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Coexpression cluster:C1839: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1839_Mast_immature_Fibroblast_Mesenchymal_Hair_tenocyte_Keratocytes
|full_id=C1839_Mast_immature_Fibroblast_Mesenchymal_Hair_tenocyte_Keratocytes
|id=C1839
|id=C1839

Revision as of 14:27, 12 September 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
mesoderm2.28e-19448
mesoderm-derived structure2.28e-19448
presumptive mesoderm2.28e-19448
somite1.50e-1883
paraxial mesoderm1.50e-1883
presomitic mesoderm1.50e-1883
presumptive segmental plate1.50e-1883
trunk paraxial mesoderm1.50e-1883
presumptive paraxial mesoderm1.50e-1883
multilaminar epithelium7.72e-1782
dermomyotome9.59e-1770
musculoskeletal system1.47e-14167
artery2.09e-1442
arterial blood vessel2.09e-1442
arterial system2.09e-1442
blood vessel4.48e-1460
epithelial tube open at both ends4.48e-1460
blood vasculature4.48e-1460
vascular cord4.48e-1460
trunk mesenchyme5.14e-14143
splanchnic layer of lateral plate mesoderm7.17e-1484
vasculature1.03e-1379
vascular system1.03e-1379
vessel2.12e-1369
skeletal muscle tissue9.37e-1361
striated muscle tissue9.37e-1361
myotome9.37e-1361
epithelial tube3.18e-12118
lateral plate mesoderm3.50e-12216
muscle tissue5.45e-1263
musculature5.45e-1263
musculature of body5.45e-1263
surface structure4.68e-1195
trunk5.72e-11216
systemic artery1.10e-1033
systemic arterial system1.10e-1033
integument1.72e-1045
integumental system1.72e-1045
mesenchyme7.21e-10238
entire embryonic mesenchyme7.21e-10238
multi-cellular organism1.69e-09659
skin of body3.19e-0940
unilaminar epithelium3.63e-09138
anatomical system4.10e-09625
anatomical group5.89e-09626
cardiovascular system1.79e-08110
circulatory system3.97e-08113


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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