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Coexpression cluster:C2969: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2969_Melanocyte_Meningeal_Fibroblast_gall_breast_glioblastoma_melanoma
|full_id=C2969_Melanocyte_Meningeal_Fibroblast_gall_breast_glioblastoma_melanoma
|id=C2969
|id=C2969

Revision as of 15:47, 12 September 2012


Full id: C2969_Melanocyte_Meningeal_Fibroblast_gall_breast_glioblastoma_melanoma



Phase1 CAGE Peaks

Hg19::chr10:102106933..102106948,+p4@SCD
Hg19::chr10:102106957..102106970,+p5@SCD
Hg19::chr10:102106982..102107015,+p1@SCD


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>disease_data<br>

Cell Type
Ontology termp-valuen
epithelial cell1.28e-16254
ectodermal cell2.66e-1271
embryonic cell3.23e-10248
neurectodermal cell1.82e-0859
migratory neural crest cell4.93e-0841
ecto-epithelial cell3.94e-0733
Uber Anatomy
Ontology termp-valuen
ectoderm-derived structure1.07e-19169
ectoderm1.72e-19173
presumptive ectoderm1.72e-19173
organism subdivision5.16e-17365
head4.97e-15123
anterior region of body7.24e-13129
craniocervical region7.24e-13129
regional part of nervous system1.19e-1194
nervous system1.19e-1194
multi-tissue structure1.51e-11347
organ part2.04e-11219
cell layer3.21e-11312
epithelium2.80e-10309
central nervous system5.51e-1082
brain2.78e-0869
future brain2.78e-0869
neural plate3.63e-0886
presumptive neural plate3.63e-0886
neurectoderm5.40e-0890
subdivision of head2.50e-0748
organ segment3.76e-0797
anatomical cluster6.08e-07286
Disease
Ontology termp-valuen
disease of cellular proliferation9.09e-13239
cancer9.13e-13235
cell type cancer7.65e-11143
carcinoma2.24e-08106


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#90536.336201576962630.003930750035764890.0188989781320896
CHD2#1106310.34402283411690.0009033701102746880.00658112939083274
E2F1#186934.907389214879320.008460985347239390.0323257553658302
EBF1#187938.9064668465690.00141523283560980.00912267017147589
ELF1#199734.258097958807540.01295179875054610.0459670679888634
EP300#203336.77394172622320.003216880500103790.0166733390843841
FOS#235338.99795530889440.001372499272417130.00894381053921336
FOSL2#2355316.93020060456170.0002060162053171620.00242244161980625
FOXA1#3169311.08141974938550.000734755275698670.0057914797161278
GTF2F1#2962312.73966087675770.0004835525047438590.00432563083879605
HDAC2#3066313.41562023662630.0004140761399857210.00389741330064606
HNF4A#3172323.13229036295378.07584663437677e-050.00122431898192434
IRF1#365937.63716375356390.002244692747297240.0127520379588216
MAX#414936.452555509007120.003721913834265510.0185605194545602
MYC#460935.22228187160940.007020843755740150.0292983538181063
NFKB1#479035.488063424193840.006049381815655430.0268390563910466
NFYA#4800318.42558069983050.0001598135507814160.00198960155323166
NFYB#4801316.75979325353650.0002123649923296180.00244884480886751
POU2F2#545239.106124057742520.001324165192682130.00879120771460994
REST#597839.650028716128020.001112636247114590.00765044552060048
RFX5#5993312.04791082719510.0005717246050312580.00482819972708495
SIN3A#2594235.408884726815140.006318961977991520.0275229823179355
SP1#666735.69838137814090.005403962701712170.0245267246362225
SREBF1#6720347.00584944048839.62099323994382e-060.000253995680734705
SREBF2#67213436.9432624113481.19027063774682e-088.89203684804295e-07
TCF7L2#6934310.77017656313730.0008003181298398380.00611354777372315
TFAP2A#7020316.5186343730450.0002218033880766340.00247250763660322
TFAP2C#7022310.80922860986020.0007916746575753130.00612593239701475
USF1#739136.361499277207960.00388404057290560.0189376897009191
ZNF263#1012738.221841637010680.001799043925565870.0108858834613079



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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