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Coexpression cluster:C2925

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Full id: C2925_optic_smooth_colon_corpus_globus_thalamus_ductus



Phase1 CAGE Peaks

Hg19::chr8:38614412..38614456,+p7@TACC1
Hg19::chr8:38614754..38614774,+p13@TACC1
Hg19::chr8:38614778..38614806,+p5@TACC1
Hg19::chr8:38614807..38614824,+p10@TACC1


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
adult organism6.34e-38114
anatomical cluster1.43e-26373
multi-tissue structure2.78e-20342
anatomical conduit3.19e-19240
organ system subdivision6.59e-19223
neurectoderm9.24e-1786
neural tube1.63e-1656
neural rod1.63e-1656
future spinal cord1.63e-1656
neural keel1.63e-1656
neural plate8.48e-1682
presumptive neural plate8.48e-1682
structure with developmental contribution from neural crest1.00e-15132
regional part of nervous system3.23e-1553
regional part of brain3.23e-1553
multi-cellular organism4.74e-15656
cell layer9.92e-15309
epithelium2.97e-14306
tube3.45e-14192
anatomical system1.53e-13624
brain grey matter1.75e-1334
gray matter1.75e-1334
telencephalon2.02e-1334
anatomical group2.74e-13625
regional part of forebrain1.39e-1241
forebrain1.39e-1241
anterior neural tube1.39e-1241
future forebrain1.39e-1241
regional part of telencephalon2.63e-1232
cerebral hemisphere3.88e-1232
brain1.23e-1168
future brain1.23e-1168
central nervous system2.85e-1181
nervous system6.58e-1189
pre-chordal neural plate6.85e-1161
embryo1.26e-10592
organ part2.23e-10218
ecto-epithelium2.97e-10104
ectoderm-derived structure1.25e-09171
ectoderm1.25e-09171
presumptive ectoderm1.25e-09171
developing anatomical structure2.05e-09581
embryonic structure4.85e-09564
blood vessel endothelium5.19e-0918
endothelium5.19e-0918
cardiovascular system endothelium5.19e-0918
germ layer5.65e-09560
germ layer / neural crest5.65e-09560
embryonic tissue5.65e-09560
presumptive structure5.65e-09560
germ layer / neural crest derived structure5.65e-09560
epiblast (generic)5.65e-09560
cerebral cortex1.64e-0825
pallium1.64e-0825
regional part of cerebral cortex2.09e-0822
neocortex1.16e-0720
subdivision of digestive tract1.32e-07118
digestive system1.71e-07145
digestive tract1.71e-07145
primitive gut1.71e-07145
simple squamous epithelium3.44e-0722
organ5.38e-07503
squamous epithelium6.90e-0725
neural nucleus6.92e-079
nucleus of brain6.92e-079


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
CTCF#1066445.360256373075030.001211145381643620.00820303583096487
E2F1#186944.907389214879320.001724022357361790.0106851326912651
EBF1#187936.679850134926750.005184294118278910.0240651803821917
HNF4A#3172423.13229036295373.48990320893214e-060.000115966274654045



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.