTTCTCCAAAGGGTAACAG GTGTCAGCTGGCTGAGCCTAGGCTGAACCCTGAGACATGCTACCTCTGTCTTCTCATGGCTGGAGGCAGC CTTTGTAAGTCACAGAAAGTAGCTGAGGGGCTCTGGAAAAAAGACAGCCAGGGTGGAGGTAGATTGGTCC TTCTAGTTGCAGCTTCCAAGGTGCCGCCAGGTCTGGGCGTTTCACCCCACACCAAGGAGAAGCCTTTGTA ACCCAGCCCAGCTACCGACCCAAGCCCACCCCACAGCTATTTTGCGGGAGTTTCAGTGCTATAGCAGATG GTTTCTGTAACGAGGTCACCACAGGGCTGCACCTGGTGCTCCACTTCCATCGTCCTCATCTCTAATACAC TGGCCTCCTCTAGTGCTCTTTTGGCAGCCTCTCACAGTGTCCGGGCCCCTGCTTCCTTTCTCCCATTTGG TCACCTTCCCCTCTTCTAGCTAGAAGCACAGAATATGGACAGCAAACATAGCTCCAAACAAGAACTAGGA AT
>Example-9 GCTAGCCTTAGCATAGACGTTCCACTTTTTTCTAAGGTGGAGCTTACTTCTTTGATTTGATCTTTTGTGA AACTTTTGGAAATTACCCATCTTCCTAAGCTTCTGCTTCTCTCAGTTTTCTGCTTGCTCATTCCACTTTT CCAGCTGACCCTGCCCCCTACCAACATTGCTCCACAAGTACAAATTCATCCAGAGAAAATAAATTCTAAG TTTTATAGTTGTTTGGATCGCATAGGTAGCTAAAGAGGTGGCAACCCACACATCCTTAGGCATGAGCTTG ATTTTTTTTGATTTAGAACCTTCCCCTCTCTGTTCCTAGATTACATTACACATTCTGCAAGCATAGCACA GAGCAATGTTCTACTTTAATTACTTTCATTTTCTTGTATCCTCACAGCCTAGAAAATAACCTGCGTTACA GCATCCACTCAGTATCCCTTGAGCATGAGGTGACACTACTTAACATAGGGACGAGATGGTACTTTGTGTC TCCTGCTCTGTCAGCAGGGCACTGTACTTGCTGATACCAGGGAATGTTTGTTCTTAAATACCATCATTCC GGACGTGTTTGCCTTGGCCAGTTTTCCATGTACATGCAGAAAGAAGTTTGGACTGATCAATACAGTCCTC TGCCTTTAAAGCAATAGGAAAAGGCCAACTTGTCTACGTTTAGTATGTGGCTGTAGAAAGGGTATAGATA TAAAAATTAAAACTAATGAAATGGCAGTCTTACACATTTTTGGCAGCTTATTTAAAGTCTTGGTGTTAAG TACGCTGGAGCTGTCACAGCTACCAATCAGGCATGTCTGGGAATGAGTACACGGGGACC
>Example-10 GGTACCTTTTTCCCAGCAGATCCTGCTACGTCTGTCGGGTTTGTAATGTAATTTGTAATTACTGCCCTTC ATGTGGTCCGGTGCCTTGAACCATCTTTAATTAAAAGCATAATTAAGGGAAGATCTAAAGAAAGACAATT ACCAGATGGTCTTTTTTTTAGAGGCGGTAGTTGCGCAGAGAGGGGCTCGGGGTCTGTCCCCGGGACCCCA CGCCTTGGGAGGGGGCGGCGGGCCCGAACGGCGCCTGCGCACTGAGGAGGCCTTGGC
>Example-11 CAAACACTTACACCCGGTCTTCAAGGCGATCTCCAGGTTCCCACCGGAGCCTTGAGAGAAGGGCAGGGCC CCACCCTCTTGGCTCACAATTTTCAAACTTATCACCAGGTTTGCACCCTCACAGGTTCACACACAGGCTG AGAGATGCCCAGTACACAGCCAGAGCCGAGCCCCTTCATCTGGACACACACATGTCCACGAACTCACTTG TGTGTGCCCAAGAAAGACTACCCTGATATACTTTCCTACAGACTAAGGCTCTACAGTTTCCTATGAACCA ACTTGGGTCAGGGTCCCGGACTCTTCTCCTGTCCCTGTTCCCCATTTCCGTCCCATTTCCCTCCATCTGT CTGTCTCTTTCCATTAGCCAGTCTCAGGGGGACCCAGCTTACTCCTGCCCAGCCCCCTTGAGCCATCCAT CCGTCTGTCTGCAACTACCCTGGCAGGGAATCGTTCCCCACCTCACTGGGTCCTGTCCTTCATCTCAGCC ACACCCACCACAGAGGACCCCTCTCCCTTCCTCAGCAGGGCCTCTCATCACTCACCCGGACCCTCACTCA CCCCTCCCTCCTCCTCCTATCTGTTTCCCTAATCTGTCAGTCAGTCTGTCTGTACACCCATCCATCCACC CTTCCTTCCTTCCTTCCCCGCTGGGCCCCATCTCTCTCAACAATCCCAGTGTCCCATCCATCAACCTACA GACAGCCCTGTGCTGCCAGGTAGTCTCCTCCTGGCTGCTCATCTGTTTGTCTGTCCACCCGCCCATCCAT CCATCTGTCTCCAAGCCCATCCATCCATCTATCCACCAGCCCATCCATCATGCAAGCCACTTGCAAGTTC TGGTGTAGGCTTCCTCAGCAAG
3. Using the gene lists (based on published microarray data; Appendix 1 below), and the applications oPOSSUM, PScan, GenomeTrafac and ConciseScanner:
- Find the potential common transcription factor binding site clusters that could be responsible for the co-expression.
- 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).
4. Using gene list 1 from (1) above, obtain the mouse orthologs. For the mouse orthologs, download the promoter sequences.
5. How many of the genes in the gene lists 1 and 2 have a conserved NF-kappaB site (Hint: In oPOSSUM, use "select specific profiles" option and select "NF-kappaB")?
6. Use gene lists 2, 4 and 6 from Appendix 1 (see below) and identify the enriched TFBSs, in the up and down regulated genes.
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 September 13, 2015