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Coexpression cluster:C2271: Difference between revisions

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|tf_chipseq_enrich=RXRA#6256;3:15.05596285435:0.000475830799730358:0.00433716991560821!USF1#7391;3:4.77112445790597:0.0137046588718802:0.0482878738207312!USF2#7392;3:9.7441480388022:0.00171834184841007:0.010717342747453
|tf_chipseq_enrich=RXRA#6256;3:15.05596285435:0.000475830799730358:0.00433716991560821!USF1#7391;3:4.77112445790597:0.0137046588718802:0.0482878738207312!USF2#7392;3:9.7441480388022:0.00171834184841007:0.010717342747453
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|tfbs_overrepresentation_for_novel_motifs=0.590005,1.54039,0.581696,0.741427,0.534346,0.739643,0.821651,0.395818,0.392841,0.902371,0.706765,0.867962,0.341754,0.809319,0.532789,0.559384,1.05593,0.471262,0.938585,1.85448,1.42279,0.169357,0.731221,0.528529,1.53003,0.892087,0.316693,0.728867,0.537869,1.46495,0.682839,1.09415,0.433165,0.911389,0.49475,0.598278,0.491074,0.740899,0.463978,0.971732,0.493145,0.66492,0.539378,3.33079,0.648765,0.61613,0.822818,0.694903,0.173425,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.806003,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,2.45549,1.62905,0.650393,0.402607,0.248021,1.32819,0.336329,2.35456,0.305238,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,0.399165,1.27559,0.716653,0.221873,0.793068,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.354969,1.15558,0.939507,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,0.632569,0.516141,1.44917,1.14697,0.575476,0.717043,1.46636,0.489254,0.393155,0.681522,0.988625,0.444962,1.31973,0.932085,1.74599,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,1.15964,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,1.91113,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,0.234974,0.175846,1.24902,0.383416,1.92786,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,2.75236,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,0.0401987
}}
}}

Revision as of 15:23, 26 November 2012


Full id: C2271_heart_occipital_left_parietal_temporal_medial_caudate



Phase1 CAGE Peaks

Hg19::chr13:76378357..76378382,+p11@LMO7
Hg19::chr6:13013780..13013794,+p@chr6:13013780..13013794
+
Hg19::chr6:13013826..13013837,+p@chr6:13013826..13013837
+
Hg19::chr6:13013854..13013868,+p@chr6:13013854..13013868
+


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 organism2.22e-62114
regional part of forebrain2.99e-5641
forebrain2.99e-5641
anterior neural tube2.99e-5641
future forebrain2.99e-5641
telencephalon3.49e-5334
cerebral hemisphere3.77e-5332
regional part of nervous system8.11e-5353
regional part of brain8.11e-5353
neural tube1.94e-4956
neural rod1.94e-4956
future spinal cord1.94e-4956
neural keel1.94e-4956
brain grey matter3.94e-4934
gray matter3.94e-4934
regional part of telencephalon5.31e-4932
regional part of cerebral cortex6.74e-4922
brain7.70e-4668
future brain7.70e-4668
neocortex1.72e-4420
cerebral cortex1.89e-4225
pallium1.89e-4225
central nervous system5.92e-4181
neural plate1.19e-3882
presumptive neural plate1.19e-3882
pre-chordal neural plate4.86e-3761
neurectoderm2.60e-3686
nervous system9.95e-3689
structure with developmental contribution from neural crest3.03e-29132
ecto-epithelium5.04e-28104
organ system subdivision2.62e-19223
ectoderm-derived structure3.15e-17171
ectoderm3.15e-17171
presumptive ectoderm3.15e-17171
tube4.34e-17192
gyrus3.42e-156
anatomical cluster1.68e-14373
occipital lobe3.63e-135
parietal lobe3.90e-135
temporal lobe1.01e-126
anatomical conduit1.50e-12240
limbic system2.16e-125
multi-tissue structure3.68e-12342
basal ganglion3.82e-129
nuclear complex of neuraxis3.82e-129
aggregate regional part of brain3.82e-129
collection of basal ganglia3.82e-129
cerebral subcortex3.82e-129
organ part3.05e-10218
organ3.15e-10503
epithelium6.24e-10306
cell layer1.05e-09309
neural nucleus8.93e-099
nucleus of brain8.93e-099
frontal cortex2.63e-083
telencephalic nucleus2.74e-087
valve4.58e-083
cardiac mesenchyme4.58e-083
cardial valve4.58e-083
tunica intima4.58e-083
heart layer4.58e-083
endocardium4.58e-083
endocardial cushion4.58e-083
presumptive endocardium4.58e-083
cardiac chamber7.71e-083


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
RXRA#6256315.055962854350.0004758307997303580.00433716991560821
USF1#739134.771124457905970.01370465887188020.0482878738207312
USF2#739239.74414803880220.001718341848410070.010717342747453



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.