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Coexpression cluster:C3963: Difference between revisions

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|tf_chipseq_enrich=CTCFL#140690;3:19.7464743589744:0.000129837200555116:0.00171907548032148!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0167615137971632!FOSL2#2355;3:16.9302006045617:0.000206016205317162:0.00243202514605166!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.0058173835371612!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0154235830260596!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00391470064125724!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0108800314432994!HNF4A#3172;3:23.1322903629537:8.07584663437677e-05:0.00122877818567552!HNF4G#3174;3:28.7534225264468:4.20470658818262e-05:0.000757129916143457!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0128189777906265!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156907946533422!NR3C1#2908;3:14.973023331173:0.000297833119467548:0.00309168006799238!PBX3#5090;3:21.9145126867441:9.49854535978121e-05:0.00136735848219185!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.027707870938763!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0246768598051732!SP2#6668;3:26.1535304938446:5.58768218891694e-05:0.000940789843830882
|tf_chipseq_enrich=CTCFL#140690;3:19.7464743589744:0.000129837200555116:0.00171907548032148!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0167615137971632!FOSL2#2355;3:16.9302006045617:0.000206016205317162:0.00243202514605166!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.0058173835371612!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0154235830260596!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00391470064125724!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0108800314432994!HNF4A#3172;3:23.1322903629537:8.07584663437677e-05:0.00122877818567552!HNF4G#3174;3:28.7534225264468:4.20470658818262e-05:0.000757129916143457!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0128189777906265!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156907946533422!NR3C1#2908;3:14.973023331173:0.000297833119467548:0.00309168006799238!PBX3#5090;3:21.9145126867441:9.49854535978121e-05:0.00136735848219185!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.027707870938763!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0246768598051732!SP2#6668;3:26.1535304938446:5.58768218891694e-05:0.000940789843830882
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}}
}}

Revision as of 16:27, 26 November 2012


Full id: C3963_Mesenchymal_Smooth_Fibroblast_Alveolar_Keratocytes_Hair_Renal



Phase1 CAGE Peaks

Hg19::chr1:27320176..27320200,+p1@TRNP1
Hg19::chr1:27320224..27320235,+p3@TRNP1
Hg19::chr1:27320382..27320395,+p2@TRNP1


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
cell layer8.04e-29309
epithelium1.02e-27306
multi-cellular organism3.67e-24656
multi-tissue structure3.59e-22342
anatomical system1.35e-21624
anatomical group3.23e-21625
mesenchyme1.23e-18160
entire embryonic mesenchyme1.23e-18160
organism subdivision2.39e-18264
trunk mesenchyme5.07e-16122
epithelial vesicle8.24e-1678
trunk1.60e-15199
surface structure4.82e-1599
anatomical cluster6.20e-15373
anatomical conduit2.66e-14240
embryo3.98e-14592
developing anatomical structure5.40e-14581
dense mesenchyme tissue4.66e-1373
organ part4.67e-13218
paraxial mesoderm5.11e-1372
presumptive paraxial mesoderm5.11e-1372
unilaminar epithelium7.11e-13148
somite7.69e-1371
presomitic mesoderm7.69e-1371
presumptive segmental plate7.69e-1371
dermomyotome7.69e-1371
trunk paraxial mesoderm7.69e-1371
integument2.23e-1246
integumental system2.23e-1246
multilaminar epithelium4.22e-1283
organ4.54e-12503
tube7.48e-12192
embryonic structure3.12e-11564
skin of body4.55e-1141
germ layer6.02e-11560
germ layer / neural crest6.02e-11560
embryonic tissue6.02e-11560
presumptive structure6.02e-11560
germ layer / neural crest derived structure6.02e-11560
epiblast (generic)6.02e-11560
epithelial tube1.62e-10117
skeletal muscle tissue1.70e-0962
striated muscle tissue1.70e-0962
myotome1.70e-0962
muscle tissue2.96e-0964
musculature2.96e-0964
musculature of body2.96e-0964
nephron epithelium3.74e-0915
renal tubule3.74e-0915
nephron tubule3.74e-0915
nephron3.74e-0915
uriniferous tubule3.74e-0915
nephrogenic mesenchyme3.74e-0915
structure with developmental contribution from neural crest4.51e-09132
renal system1.18e-0848
urinary system structure1.49e-0847
excretory tube1.69e-0816
kidney epithelium1.69e-0816
vasculature5.49e-0878
vascular system5.49e-0878
ecto-epithelium8.51e-08104
cortex of kidney9.17e-0812
renal parenchyma9.17e-0812
splanchnic layer of lateral plate mesoderm1.79e-0783
parenchyma2.87e-0715
ectoderm-derived structure3.88e-07171
ectoderm3.88e-07171
presumptive ectoderm3.88e-07171
cortex4.39e-0715
nephron tubule epithelium5.25e-0710


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
CTCFL#140690319.74647435897440.0001298372005551160.00171907548032148
EP300#203336.77394172622320.003216880500103790.0167615137971632
FOSL2#2355316.93020060456170.0002060162053171620.00243202514605166
FOXA1#3169311.08141974938550.000734755275698670.0058173835371612
GABPB1#255337.067683836182170.002832212825417420.0154235830260596
HDAC2#3066313.41562023662630.0004140761399857210.00391470064125724
HMGN3#932438.178547723350590.001827766942164210.0108800314432994
HNF4A#3172323.13229036295378.07584663437677e-050.00122877818567552
HNF4G#3174328.75342252644684.20470658818262e-050.000757129916143457
IRF1#365937.63716375356390.002244692747297240.0128189777906265
JUND#372736.994663941871030.002921845042734990.0156907946533422
NR3C1#2908314.9730233311730.0002978331194675480.00309168006799238
PBX3#5090321.91451268674419.49854535978121e-050.00136735848219185
SIN3A#2594235.408884726815140.006318961977991520.027707870938763
SP1#666735.69838137814090.005403962701712170.0246768598051732
SP2#6668326.15353049384465.58768218891694e-050.000940789843830882



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.