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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4140_Mast_medulla_gall_retina_occipital_pituitary_epididymis
|full_id=C4140_Mast_medulla_gall_retina_occipital_pituitary_epididymis
|id=C4140
|id=C4140

Revision as of 17:11, 12 September 2012


Full id: C4140_Mast_medulla_gall_retina_occipital_pituitary_epididymis



Phase1 CAGE Peaks

Hg19::chr2:165811983..165812008,-p2@SLC38A11
Hg19::chr2:165812028..165812040,-p1@SLC38A11
Hg19::chr2:165812051..165812061,-p4@SLC38A11


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
adult organism1.22e-61115
neural tube9.26e-4957
neural rod9.26e-4957
future spinal cord9.26e-4957
neural keel9.26e-4957
regional part of brain2.66e-4259
neural plate2.59e-4086
presumptive neural plate2.59e-4086
anterior neural tube2.94e-4042
regional part of forebrain1.13e-3941
forebrain1.13e-3941
future forebrain1.13e-3941
central nervous system1.35e-3782
neurectoderm2.16e-3790
regional part of nervous system2.67e-3794
nervous system2.67e-3794
brain1.08e-3569
future brain1.08e-3569
telencephalon2.18e-3334
pre-chordal neural plate3.52e-3361
gray matter7.53e-3334
brain grey matter7.53e-3334
regional part of telencephalon2.66e-3233
cerebral hemisphere1.28e-3132
cerebral cortex6.38e-2525
pallium6.38e-2525
regional part of cerebral cortex4.58e-2422
anterior region of body6.26e-24129
craniocervical region6.26e-24129
head6.71e-23123
neocortex2.54e-2220
ectoderm-derived structure4.26e-20169
ectoderm5.00e-19173
presumptive ectoderm5.00e-19173
organ part8.37e-14219
organ5.35e-11511
organism subdivision1.27e-10365
multi-tissue structure1.86e-10347
posterior neural tube9.31e-1015
chordal neural plate9.31e-1015
basal ganglion1.02e-099
nuclear complex of neuraxis1.02e-099
aggregate regional part of brain1.02e-099
collection of basal ganglia1.02e-099
cerebral subcortex1.02e-099
temporal lobe1.92e-097
nucleus of brain2.65e-099
neural nucleus2.65e-099
segmental subdivision of nervous system1.21e-0813
brainstem1.26e-088
tube1.69e-08194
epithelium4.17e-08309
anatomical conduit4.34e-08241
cell layer4.41e-08312
gyrus5.65e-086
telencephalic nucleus6.95e-087
segmental subdivision of hindbrain8.60e-0812
hindbrain8.60e-0812
presumptive hindbrain8.60e-0812
diencephalon1.33e-077
future diencephalon1.33e-077
anatomical cluster1.35e-07286
multi-cellular organism5.06e-07659


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#1066435.360256373075030.0064925092527670.0280078964828473
NR3C1#2908314.9730233311730.0002978331194675480.003093524929296



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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