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Coexpression cluster:C1304: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.44418,0.143275,0.436508,0.58616,1.80086,0.584466,0.662701,0.269608,0.267027,0.075749,0.553339,0.707204,0.223349,0.650887,0.391663,0.415981,0.889639,1.60251,0.236034,0.800617,0.436569,0.29639,0.576478,1.00694,0.483957,0.730467,0.202389,0.574247,0.396295,0.186644,0.530785,0.92701,0.302275,0.640661,0.35719,0.0334022,0.35388,0.585658,0.329602,0.248856,0.355745,0.513952,0.0979105,0.390088,0.154075,0.468392,0.66382,0.542147,0.304272,0.396429,0.745008,0.675919,0.149032,1.00488,1.15929,0.653901,0.400834,0.62023,1.04504,0.619193,0.968558,0.666252,0.267534,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.275507,0.146905,1.15727,0.218784,0.594475,0.192925,0.84426,2.10892,2.08653,0.240887,0.86037,1.63739,0.272514,1.10535,0.0481066,0.398737,0.181871,0.771626,1.71797,2.97901,1.07807,0.94406,0.83374,0.393853,0.32338,0.661488,0.987239,0.776336,0.166235,0.330999,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,0.647343,0.483695,0.376529,0.44815,0.978783,0.430775,0.563054,1.29401,0.352243,0.0577227,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,0.324369,1.07876,0.53374,1.20639,1.65434,1.35529,0.520084,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,0.306342,0.136746,0.0926553,1.07915,0.258882,0.665754,1.48627,0.755083,0.378604,0.484017,0.454152,1.27379,1.06043,0.912368,0.457485,1.94435,0.683502,0.29379,1.58953,0.0115686
}}
}}

Revision as of 14:48, 26 November 2012


Full id: C1304_pons_medial_frontal_paracentral_hippocampus_nucleus_insula



Phase1 CAGE Peaks

Hg19::chr10:134760770..134760781,-p@chr10:134760770..134760781
-
Hg19::chr16:47920797..47920838,-p1@uc002eex.1
Hg19::chr3:120628150..120628164,+p4@STXBP5L
Hg19::chr4:86068867..86068880,+p@chr4:86068867..86068880
+
Hg19::chr4:86068886..86068893,+p@chr4:86068886..86068893
+
Hg19::chrX:85969610..85969619,+p4@DACH2


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
neural tube1.15e-10656
neural rod1.15e-10656
future spinal cord1.15e-10656
neural keel1.15e-10656
regional part of nervous system7.03e-9553
regional part of brain7.03e-9553
central nervous system7.37e-8481
brain7.78e-8168
future brain7.78e-8168
regional part of forebrain7.18e-7741
forebrain7.18e-7741
anterior neural tube7.18e-7741
future forebrain7.18e-7741
neural plate5.99e-7582
presumptive neural plate5.99e-7582
nervous system6.49e-7589
telencephalon1.17e-7334
brain grey matter1.57e-7334
gray matter1.57e-7334
neurectoderm3.70e-7186
cerebral hemisphere4.50e-6632
regional part of telencephalon1.25e-6532
adult organism5.60e-59114
ecto-epithelium1.14e-57104
pre-chordal neural plate6.30e-5461
regional part of cerebral cortex1.62e-5022
structure with developmental contribution from neural crest1.29e-46132
cerebral cortex2.95e-4425
pallium2.95e-4425
neocortex2.79e-4220
ectoderm-derived structure4.65e-38171
ectoderm4.65e-38171
presumptive ectoderm4.65e-38171
neural nucleus3.22e-329
nucleus of brain3.22e-329
posterior neural tube3.40e-2915
chordal neural plate3.40e-2915
gyrus4.10e-296
organ system subdivision2.04e-27223
tube3.36e-26192
basal ganglion4.75e-259
nuclear complex of neuraxis4.75e-259
aggregate regional part of brain4.75e-259
collection of basal ganglia4.75e-259
cerebral subcortex4.75e-259
telencephalic nucleus7.50e-247
brainstem6.59e-206
corpus striatum6.62e-204
striatum6.62e-204
ventral part of telencephalon6.62e-204
future corpus striatum6.62e-204
anatomical conduit1.87e-19240
segmental subdivision of hindbrain2.44e-1812
hindbrain2.44e-1812
presumptive hindbrain2.44e-1812
segmental subdivision of nervous system7.38e-1713
limbic system3.61e-165
frontal cortex2.10e-153
caudate-putamen3.74e-153
dorsal striatum3.74e-153
pons4.98e-153
epithelium1.21e-14306
cell layer1.99e-14309
spinal cord2.25e-143
dorsal region element2.25e-143
dorsum2.25e-143
anatomical cluster2.66e-14373
organ part3.76e-14218
regional part of metencephalon8.76e-139
metencephalon8.76e-139
future metencephalon8.76e-139
temporal lobe2.07e-116
Ammon's horn7.23e-112
lobe parts of cerebral cortex7.23e-112
hippocampal formation7.23e-112
limbic lobe7.23e-112
middle temporal gyrus8.36e-112
middle frontal gyrus1.01e-102
caudate nucleus1.42e-102
future caudate nucleus1.42e-102
multi-tissue structure2.11e-10342
locus ceruleus3.18e-102
brainstem nucleus3.18e-102
hindbrain nucleus3.18e-102
parietal lobe2.37e-095
occipital lobe4.39e-095
organ9.30e-08503
medulla oblongata2.25e-073
myelencephalon2.25e-073
future myelencephalon2.25e-073
germ layer8.98e-07560
germ layer / neural crest8.98e-07560
embryonic tissue8.98e-07560
presumptive structure8.98e-07560
germ layer / neural crest derived structure8.98e-07560
epiblast (generic)8.98e-07560


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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