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Coexpression cluster:C1657: Difference between revisions

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|tf_chipseq_enrich=CTBP2#1488;2:25.0868001357313:0.00246143859967838:0.0138447967423422!POU5F1#5460;2:134.175680580762:8.81868530743257e-05:0.00130141963377554!REST#5978;3:5.79001722967681:0.00946878869443394:0.0356904440038251
|tf_chipseq_enrich=CTBP2#1488;2:25.0868001357313:0.00246143859967838:0.0138447967423422!POU5F1#5460;2:134.175680580762:8.81868530743257e-05:0.00130141963377554!REST#5978;3:5.79001722967681:0.00946878869443394:0.0356904440038251
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|tfbs_overrepresentation_for_novel_motifs=0.508327,0.452433,0.500341,0.654974,0.454983,0.653236,0.733342,0.324142,0.321368,2.98939,0.621241,0.778743,0.752887,0.721271,0.453496,1.20439,0.963929,0.395009,1.42981,0.501863,0.500405,0.384437,0.645033,0.44943,0.549618,0.802434,0.25115,0.642741,0.458349,0.659743,0.598009,1.00172,1.68319,0.758594,0.417272,3.37137,1.87167,0.654459,0.388123,1.48009,0.415749,0.580638,0.414516,0.451846,1.25074,0.533483,0.734485,0.609718,0.124583,0.458489,0.817229,0.746838,1.06581,1.08035,1.2359,0.724351,0.4631,0.689906,1.22844,0.688844,1.04369,0.736968,0.86107,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,1.39076,0.330474,1.66643,1.23387,2.09345,0.255232,0.675933,2.11876,0.987729,0.543014,0.293154,0.934302,0.755403,0.327263,1.18161,0.536557,2.19312,0.228496,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,0.455791,0.381528,0.28626,1.06255,0.849074,1.14173,0.389604,1.01316,1.05685,0.967698,0.88799,1.49565,0.951411,0.717647,2.32322,2.90764,0.512457,1.05402,0.494368,1.52665,1.37132,1.05995,1.00558,0.596731,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.995523,1.15483,0.601055,1.28328,0.763715,1.43285,0.629991,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,1.7291,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,1.69829,0.526389,3.25206,1.15522,2.31232,0.736459,1.56426,0.827475,0.439798,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,2.49515,0.731946,1.45393
}}
}}

Revision as of 15:01, 26 November 2012


Full id: C1657_pineal_cerebellum_temporal_occipital_duodenum_middle_brain



Phase1 CAGE Peaks

Hg19::chr12:119419286..119419293,+p4@SRRM4
Hg19::chr12:119419294..119419308,+p2@SRRM4
Hg19::chr15:89147826..89147846,+p@chr15:89147826..89147846
+
Hg19::chr20:61808928..61808938,+p@chr20:61808928..61808938
+
Hg19::chr3:52001995..52002004,-p@chr3:52001995..52002004
-


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
neuronal stem cell2.52e-088
neuron2.80e-076
neuroblast2.80e-076
electrically signaling cell2.80e-076
Uber Anatomy
Ontology termp-valuen
central nervous system1.25e-9381
nervous system5.55e-9389
regional part of nervous system3.86e-9053
regional part of brain3.86e-9053
neural tube3.93e-8956
neural rod3.93e-8956
future spinal cord3.93e-8956
neural keel3.93e-8956
brain6.34e-8568
future brain6.34e-8568
regional part of forebrain3.39e-7741
forebrain3.39e-7741
anterior neural tube3.39e-7741
future forebrain3.39e-7741
brain grey matter3.76e-6834
gray matter3.76e-6834
telencephalon7.68e-6834
neural plate4.00e-6682
presumptive neural plate4.00e-6682
cerebral hemisphere1.90e-6332
regional part of telencephalon3.51e-6332
neurectoderm1.67e-6286
regional part of cerebral cortex1.61e-5822
pre-chordal neural plate2.80e-5861
neocortex9.69e-5320
ecto-epithelium6.30e-52104
cerebral cortex5.19e-5125
pallium5.19e-5125
ectoderm-derived structure9.14e-48171
ectoderm9.14e-48171
presumptive ectoderm9.14e-48171
adult organism3.85e-40114
structure with developmental contribution from neural crest1.75e-38132
organ system subdivision2.18e-36223
tube3.26e-20192
basal ganglion9.63e-199
nuclear complex of neuraxis9.63e-199
aggregate regional part of brain9.63e-199
collection of basal ganglia9.63e-199
cerebral subcortex9.63e-199
neural nucleus3.90e-189
nucleus of brain3.90e-189
anatomical cluster1.01e-17373
gyrus1.13e-176
limbic system2.29e-155
temporal lobe3.17e-156
occipital lobe3.87e-155
parietal lobe6.89e-155
segmental subdivision of hindbrain3.84e-1412
hindbrain3.84e-1412
presumptive hindbrain3.84e-1412
posterior neural tube5.40e-1415
chordal neural plate5.40e-1415
anatomical conduit7.28e-14240
telencephalic nucleus2.12e-137
organ part2.90e-13218
segmental subdivision of nervous system6.09e-1313
gland of diencephalon6.73e-134
neuroendocrine gland6.73e-134
regional part of metencephalon2.18e-119
metencephalon2.18e-119
future metencephalon2.18e-119
epithelium4.10e-11306
brainstem4.78e-116
cell layer6.85e-11309
diencephalon1.13e-107
future diencephalon1.13e-107
frontal cortex7.11e-103
multi-tissue structure2.47e-09342
pons8.44e-093
germ layer6.38e-08560
germ layer / neural crest6.38e-08560
embryonic tissue6.38e-08560
presumptive structure6.38e-08560
germ layer / neural crest derived structure6.38e-08560
epiblast (generic)6.38e-08560
embryonic structure9.29e-08564
pineal body1.66e-072
regional part of epithalamus1.66e-072
secretory circumventricular organ1.66e-072
circumventricular organ1.66e-072
epithalamus1.66e-072
regional part of diencephalon2.21e-074
Ammon's horn2.25e-072
lobe parts of cerebral cortex2.25e-072
hippocampal formation2.25e-072
limbic lobe2.25e-072
middle temporal gyrus3.04e-072
amygdala3.04e-072
embryo3.14e-07592
middle frontal gyrus3.33e-072
developing anatomical structure4.33e-07581
pituitary gland4.61e-072
corpus striatum6.87e-074
striatum6.87e-074
ventral part of telencephalon6.87e-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
CTBP2#1488225.08680013573130.002461438599678380.0138447967423422
POU5F1#54602134.1756805807628.81868530743257e-050.00130141963377554
REST#597835.790017229676810.009468788694433940.0356904440038251



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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