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Coexpression cluster:C2174: Difference between revisions

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|tf_chipseq_enrich=CTBP2#1488;3:47.0377502544961:1.60047699357395e-05:0.000370215319450432!ZNF263#10127;3:6.16638122775801:0.00653981434797598:0.0279601961146333
|tf_chipseq_enrich=CTBP2#1488;3:47.0377502544961:1.60047699357395e-05:0.000370215319450432!ZNF263#10127;3:6.16638122775801:0.00653981434797598:0.0279601961146333
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|tfbs_overrepresentation_for_novel_motifs=1.44014,1.03954,0.581696,0.741427,0.534346,0.739643,0.821651,0.395818,0.392841,0.902371,0.706765,0.867962,0.905351,0.809319,0.532789,0.559384,2.39977,0.471262,0.356737,0.635753,0.581762,0.505745,0.731221,0.528529,0.632849,0.892087,0.316693,0.728867,0.537869,0.297585,0.682839,1.09415,1.93746,0.911389,0.49475,1.00622,1.23038,0.740899,0.463978,1.72725,0.493145,0.66492,0.183156,0.53106,0.648765,0.61613,0.822818,0.694903,0.515703,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,1.90242,0.54284,0.777235,0.297448,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.248021,1.32819,0.336329,2.35456,0.305238,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,0.399165,1.27559,0.353274,0.221873,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,2.27689,0.456994,0.934671,1.15558,0.939507,1.37313,0.465545,1.1057,4.20395,1.05974,0.979006,1.67377,1.04326,0.805616,5.05604,1.28386,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,0.393155,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,3.02112,0.458105,1.24863,0.68598,3.05064,0.852645,1.52813,0.774456,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,0.234974,0.521611,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,1.08488,0.820225,1.00378
}}
}}

Revision as of 15:20, 26 November 2012


Full id: C2174_parietal_occipital_Saos2_caudate_lung_small_putamen



Phase1 CAGE Peaks

Hg19::chr11:91957816..91957827,+p@chr11:91957816..91957827
+
Hg19::chr11:91957916..91957921,+p@chr11:91957916..91957921
+
Hg19::chr11:91957974..91957992,+p@chr11:91957974..91957992
+
Hg19::chr11:92145586..92145591,+p@chr11:92145586..92145591
+


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 cell3.85e-078
Uber Anatomy
Ontology termp-valuen
nervous system1.67e-4189
central nervous system6.56e-4181
neural tube5.42e-3856
neural rod5.42e-3856
future spinal cord5.42e-3856
neural keel5.42e-3856
regional part of nervous system1.99e-3553
regional part of brain1.99e-3553
regional part of forebrain6.62e-3341
forebrain6.62e-3341
anterior neural tube6.62e-3341
future forebrain6.62e-3341
brain1.36e-3168
future brain1.36e-3168
neurectoderm4.10e-3086
neural plate5.57e-3082
presumptive neural plate5.57e-3082
brain grey matter9.74e-3034
gray matter9.74e-3034
telencephalon1.27e-2934
cerebral hemisphere3.59e-2832
regional part of telencephalon6.06e-2832
pre-chordal neural plate1.36e-2661
adult organism2.42e-24114
cerebral cortex1.23e-2325
pallium1.23e-2325
regional part of cerebral cortex5.84e-2122
ecto-epithelium6.87e-21104
ectoderm-derived structure4.53e-20171
ectoderm4.53e-20171
presumptive ectoderm4.53e-20171
neocortex5.43e-1920
organ system subdivision2.98e-17223
structure with developmental contribution from neural crest2.75e-16132
multi-cellular organism6.87e-08656
basal ganglion1.05e-079
nuclear complex of neuraxis1.05e-079
aggregate regional part of brain1.05e-079
collection of basal ganglia1.05e-079
cerebral subcortex1.05e-079
neural nucleus1.43e-079
nucleus of brain1.43e-079
anatomical cluster1.93e-07373
gyrus4.29e-076
posterior neural tube7.24e-0715
chordal neural plate7.24e-0715


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#1488347.03775025449611.60047699357395e-050.000370215319450432
ZNF263#1012736.166381227758010.006539814347975980.0279601961146333



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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