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Coexpression cluster:C733: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.253158,0.306045,0.246925,0.975357,0.21227,0.371921,0.44126,0.384145,0.762093,0.0713737,0.344881,0.481459,0.0905352,0.430675,0.606477,0.230406,0.650562,0.168654,0.0986515,0.14663,0.246975,0.423587,0.36495,0.20812,0.779948,0.50266,0.267398,0.363006,0.214796,0.24094,0.325512,0.685875,0.14393,0.0919867,0.184525,0.285028,0.182011,0.372963,0.492146,0.706689,0.540033,0.311187,0.471149,0.209923,0.00493315,0.273032,0.442265,0.335245,1.8813,0.214901,0.515974,0.453148,0.179579,0.760015,0.908824,0.433372,0.218374,0.40339,0.0681812,0.402472,0.725346,0.444449,0.119615,0.624068,0.461047,0.591283,0.99547,1.35949,0.675894,1.19869,0.299692,1.28337,0.0464399,0.906867,0.0876634,0.576459,0.071925,0.607953,0.672773,0.280653,0.333602,0.623044,1.16527,0.123028,0.856604,0.0372554,3.53066,0.0654897,0.540459,1.45821,1.08742,0.830286,0.702047,0.456075,0.212875,1.49285,1.10159,0.743159,0.544807,0.792069,0.164861,0.696605,0.737766,0.654073,0.580349,0.340854,0.638916,0.427507,0.285742,0.199366,0.712243,0.735091,0.242288,0.353283,1.04009,0.180771,0.0096263,0.324453,0.58906,0.901377,0.898765,0.538171,0.966635,0.471181,1.14929,0.608677,0.435413,0.706859,0.940494,0.159968,0.830959,0.328039,0.954592,0.468088,1.10012,1.26269,1.54623,0.363513,1.05827,1.9115,1.51034,1.02151,0.437004,1.7524,0.582016,0.395692,0.566218,1.75262,0.830443,0.146851,0.0413159,0.0216333,1.94121,0.113748,0.444001,1.22899,0.525224,0.582239,0.286011,0.261307,1.02032,0.813307,1.6118,0.264042,0.597299,0.459987,0.137885,0.440034,0.000550667
}}
}}

Revision as of 14:26, 26 November 2012


Full id: C733_pineal_neuroectodermal_anaplastic_epithelioid_papillary_parietal_middle



Phase1 CAGE Peaks

Hg19::chr11:126565298..126565302,-p@chr11:126565298..126565302
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Hg19::chr11:126605112..126605121,-p@chr11:126605112..126605121
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Hg19::chr11:126669389..126669406,-p@chr11:126669389..126669406
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Hg19::chr11:126724227..126724237,-p@chr11:126724227..126724237
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Hg19::chr11:126792092..126792107,-p@chr11:126792092..126792107
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Hg19::chr11:126792108..126792125,-p@chr11:126792108..126792125
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Hg19::chr11:126794867..126794870,-p@chr11:126794867..126794870
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Hg19::chr11:126794895..126794906,-p@chr11:126794895..126794906
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Hg19::chr11:126798945..126798948,-p@chr11:126798945..126798948
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Hg19::chr11:126824157..126824162,-p@chr11:126824157..126824162
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Hg19::chr11:126842992..126842996,-p@chr11:126842992..126842996
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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>disease_data<br>

Cell Type
Ontology termp-valuen
skin fibroblast2.29e-1123
Uber Anatomy
Ontology termp-valuen
neural tube1.71e-6856
neural rod1.71e-6856
future spinal cord1.71e-6856
neural keel1.71e-6856
regional part of nervous system1.12e-6253
regional part of brain1.12e-6253
regional part of forebrain9.87e-5641
forebrain9.87e-5641
anterior neural tube9.87e-5641
future forebrain9.87e-5641
brain3.99e-5368
future brain3.99e-5368
central nervous system3.49e-5281
brain grey matter3.72e-5234
gray matter3.72e-5234
telencephalon9.89e-5234
nervous system2.23e-5089
neurectoderm1.11e-4986
regional part of telencephalon7.46e-4832
neural plate1.01e-4782
presumptive neural plate1.01e-4782
cerebral hemisphere1.23e-4732
pre-chordal neural plate2.57e-3961
regional part of cerebral cortex6.28e-3822
ecto-epithelium1.10e-36104
neocortex1.81e-3320
cerebral cortex7.46e-3325
pallium7.46e-3325
structure with developmental contribution from neural crest2.26e-29132
adult organism5.73e-26114
ectoderm-derived structure1.35e-23171
ectoderm1.35e-23171
presumptive ectoderm1.35e-23171
basal ganglion1.15e-219
nuclear complex of neuraxis1.15e-219
aggregate regional part of brain1.15e-219
collection of basal ganglia1.15e-219
cerebral subcortex1.15e-219
neural nucleus1.94e-219
nucleus of brain1.94e-219
telencephalic nucleus3.89e-177
organ system subdivision1.34e-16223
tube4.72e-14192
posterior neural tube9.60e-1415
chordal neural plate9.60e-1415
limbic system7.71e-135
parietal lobe1.92e-125
temporal lobe1.92e-126
corpus striatum9.34e-114
striatum9.34e-114
ventral part of telencephalon9.34e-114
future corpus striatum9.34e-114
segmental subdivision of nervous system1.01e-1013
brainstem1.08e-096
gyrus1.26e-096
anatomical conduit5.89e-09240
segmental subdivision of hindbrain7.33e-0912
hindbrain7.33e-0912
presumptive hindbrain7.33e-0912
caudate-putamen1.14e-083
dorsal striatum1.14e-083
pons6.85e-083
occipital lobe8.12e-085
epithelium1.10e-07306
organ part1.34e-07218
cell layer1.70e-07309
spinal cord2.13e-073
dorsal region element2.13e-073
dorsum2.13e-073
organ6.97e-07503
regional part of diencephalon9.56e-074
Disease
Ontology termp-valuen
musculoskeletal system disease4.19e-115
myotonic disease4.19e-115
muscle tissue disease4.19e-115
myopathy4.19e-115
muscular disease4.19e-115
myotonic dystrophy4.19e-115


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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