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Coexpression cluster:C4186

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Full id: C4186_retina_corpus_Retinal_medulla_eye_pons_spinal



Phase1 CAGE Peaks

Hg19::chr2:219610834..219610846,+p11@TTLL4
Hg19::chr2:219610848..219610865,+p6@TTLL4
Hg19::chr2:219610868..219610888,+p9@TTLL4


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>


Cell Type
Ontology termp-valuen
pigment cell1.96e-0814
visual pigment cell4.32e-074
Uber Anatomy
Ontology termp-valuen
neural tube5.81e-5757
neural rod5.81e-5757
future spinal cord5.81e-5757
neural keel5.81e-5757
regional part of nervous system1.50e-4994
nervous system1.50e-4994
central nervous system6.17e-4982
neural plate5.82e-4786
presumptive neural plate5.82e-4786
regional part of brain8.56e-4759
brain4.62e-4569
future brain4.62e-4569
regional part of forebrain8.93e-4541
forebrain8.93e-4541
future forebrain8.93e-4541
neurectoderm4.99e-4490
telencephalon1.82e-4334
anterior neural tube2.02e-4342
gray matter3.40e-4334
brain grey matter3.40e-4334
regional part of telencephalon7.10e-4233
adult organism7.55e-41115
cerebral hemisphere2.98e-4032
pre-chordal neural plate5.35e-3661
ectoderm-derived structure1.74e-34169
head4.77e-34123
ectoderm3.72e-33173
presumptive ectoderm3.72e-33173
anterior region of body9.24e-33129
craniocervical region9.24e-33129
cerebral cortex4.35e-3025
pallium4.35e-3025
regional part of cerebral cortex6.78e-2722
neocortex3.38e-2420
tube5.64e-20194
anatomical conduit5.19e-16241
nucleus of brain1.60e-149
neural nucleus1.60e-149
basal ganglion2.30e-149
nuclear complex of neuraxis2.30e-149
aggregate regional part of brain2.30e-149
collection of basal ganglia2.30e-149
cerebral subcortex2.30e-149
posterior neural tube3.70e-1415
chordal neural plate3.70e-1415
epithelium3.24e-12309
cell layer6.82e-12312
organism subdivision8.64e-12365
telencephalic nucleus1.25e-117
segmental subdivision of nervous system1.61e-1113
organ part1.84e-11219
anatomical cluster1.86e-11286
brainstem1.50e-108
segmental subdivision of hindbrain3.59e-1012
hindbrain3.59e-1012
presumptive hindbrain3.59e-1012
organ4.16e-10511
gyrus5.24e-106
temporal lobe1.83e-097
multi-tissue structure1.92e-09347
limbic system1.28e-085
parietal lobe1.67e-085
embryo7.63e-08612
corpus striatum2.06e-074
striatum2.06e-074
ventral part of telencephalon2.06e-074
future corpus striatum2.06e-074


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
EP300#203336.77394172622320.003216880500103790.016781607519997
FOSL2#2355316.93020060456170.0002060162053171620.00243505279166128
HDAC2#3066313.41562023662630.0004140761399857210.00392144522886912
HNF4A#3172323.13229036295378.07584663437677e-050.00123039146119282
HNF4G#3174328.75342252644684.20470658818262e-050.000758175675696141
RAD21#5885310.35503389545630.0009004912073565420.00665768095746212
SP1#666735.69838137814090.005403962701712170.0247103529161172
TCF7L2#6934310.77017656313730.0008003181298398380.00615224681012387



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.