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Coexpression cluster:C1467: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.44418,0.0360157,0.436508,0.58616,1.01854,1.42848,0.662701,0.742622,0.267027,0.075749,0.553339,0.707204,0.223349,0.650887,0.391663,1.06849,0.889639,0.336106,0.236034,0.127969,1.11315,0.0880431,0.576478,0.387783,0.483957,0.730467,0.202389,0.574247,0.396295,0.547818,0.530785,0.92701,0.302275,0.640661,0.35719,0.0334022,0.35388,0.585658,0.329602,0.248856,1.6715,0.513952,0.0979105,0.390088,0.0393783,0.468392,0.66382,0.542147,0.0909286,1.81235,0.745008,0.675919,0.149032,1.00488,1.15929,0.653901,0.400834,0.62023,0.186533,0.619193,0.968558,0.666252,1.35522,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,2.12614,0.146905,1.15727,0.218784,0.206105,0.192925,0.84426,0.913168,0.477584,0.676305,0.86037,0.684313,0.272514,1.10535,0.0481066,0.126687,0.181871,0.771626,1.71797,1.34233,1.07807,0.94406,0.30974,0.393853,0.864356,0.234532,0.987239,1.82799,0.166235,1.58445,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,0.647343,0.483695,0.376529,0.44815,0.978783,0.430775,0.563054,1.29401,0.352243,0.0577227,0.529546,0.824029,0.312699,1.14892,1.81315,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,0.324369,1.07876,0.53374,1.20639,0.692462,1.35529,0.175219,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,0.306342,0.136746,0.0926553,1.07915,0.258882,0.665754,1.48627,0.755083,0.378604,0.484017,0.454152,1.27379,1.06043,0.912368,0.457485,0.83286,0.683502,0.29379,0.661335,0.0115686
}}
}}

Revision as of 14:54, 26 November 2012


Full id: C1467_hippocampus_locus_occipital_skeletal_optic_thalamus_medulla



Phase1 CAGE Peaks

Hg19::chr1:169101089..169101109,+p@chr1:169101089..169101109
+
Hg19::chr1:169101118..169101155,+p@chr1:169101118..169101155
+
Hg19::chr1:169101157..169101169,+p@chr1:169101157..169101169
+
Hg19::chr1:169101171..169101205,+p@chr1:169101171..169101205
+
Hg19::chr1:169101209..169101238,+p@chr1:169101209..169101238
+
Hg19::chr1:169101479..169101501,+p@chr1:169101479..169101501
+


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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
adult organism3.72e-39114
organ system subdivision1.07e-32223
neural tube1.99e-2756
neural rod1.99e-2756
future spinal cord1.99e-2756
neural keel1.99e-2756
regional part of nervous system7.58e-2553
regional part of brain7.58e-2553
regional part of forebrain3.10e-2141
forebrain3.10e-2141
anterior neural tube3.10e-2141
future forebrain3.10e-2141
anatomical cluster1.65e-20373
neural plate1.66e-2082
presumptive neural plate1.66e-2082
brain1.96e-2068
future brain1.96e-2068
central nervous system1.01e-1981
nervous system1.40e-1989
multi-tissue structure2.18e-19342
neurectoderm1.18e-1886
brain grey matter2.31e-1834
gray matter2.31e-1834
telencephalon1.50e-1734
regional part of telencephalon1.76e-1632
cerebral hemisphere2.57e-1632
subdivision of digestive tract2.12e-15118
regional part of cerebral cortex3.12e-1522
organ4.66e-15503
digestive system1.51e-14145
digestive tract1.51e-14145
primitive gut1.51e-14145
ecto-epithelium1.87e-14104
pre-chordal neural plate1.31e-1361
structure with developmental contribution from neural crest2.98e-13132
neocortex3.08e-1320
endoderm-derived structure3.44e-13160
endoderm3.44e-13160
presumptive endoderm3.44e-13160
tube3.87e-13192
anatomical conduit6.69e-13240
cerebral cortex1.47e-1225
pallium1.47e-1225
organ part4.82e-12218
embryo3.34e-10592
foregut8.48e-1087
ectoderm-derived structure1.86e-09171
ectoderm1.86e-09171
presumptive ectoderm1.86e-09171
multi-cellular organism8.65e-09656
developing anatomical structure9.88e-09581
anatomical system1.38e-08624
anatomical group1.72e-08625
respiratory tract7.77e-0854
respiratory primordium1.12e-0738
endoderm of foregut1.12e-0738
embryonic structure1.79e-07564
neural nucleus1.91e-079
nucleus of brain1.91e-079
germ layer1.94e-07560
germ layer / neural crest1.94e-07560
embryonic tissue1.94e-07560
presumptive structure1.94e-07560
germ layer / neural crest derived structure1.94e-07560
epiblast (generic)1.94e-07560
posterior neural tube2.18e-0715
chordal neural plate2.18e-0715
basal ganglion2.60e-079
nuclear complex of neuraxis2.60e-079
aggregate regional part of brain2.60e-079
collection of basal ganglia2.60e-079
cerebral subcortex2.60e-079
brainstem2.61e-076
endo-epithelium4.87e-0782
gastrointestinal system5.54e-0725
organ segment6.14e-0798
gyrus8.05e-076
larynx9.92e-079
Disease
Ontology termp-valuen
carcinoma2.93e-16106
cell type cancer4.34e-15143


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

No analysis results for this cluster

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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