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Coexpression cluster:C755: Difference between revisions

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|tf_chipseq_enrich=CTBP2#1488;3:17.1046364561804:0.000607092865199348:0.00506787401075491
|tf_chipseq_enrich=CTBP2#1488;3:17.1046364561804:0.000607092865199348:0.00506787401075491
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}}
}}

Revision as of 14:27, 26 November 2012


Full id: C755_cerebellum_parietal_temporal_occipital_duodenum_brain_hippocampus



Phase1 CAGE Peaks

Hg19::chr14:23982181..23982193,-p@chr14:23982181..23982193
-
Hg19::chr17:2679600..2679618,+p@chr17:2679600..2679618
+
Hg19::chr19:42817494..42817510,+p5@TMEM145
Hg19::chr1:42384322..42384336,-p5@HIVEP3
Hg19::chr5:87979375..87979388,-p@chr5:87979375..87979388
-
Hg19::chr5:87980660..87980676,-p8@LINC00461
Hg19::chr5:87980761..87980821,-p4@LINC00461
Hg19::chr7:82753269..82753271,-p@chr7:82753269..82753271
-
Hg19::chr8:10192782..10192787,+p@chr8:10192782..10192787
+
Hg19::chr8:85114625..85114629,+p@chr8:85114625..85114629
+
Hg19::chr8:9970823..9970828,+p@chr8:9970823..9970828
+


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 tube4.62e-10956
neural rod4.62e-10956
future spinal cord4.62e-10956
neural keel4.62e-10956
regional part of nervous system1.00e-10453
regional part of brain1.00e-10453
central nervous system8.47e-9181
brain4.36e-8768
future brain4.36e-8768
regional part of forebrain4.78e-8741
forebrain4.78e-8741
anterior neural tube4.78e-8741
future forebrain4.78e-8741
nervous system1.98e-8489
telencephalon8.83e-8234
brain grey matter1.27e-8134
gray matter1.27e-8134
cerebral hemisphere1.42e-7532
neural plate2.95e-7582
presumptive neural plate2.95e-7582
regional part of telencephalon3.09e-7532
neurectoderm9.95e-7586
ecto-epithelium3.64e-60104
pre-chordal neural plate8.55e-6061
cerebral cortex2.71e-5825
pallium2.71e-5825
regional part of cerebral cortex5.41e-5522
neocortex3.17e-5420
structure with developmental contribution from neural crest9.71e-48132
ectoderm-derived structure2.24e-45171
ectoderm2.24e-45171
presumptive ectoderm2.24e-45171
adult organism1.04e-43114
organ system subdivision1.71e-32223
tube1.77e-26192
basal ganglion7.52e-259
nuclear complex of neuraxis7.52e-259
aggregate regional part of brain7.52e-259
collection of basal ganglia7.52e-259
cerebral subcortex7.52e-259
neural nucleus3.30e-249
nucleus of brain3.30e-249
posterior neural tube3.35e-2215
chordal neural plate3.35e-2215
brainstem1.03e-206
temporal lobe3.60e-196
anatomical conduit3.69e-19240
parietal lobe5.06e-195
segmental subdivision of hindbrain3.27e-1812
hindbrain3.27e-1812
presumptive hindbrain3.27e-1812
telencephalic nucleus5.07e-187
segmental subdivision of nervous system1.05e-1613
anatomical cluster5.12e-16373
gyrus1.08e-156
organ part5.36e-15218
epithelium1.25e-14306
cell layer2.18e-14309
limbic system2.15e-125
occipital lobe2.34e-125
medulla oblongata2.27e-113
myelencephalon2.27e-113
future myelencephalon2.27e-113
multi-tissue structure3.07e-11342
pons4.44e-113
regional part of metencephalon4.60e-109
metencephalon4.60e-109
future metencephalon4.60e-109
corpus striatum7.25e-094
striatum7.25e-094
ventral part of telencephalon7.25e-094
future corpus striatum7.25e-094
amygdala9.93e-092
middle temporal gyrus1.24e-082
globus pallidus3.60e-082
pallidum3.60e-082
germ layer4.35e-08560
germ layer / neural crest4.35e-08560
embryonic tissue4.35e-08560
presumptive structure4.35e-08560
germ layer / neural crest derived structure4.35e-08560
epiblast (generic)4.35e-08560
diencephalon5.24e-087
future diencephalon5.24e-087
locus ceruleus5.54e-082
brainstem nucleus5.54e-082
hindbrain nucleus5.54e-082
embryonic structure6.00e-08564
organ1.31e-07503
meninx1.82e-072
membrane organ1.82e-072
meningeal cluster1.82e-072
developing anatomical structure2.26e-07581
embryo5.11e-07592


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
CTBP2#1488317.10463645618040.0006070928651993480.00506787401075491



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.