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Coexpression cluster:C1879

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Full id: C1879_ovary_MCF7_breast_hepatocellular_uterus_epididymis_testis



Phase1 CAGE Peaks

Hg19::chr2:11679770..11679781,+p7@GREB1
Hg19::chr2:11679938..11679951,+p1@GREB1
Hg19::chr2:11680114..11680122,+p15@GREB1
Hg19::chr2:11680148..11680159,+p10@GREB1
Hg19::chr2:11680181..11680197,+p13@GREB1


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><br>uberon_data<br>disease_data<br>


Uber Anatomy
Ontology termp-valuen
male reproductive organ9.22e-2011
male genital duct2.59e-193
internal male genitalia2.59e-193
adult organism3.18e-15114
duct of male reproductive system1.26e-144
male organism7.09e-1322
male reproductive system7.09e-1322
testis1.59e-128
reproductive organ3.42e-1148
reproductive structure1.17e-1059
reproductive system1.17e-1059
medulla oblongata7.01e-093
myelencephalon7.01e-093
future myelencephalon7.01e-093
internal genitalia1.82e-0825
uterus or analog7.03e-081
epididymis9.10e-081
seminal vesicle1.72e-071
seminal fluid secreting gland1.72e-071
vas deferens1.83e-071
spermatic cord1.83e-071
maxillary sinus2.35e-071
paranasal sinus2.35e-071
substantia nigra2.83e-071
midbrain nucleus2.83e-071
regional part of midbrain2.83e-071
midbrain2.83e-071
presumptive midbrain2.83e-071
midbrain neural tube2.83e-071
dura mater3.01e-071
future meninx3.01e-071
ectomeninx3.01e-071
future dura mater3.01e-071
gonad3.36e-0721
indifferent external genitalia3.36e-0721
indifferent gonad3.36e-0721
gonad primordium3.36e-0721
corpus callosum4.34e-071
central nervous system cell part cluster4.34e-071
axon tract4.34e-071
intercerebral commissure4.34e-071
dorsal telencephalic commissure4.34e-071
brain white matter4.34e-071
brain commissure4.34e-071
white matter4.34e-071
nervous system commissure4.34e-071
cerebral hemisphere white matter4.34e-071
nucleus accumbens4.61e-071
ventral striatum4.61e-071
external genitalia7.34e-0722
Disease
Ontology termp-valuen
thoracic cancer2.96e-154
breast cancer2.96e-154
paranasal sinus cancer2.35e-071
maxillary sinus cancer2.35e-071


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
BHLHE40#8553217.9487254187910.004747812859838950.0223198067729888
E2F1#186954.907389214879320.0003512818099256460.00353104147707647
EP300#203345.419153380978560.00209386927943890.0121213687531356
ESR1#2099530.76860329615453.62044058097993e-082.40991200660907e-06
FOXA1#3169511.08141974938555.98116883436141e-060.000179141752765091
FOXA2#3170524.63046375266521.10174651693954e-076.40675414714079e-06
HDAC2#3066513.41562023662632.29961139448262e-068.18014694919519e-05
HEY1#2346254.040111043105710.0009288852205177990.00674630344545608
HNF4A#3172523.13229036295371.50794906621644e-078.4808127370263e-06
HNF4G#3174211.50136901057870.01127438304921050.0413820654838157
NR3C1#290838.983813998703820.002687995788940450.0147979332771679
RXRA#6256312.044770283480.001145262162836830.0078366006043711
TBP#690853.706770687096390.001428755106721120.00919621315116771
TCF7L2#6934510.77017656313736.89693748574565e-060.000199919304488978



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.