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Coexpression cluster:C3267: Difference between revisions

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|tf_chipseq_enrich=ZZZ3#26009;1:79.8044041450777:0.012478437908258:0.0451555932469615
|tf_chipseq_enrich=ZZZ3#26009;1:79.8044041450777:0.012478437908258:0.0451555932469615
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}}
}}

Revision as of 16:01, 26 November 2012


Full id: C3267_temporal_parietal_duodenum_Chondrocyte_colon_occipital_Neural



Phase1 CAGE Peaks

Hg19::chr12:24097201..24097216,-p10@SOX5
Hg19::chr12:24097236..24097256,-p9@SOX5
Hg19::chr12:24102576..24102623,-p2@SOX5


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
astrocyte of the cerebral cortex1.55e-083
collagen secreting cell6.35e-086
chondroblast6.35e-086
chondrocyte6.35e-086
GAG secreting cell9.93e-089
carbohydrate secreting cell9.93e-089
Uber Anatomy
Ontology termp-valuen
neural tube1.25e-5856
neural rod1.25e-5856
future spinal cord1.25e-5856
neural keel1.25e-5856
telencephalon1.61e-5734
brain grey matter2.82e-5734
gray matter2.82e-5734
cerebral hemisphere3.39e-5732
regional part of nervous system1.55e-5553
regional part of brain1.55e-5553
regional part of telencephalon1.15e-5232
central nervous system5.28e-5281
regional part of forebrain4.57e-5041
forebrain4.57e-5041
anterior neural tube4.57e-5041
future forebrain4.57e-5041
brain5.38e-4668
future brain5.38e-4668
nervous system9.07e-4689
cerebral cortex4.53e-4425
pallium4.53e-4425
neural plate1.71e-4182
presumptive neural plate1.71e-4182
neurectoderm4.32e-3986
regional part of cerebral cortex2.85e-3722
neocortex1.03e-3620
pre-chordal neural plate1.76e-3361
ecto-epithelium1.48e-30104
adult organism3.09e-28114
organ system subdivision8.88e-27223
structure with developmental contribution from neural crest1.92e-26132
ectoderm-derived structure4.10e-21171
ectoderm4.10e-21171
presumptive ectoderm4.10e-21171
brainstem7.71e-166
temporal lobe5.84e-156
tube5.91e-15192
basal ganglion6.48e-159
nuclear complex of neuraxis6.48e-159
aggregate regional part of brain6.48e-159
collection of basal ganglia6.48e-159
cerebral subcortex6.48e-159
neural nucleus2.21e-149
nucleus of brain2.21e-149
organ part1.61e-13218
anatomical cluster1.78e-13373
gyrus3.25e-126
corpus striatum6.15e-124
striatum6.15e-124
ventral part of telencephalon6.15e-124
future corpus striatum6.15e-124
posterior neural tube2.99e-1015
chordal neural plate2.99e-1015
telencephalic nucleus4.63e-107
multi-tissue structure4.64e-10342
parietal lobe5.51e-105
anatomical conduit6.45e-10240
limbic system8.48e-105
occipital lobe2.69e-095
caudate-putamen3.43e-093
dorsal striatum3.43e-093
pons5.35e-093
medulla oblongata1.55e-083
myelencephalon1.55e-083
future myelencephalon1.55e-083
epithelium7.11e-08306
cell layer1.07e-07309
segmental subdivision of hindbrain1.43e-0712
hindbrain1.43e-0712
presumptive hindbrain1.43e-0712
amygdala5.88e-072
segmental subdivision of nervous system6.16e-0713
middle temporal gyrus7.84e-072


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
ZZZ3#26009179.80440414507770.0124784379082580.0451555932469615



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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