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Coexpression cluster:C1839: Difference between revisions

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|tf_chipseq_enrich=CCNT2#905;5:6.33620157696263:9.78880505817628e-05:0.00139111853513522!E2F6#1876;5:5.01715573169739:0.000314497859929779:0.00322904463165613!EGR1#1958;5:4.98817909481014:0.000323739800059071:0.0033092944091582!FOS#2353;5:8.9979553088944:1.69470025615156e-05:0.000389251814497939!FOSL1#8061;5:39.713579716373:1.01017090471068e-08:7.64501732732457e-07!FOSL2#2355;5:16.9302006045617:7.18315284751475e-07:3.20873096767148e-05!GTF2F1#2962;5:12.7396608767577:2.97806917252935e-06:0.000101081107023007!HEY1#23462;5:4.04011104310571:0.000928885220517799:0.00674536528616732!HMGN3#9324;5:8.17854772335059:2.73180911341838e-05:0.000582260024482249!IRF1#3659;5:7.6371637535639:3.84754333311872e-05:0.000724677327624142!JUN#3725;5:12.5128291923363:3.25800591331781e-06:0.000109128569461514!JUND#3727;5:6.99466394187103:5.97069468343598e-05:0.000984641373824996!MAX#4149;5:6.45255550900712:8.93743970843928e-05:0.00130694100491415!MXI1#4601;5:9.9615716287593:1.01894348670516e-05:0.000266576750521042!MYC#4609;5:5.2222818716094:0.000257394484885061:0.00276564018589618!NFYB#4801;5:16.7597932535365:7.55590255814554e-07:3.32545683636815e-05!NR3C1#2908;3:8.98381399870382:0.00268799578894045:0.0147971532891183!POU2F2#5452;5:9.10612405774252:1.59639992500654e-05:0.000369763610041602!REST#5978;5:9.65002871612802:1.19441074361324e-05:0.000301530248132035!RFX5#5993;5:12.0479108271951:3.93714721313598e-06:0.0001275013078427!SIN3A#25942;5:5.40888472681514:0.000215952267165727:0.0024819895268539!SMARCA4#6597;5:156.765903307888:1.04731463528549e-11:1.30681592825068e-09!SMARCB1#6598;4:14.6021726249259:4.30486693344344e-05:0.000768540166943417!SMARCC1#6599;5:43.6633593196315:6.28653634995012e-09:4.97393613524577e-07!STAT1#6772;4:16.5652699977594:2.61308619905866e-05:0.00056385973046175!TAF1#6872;5:3.34304628574529:0.00239460009087031:0.0135439826098242!TAF7#6879;5:11.4330694049239:5.11611886715123e-06:0.000157431449135653!TBP#6908;5:3.70677068709639:0.00142875510672112:0.00919224755688088!TCF12#6938;5:10.6344649021864:7.34844389925727e-06:0.00021113181083756!TFAP2C#7022;4:8.64738288788818:0.000339051887817405:0.00344860149121172
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}}
}}

Revision as of 15:08, 26 November 2012


Full id: C1839_Mast_immature_Fibroblast_Mesenchymal_Hair_tenocyte_Keratocytes



Phase1 CAGE Peaks

Hg19::chr1:156084491..156084510,+p1@LMNA
Hg19::chr1:156084522..156084529,+p5@LMNA
Hg19::chr1:156084534..156084545,+p4@LMNA
Hg19::chr1:156084552..156084561,+p3@LMNA
Hg19::chr1:156084564..156084580,+p2@LMNA


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
epithelial vesicle8.38e-1978
mesoderm2.39e-18315
mesoderm-derived structure2.39e-18315
presumptive mesoderm2.39e-18315
somite4.18e-1771
presomitic mesoderm4.18e-1771
presumptive segmental plate4.18e-1771
dermomyotome4.18e-1771
trunk paraxial mesoderm4.18e-1771
multilaminar epithelium6.05e-1783
dense mesenchyme tissue1.37e-1673
musculoskeletal system2.46e-16167
paraxial mesoderm2.68e-1672
presumptive paraxial mesoderm2.68e-1672
artery6.69e-1542
arterial blood vessel6.69e-1542
arterial system6.69e-1542
epithelial tube open at both ends1.46e-1459
blood vessel1.46e-1459
blood vasculature1.46e-1459
vascular cord1.46e-1459
splanchnic layer of lateral plate mesoderm2.53e-1483
vasculature6.67e-1478
vascular system6.67e-1478
vessel9.48e-1468
skeletal muscle tissue4.39e-1362
striated muscle tissue4.39e-1362
myotome4.39e-1362
unilaminar epithelium2.50e-12148
muscle tissue2.71e-1264
musculature2.71e-1264
musculature of body2.71e-1264
lateral plate mesoderm4.25e-12203
epithelial tube4.34e-12117
trunk mesenchyme2.58e-11122
systemic artery4.67e-1133
systemic arterial system4.67e-1133
surface structure6.64e-1199
integument8.76e-1146
integumental system8.76e-1146
mesenchyme1.53e-10160
entire embryonic mesenchyme1.53e-10160
anatomical system8.28e-10624
trunk8.92e-10199
anatomical group1.22e-09625
skin of body1.26e-0941
multi-cellular organism1.72e-09656
organism subdivision1.93e-09264
cardiovascular system1.88e-08109
circulatory system4.79e-08112


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CCNT2#90556.336201576962639.78880505817628e-050.00139111853513522
E2F6#187655.017155731697390.0003144978599297790.00322904463165613
EGR1#195854.988179094810140.0003237398000590710.0033092944091582
FOS#235358.99795530889441.69470025615156e-050.000389251814497939
FOSL1#8061539.7135797163731.01017090471068e-087.64501732732457e-07
FOSL2#2355516.93020060456177.18315284751475e-073.20873096767148e-05
GTF2F1#2962512.73966087675772.97806917252935e-060.000101081107023007
HEY1#2346254.040111043105710.0009288852205177990.00674536528616732
HMGN3#932458.178547723350592.73180911341838e-050.000582260024482249
IRF1#365957.63716375356393.84754333311872e-050.000724677327624142
JUN#3725512.51282919233633.25800591331781e-060.000109128569461514
JUND#372756.994663941871035.97069468343598e-050.000984641373824996
MAX#414956.452555509007128.93743970843928e-050.00130694100491415
MXI1#460159.96157162875931.01894348670516e-050.000266576750521042
MYC#460955.22228187160940.0002573944848850610.00276564018589618
NFYB#4801516.75979325353657.55590255814554e-073.32545683636815e-05
NR3C1#290838.983813998703820.002687995788940450.0147971532891183
POU2F2#545259.106124057742521.59639992500654e-050.000369763610041602
REST#597859.650028716128021.19441074361324e-050.000301530248132035
RFX5#5993512.04791082719513.93714721313598e-060.0001275013078427
SIN3A#2594255.408884726815140.0002159522671657270.0024819895268539
SMARCA4#65975156.7659033078881.04731463528549e-111.30681592825068e-09
SMARCB1#6598414.60217262492594.30486693344344e-050.000768540166943417
SMARCC1#6599543.66335931963156.28653634995012e-094.97393613524577e-07
STAT1#6772416.56526999775942.61308619905866e-050.00056385973046175
TAF1#687253.343046285745290.002394600090870310.0135439826098242
TAF7#6879511.43306940492395.11611886715123e-060.000157431449135653
TBP#690853.706770687096390.001428755106721120.00919224755688088
TCF12#6938510.63446490218647.34844389925727e-060.00021113181083756
TFAP2C#702248.647382887888180.0003390518878174050.00344860149121172



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

This analysis result is provided for C0 - C305 clusters.

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