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Coexpression cluster:C2108: Difference between revisions

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|tf_chipseq_enrich=HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0185510156538771!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0321207697408952
|tf_chipseq_enrich=HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0185510156538771!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0321207697408952
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}}
}}

Revision as of 15:18, 26 November 2012


Full id: C2108_hepatocellular_hippocampus_amygdala_medulla_medial_middle_thalamus



Phase1 CAGE Peaks

Hg19::chr11:124806196..124806206,-p7@HEPACAM
Hg19::chr11:124806212..124806292,-p3@HEPACAM
Hg19::chr11:124806297..124806320,-p6@HEPACAM
Hg19::chr22:29279602..29279621,+p2@ZNRF3


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><br>


Uber Anatomy
Ontology termp-valuen
neural tube1.53e-8456
neural rod1.53e-8456
future spinal cord1.53e-8456
neural keel1.53e-8456
regional part of nervous system8.94e-7953
regional part of brain8.94e-7953
central nervous system1.20e-7381
brain8.81e-6668
future brain8.81e-6668
nervous system1.18e-6489
regional part of forebrain1.73e-6441
forebrain1.73e-6441
anterior neural tube1.73e-6441
future forebrain1.73e-6441
adult organism2.88e-61114
telencephalon4.72e-5934
brain grey matter8.09e-5934
gray matter8.09e-5934
neural plate1.41e-5782
presumptive neural plate1.41e-5782
cerebral hemisphere2.58e-5532
regional part of telencephalon3.71e-5532
neurectoderm3.66e-5486
ecto-epithelium4.78e-42104
pre-chordal neural plate6.79e-4261
cerebral cortex9.47e-4225
pallium9.47e-4225
regional part of cerebral cortex7.73e-4122
structure with developmental contribution from neural crest5.50e-37132
neocortex1.19e-3620
ectoderm-derived structure1.60e-30171
ectoderm1.60e-30171
presumptive ectoderm1.60e-30171
organ system subdivision1.06e-29223
tube1.23e-23192
posterior neural tube3.67e-2015
chordal neural plate3.67e-2015
anatomical conduit1.64e-19240
basal ganglion9.11e-199
nuclear complex of neuraxis9.11e-199
aggregate regional part of brain9.11e-199
collection of basal ganglia9.11e-199
cerebral subcortex9.11e-199
anatomical cluster1.79e-18373
neural nucleus3.03e-189
nucleus of brain3.03e-189
segmental subdivision of hindbrain5.90e-1512
hindbrain5.90e-1512
presumptive hindbrain5.90e-1512
telencephalic nucleus9.64e-157
segmental subdivision of nervous system1.27e-1313
gyrus3.56e-136
epithelium7.92e-13306
cell layer1.55e-12309
brainstem3.35e-126
multi-tissue structure9.56e-12342
limbic system1.05e-115
temporal lobe3.60e-116
parietal lobe1.17e-105
occipital lobe1.29e-105
regional part of metencephalon7.23e-109
metencephalon7.23e-109
future metencephalon7.23e-109
organ part1.28e-09218
corpus striatum2.15e-094
striatum2.15e-094
ventral part of telencephalon2.15e-094
future corpus striatum2.15e-094
regional part of diencephalon8.28e-094
organ1.29e-07503
caudate-putamen1.50e-073
dorsal striatum1.50e-073
frontal cortex2.28e-073
diencephalon2.29e-077
future diencephalon2.29e-077
medulla oblongata4.51e-073
myelencephalon4.51e-073
future myelencephalon4.51e-073
spinal cord4.79e-073
dorsal region element4.79e-073
dorsum4.79e-073
pons8.92e-073


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
HEY1#2346244.040111043105710.00375304636917980.0185510156538771
TAF1#687243.343046285745290.008005664898701650.0321207697408952



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.