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Coexpression cluster:C1161: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=1.01633,0.247072,0.384703,0.529489,0.90845,0.52784,0.604235,0.226729,0.637583,0.443077,0.497563,0.647852,0.541517,0.592674,0.341795,0.956905,0.827563,0.28906,0.569568,0.66776,0.384762,0.23059,0.520063,0.338096,0.430372,0.670692,0.957451,0.517892,0.915262,0.150685,0.475674,0.864517,0.714156,0.546594,0.309012,0.0934825,0.305874,0.529001,1.4117,0.207499,0.307642,0.459366,0.0729319,0.902101,0.0257952,0.415364,0.60533,0.486696,1.3209,0.346342,0.684981,1.49721,0.752493,0.941629,1.09491,0.595623,0.924875,0.562713,0.150585,0.561701,0.905643,0.60771,0.224801,0.799729,0.625758,0.76514,1.18348,1.55228,1.98793,1.38987,1.13397,1.90083,0.369103,1.0929,0.179863,0.503161,0.921933,0.782748,0.850825,0.424224,1.72677,0.798651,0.625403,0.649554,1.04131,0.0324537,0.097572,0.448771,0.711163,1.65172,1.27705,1.01423,0.881388,1.34301,0.343884,0.759662,0.194299,0.924148,0.715799,0.81992,0.28424,0.875714,0.918549,0.831244,2.97738,0.493026,0.815341,0.589207,0.43012,0.873303,0.395884,0.915771,0.379203,1.2644,1.22894,0.304323,0.039977,0.474472,0.762789,0.736663,1.0846,0.708722,0.525076,0.636741,1.33983,0.783512,0.597853,0.886402,1.12733,0.27799,1.01492,0.47854,1.14174,0.633392,1.28996,0.140417,0.469685,0.518459,1.24743,2.10682,1.70417,1.21002,0.59959,0.920609,0.755332,0.554217,0.738579,1.94751,0.456039,0.26104,0.345641,0.0685123,1.0153,1.16378,0.607223,1.42052,0.694887,0.329354,1.09986,0.401655,1.2088,0.996724,0.850033,0.404861,0.7715,0.624608,0.24928,0.602897,0.033943
}}
}}

Revision as of 14:43, 26 November 2012


Full id: C1161_osteosarcoma_Melanocyte_cerebellum_substantia_thalamus_globus_occipital



Phase1 CAGE Peaks

Hg19::chr12:110510751..110510754,-p@chr12:110510751..110510754
-
Hg19::chr12:110511424..110511445,-p5@C12orf76
Hg19::chr13:113698946..113698993,+p1@MCF2L
Hg19::chr13:113698996..113699013,+p6@MCF2L
Hg19::chr13:113699029..113699040,+p11@MCF2L
Hg19::chr16:27730331..27730353,+p@chr16:27730331..27730353
+
Hg19::chr8:112039622..112039629,-p1@ENST00000523557


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

GO IDGO nameFDR corrected p-value
GO:0005089Rho guanyl-nucleotide exchange factor activity0.0332038149063935
GO:0035023regulation of Rho protein signal transduction0.0332038149063935
GO:0005088Ras guanyl-nucleotide exchange factor activity0.0332038149063935
GO:0007266Rho protein signal transduction0.0332038149063935
GO:0005085guanyl-nucleotide exchange factor activity0.0372071117390792
GO:0046578regulation of Ras protein signal transduction0.0372071117390792
GO:0007265Ras protein signal transduction0.0372071117390792
GO:0005083small GTPase regulator activity0.0372071117390792
GO:0051056regulation of small GTPase mediated signal transduction0.0372071117390792
GO:0030695GTPase regulator activity0.049452490286118



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
melanocyte6.92e-1610
melanoblast6.92e-1610
light melanocyte3.61e-113
pigment cell4.87e-1114
neurecto-epithelial cell2.08e-0720
Uber Anatomy
Ontology termp-valuen
neural tube6.35e-10456
neural rod6.35e-10456
future spinal cord6.35e-10456
neural keel6.35e-10456
regional part of nervous system5.83e-9553
regional part of brain5.83e-9553
central nervous system3.51e-8281
regional part of forebrain5.36e-7941
forebrain5.36e-7941
anterior neural tube5.36e-7941
future forebrain5.36e-7941
brain5.82e-7968
future brain5.82e-7968
nervous system3.04e-7689
neural plate2.83e-7182
presumptive neural plate2.83e-7182
brain grey matter7.28e-6934
gray matter7.28e-6934
telencephalon1.95e-6834
neurectoderm1.72e-6786
regional part of telencephalon1.16e-6232
cerebral hemisphere5.42e-6232
ecto-epithelium2.15e-59104
adult organism1.20e-56114
pre-chordal neural plate6.25e-5461
regional part of cerebral cortex1.75e-4822
structure with developmental contribution from neural crest1.33e-44132
neocortex1.65e-4220
cerebral cortex2.69e-4225
pallium2.69e-4225
ectoderm-derived structure3.76e-40171
ectoderm3.76e-40171
presumptive ectoderm3.76e-40171
neural nucleus4.07e-299
nucleus of brain4.07e-299
basal ganglion4.65e-299
nuclear complex of neuraxis4.65e-299
aggregate regional part of brain4.65e-299
collection of basal ganglia4.65e-299
cerebral subcortex4.65e-299
organ system subdivision2.10e-25223
posterior neural tube1.30e-2415
chordal neural plate1.30e-2415
tube4.68e-23192
telencephalic nucleus8.29e-237
brainstem2.67e-206
gyrus1.04e-196
limbic system6.99e-175
segmental subdivision of hindbrain1.26e-1612
hindbrain1.26e-1612
presumptive hindbrain1.26e-1612
anatomical conduit2.41e-16240
segmental subdivision of nervous system3.08e-1513
corpus striatum2.28e-134
striatum2.28e-134
ventral part of telencephalon2.28e-134
future corpus striatum2.28e-134
epithelium5.94e-13306
cell layer1.01e-12309
temporal lobe3.98e-126
diencephalon1.03e-117
future diencephalon1.03e-117
anatomical cluster2.02e-11373
occipital lobe2.99e-115
pons4.57e-113
parietal lobe5.06e-115
medulla oblongata5.79e-113
myelencephalon5.79e-113
future myelencephalon5.79e-113
frontal cortex8.09e-113
organ part8.77e-11218
caudate-putamen1.52e-103
dorsal striatum1.52e-103
spinal cord1.62e-103
dorsal region element1.62e-103
dorsum1.62e-103
regional part of metencephalon5.64e-099
metencephalon5.64e-099
future metencephalon5.64e-099
locus ceruleus5.11e-082
brainstem nucleus5.11e-082
hindbrain nucleus5.11e-082
dorsal plus ventral thalamus5.29e-082
thalamic complex5.29e-082
amygdala5.86e-082
middle frontal gyrus5.86e-082
middle temporal gyrus6.07e-082
Ammon's horn8.52e-082
lobe parts of cerebral cortex8.52e-082
hippocampal formation8.52e-082
limbic lobe8.52e-082
globus pallidus9.43e-082
pallidum9.43e-082
multi-tissue structure1.02e-07342
caudate nucleus1.19e-072

Disease
Ontology termp-valuen


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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