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Coexpression cluster:C3140: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0003075!4.25e-89!86;UBERON:0007284!4.25e-89!86;UBERON:0005743!7.02e-86!86;UBERON:0002346!3.85e-84!90;UBERON:0001049!3.48e-82!57;UBERON:0005068!3.48e-82!57;UBERON:0006241!3.48e-82!57;UBERON:0007135!3.48e-82!57;UBERON:0001017!3.19e-80!82;UBERON:0000073!9.77e-76!94;UBERON:0001016!9.77e-76!94;UBERON:0003056!6.04e-75!61;UBERON:0002616!1.22e-71!59;UBERON:0000955!5.85e-68!69;UBERON:0006238!5.85e-68!69;UBERON:0002780!6.21e-62!41;UBERON:0001890!6.21e-62!41;UBERON:0006240!6.21e-62!41;UBERON:0003080!3.77e-60!42;UBERON:0000033!2.71e-56!123;UBERON:0000153!3.02e-54!129;UBERON:0007811!3.02e-54!129;UBERON:0004121!2.43e-52!169;UBERON:0001893!5.26e-52!34;UBERON:0002020!7.33e-52!34;UBERON:0003528!7.33e-52!34;UBERON:0002791!9.77e-51!33;UBERON:0000924!1.45e-50!173;UBERON:0006601!1.45e-50!173;UBERON:0001869!3.99e-49!32;UBERON:0000956!2.13e-39!25;UBERON:0000203!2.13e-39!25;UBERON:0002619!3.28e-34!22;UBERON:0007023!8.72e-34!115;UBERON:0001950!2.35e-31!20;UBERON:0003076!5.31e-22!15;UBERON:0003057!5.31e-22!15;UBERON:0000064!5.21e-19!219;UBERON:0007625!3.61e-18!11;UBERON:0000970!1.93e-17!20;UBERON:0004733!2.65e-17!12;UBERON:0002028!2.65e-17!12;UBERON:0007277!2.65e-17!12;UBERON:0002104!2.19e-16!21;UBERON:0000019!6.87e-16!19;UBERON:0000047!6.87e-16!19;UBERON:0004088!6.87e-16!19;UBERON:0003072!6.87e-16!19;UBERON:0003071!6.87e-16!19;UBERON:0004128!6.87e-16!19;UBERON:0004732!1.01e-15!13;UBERON:0000483!2.09e-15!309;UBERON:0000119!4.77e-15!312;UBERON:0000025!5.96e-15!194;UBERON:0000020!1.48e-14!23;UBERON:0002420!5.55e-14!9;UBERON:0007245!5.55e-14!9;UBERON:0010009!5.55e-14!9;UBERON:0010011!5.55e-14!9;UBERON:0000454!5.55e-14!9;UBERON:0001456!5.68e-14!21;UBERON:0001032!9.26e-14!24;UBERON:0004456!9.26e-14!24;UBERON:0002308!1.15e-13!9;UBERON:0000125!1.15e-13!9;UBERON:0002680!2.53e-13!9;UBERON:0001895!2.53e-13!9;UBERON:0010092!2.53e-13!9;UBERON:0001871!2.55e-13!7;UBERON:0000475!2.93e-12!365;UBERON:0001801!3.97e-12!14;UBERON:0009663!4.30e-11!7;UBERON:0001894!4.73e-11!7;UBERON:0006222!4.73e-11!7;UBERON:0005085!2.49e-10!29;UBERON:0000200!4.30e-10!6;UBERON:0000481!8.35e-10!347;UBERON:0002037!1.15e-09!6;UBERON:0006215!1.15e-09!6;UBERON:0000062!2.40e-09!511;UBERON:0000922!3.47e-09!612;UBERON:0000477!4.21e-09!286;UBERON:0002298!4.53e-09!8;UBERON:0004111!5.68e-09!241;UBERON:0002021!6.15e-09!5;UBERON:0000349!1.17e-08!5;UBERON:0000488!1.32e-08!4;UBERON:0001872!2.83e-08!5;UBERON:0000063!5.30e-08!97;UBERON:0010077!6.08e-08!4;UBERON:0005389!6.08e-08!4;UBERON:0000484!6.08e-08!4;UBERON:0002546!6.08e-08!4;UBERON:0000965!6.08e-08!4;UBERON:0001803!6.08e-08!4;UBERON:0003073!6.08e-08!4;UBERON:0005426!6.08e-08!4;UBERON:0000468!2.49e-07!659;UBERON:0000923!2.86e-07!604;UBERON:0005291!2.86e-07!604;UBERON:0006598!2.86e-07!604;UBERON:0002532!2.86e-07!604;UBERON:0002050!3.26e-07!605;UBERON:0005423!3.26e-07!605;UBERON:0000369!3.73e-07!4;UBERON:0002435!3.73e-07!4;UBERON:0000204!3.73e-07!4;UBERON:0010082!3.73e-07!4;UBERON:0003296!4.18e-07!4;UBERON:0010133!4.18e-07!4;UBERON:0000467!5.02e-07!625;UBERON:0000480!5.70e-07!626;UBERON:0001778!7.04e-07!3;UBERON:0001775!7.04e-07!3
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}}
}}

Revision as of 18:56, 8 August 2012


Full id: C3140_argyrophil_Lens_Ciliary_eye_small_Astrocyte_Iris



Phase1 CAGE Peaks

Hg19::chr11:31827535..31827565,-p11@PAX6
Hg19::chr11:31839453..31839462,-p9@PAX6
Hg19::chr11:31839488..31839515,-p3@PAX6


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><br>

Uber Anatomy
Ontology termp-valuen
neural plate4.25e-8986
presumptive neural plate4.25e-8986
neurectoderm3.85e-8490
neural tube3.48e-8257
neural rod3.48e-8257
future spinal cord3.48e-8257
neural keel3.48e-8257
central nervous system3.19e-8082
regional part of nervous system9.77e-7694
nervous system9.77e-7694
pre-chordal neural plate6.04e-7561
regional part of brain1.22e-7159
brain5.85e-6869
future brain5.85e-6869
regional part of forebrain6.21e-6241
forebrain6.21e-6241
future forebrain6.21e-6241
anterior neural tube3.77e-6042
head2.71e-56123
anterior region of body3.02e-54129
craniocervical region3.02e-54129
ectoderm-derived structure2.43e-52169
telencephalon5.26e-5234
gray matter7.33e-5234
brain grey matter7.33e-5234
regional part of telencephalon9.77e-5133
ectoderm1.45e-50173
presumptive ectoderm1.45e-50173
cerebral hemisphere3.99e-4932
cerebral cortex2.13e-3925
pallium2.13e-3925
regional part of cerebral cortex3.28e-3422
adult organism8.72e-34115
neocortex2.35e-3120
posterior neural tube5.31e-2215
chordal neural plate5.31e-2215
organ part5.21e-19219
pigment epithelium of eye3.61e-1811
eye1.93e-1720
segmental subdivision of hindbrain2.65e-1712
hindbrain2.65e-1712
presumptive hindbrain2.65e-1712
visual system2.19e-1621
camera-type eye6.87e-1619
simple eye6.87e-1619
ocular region6.87e-1619
optic cup6.87e-1619
eye primordium6.87e-1619
optic vesicle6.87e-1619
segmental subdivision of nervous system1.01e-1513
epithelium2.09e-15309
cell layer4.77e-15312
tube5.96e-15194
sense organ1.48e-1423
basal ganglion5.55e-149
nuclear complex of neuraxis5.55e-149
aggregate regional part of brain5.55e-149
collection of basal ganglia5.55e-149
cerebral subcortex5.55e-149
face5.68e-1421
sensory system9.26e-1424
entire sense organ system9.26e-1424
nucleus of brain1.15e-139
neural nucleus1.15e-139
regional part of metencephalon2.53e-139
metencephalon2.53e-139
future metencephalon2.53e-139
temporal lobe2.55e-137
organism subdivision2.93e-12365
anterior segment of eyeball3.97e-1214
telencephalic nucleus4.30e-117
diencephalon4.73e-117
future diencephalon4.73e-117
ectodermal placode2.49e-1029
gyrus4.30e-106
multi-tissue structure8.35e-10347
cerebellum1.15e-096
rhombic lip1.15e-096
organ2.40e-09511
embryo3.47e-09612
anatomical cluster4.21e-09286
brainstem4.53e-098
anatomical conduit5.68e-09241
occipital lobe6.15e-095


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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