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Coexpression cluster:C1646: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001049!2.64e-84!56;UBERON:0005068!2.64e-84!56;UBERON:0006241!2.64e-84!56;UBERON:0007135!2.64e-84!56;UBERON:0000073!3.60e-79!53;UBERON:0002616!3.60e-79!53;UBERON:0001017!2.26e-74!81;UBERON:0002346!6.53e-72!86;UBERON:0002780!1.03e-71!41;UBERON:0001890!1.03e-71!41;UBERON:0003080!1.03e-71!41;UBERON:0006240!1.03e-71!41;UBERON:0001016!5.65e-68!89;UBERON:0003075!1.13e-64!82;UBERON:0007284!1.13e-64!82;UBERON:0000955!2.05e-63!68;UBERON:0006238!2.05e-63!68;UBERON:0003528!3.89e-59!34;UBERON:0002020!3.89e-59!34;UBERON:0001893!6.57e-59!34;UBERON:0007023!4.23e-58!114;UBERON:0001869!6.87e-56!32;UBERON:0002791!2.03e-55!32;UBERON:0003056!3.08e-54!61;UBERON:0010371!1.93e-51!104;UBERON:0004121!4.09e-44!171;UBERON:0000924!4.09e-44!171;UBERON:0006601!4.09e-44!171;UBERON:0000956!6.64e-42!25;UBERON:0000203!6.64e-42!25;UBERON:0010314!1.12e-41!132;UBERON:0002619!3.49e-41!22;UBERON:0001950!3.34e-37!20;UBERON:0011216!8.57e-28!223;UBERON:0000025!1.80e-19!192;UBERON:0002420!6.78e-19!9;UBERON:0007245!6.78e-19!9;UBERON:0010009!6.78e-19!9;UBERON:0010011!6.78e-19!9;UBERON:0000454!6.78e-19!9;UBERON:0000125!2.06e-18!9;UBERON:0002308!2.06e-18!9;UBERON:0000477!8.76e-17!373;UBERON:0004111!2.30e-15!240;UBERON:0009663!7.52e-15!7;UBERON:0003076!3.21e-14!15;UBERON:0003057!3.21e-14!15;UBERON:0001894!8.15e-14!7;UBERON:0006222!8.15e-14!7;UBERON:0000483!1.60e-13!306;UBERON:0000119!3.19e-13!309;UBERON:0000200!8.65e-13!6;UBERON:0002298!3.93e-12!6;UBERON:0000064!6.88e-12!218;UBERON:0000349!1.03e-11!5;UBERON:0000481!2.50e-11!342;UBERON:0001871!4.32e-11!6;UBERON:0001872!4.58e-11!5;UBERON:0002021!8.30e-11!5;UBERON:0000369!6.08e-10!4;UBERON:0002435!6.08e-10!4;UBERON:0000204!6.08e-10!4;UBERON:0010082!6.08e-10!4;UBERON:0004733!6.57e-10!12;UBERON:0002028!6.57e-10!12;UBERON:0007277!6.57e-10!12;UBERON:0000922!4.69e-09!592;UBERON:0004732!5.05e-09!13;UBERON:0002050!5.63e-09!564;UBERON:0000923!1.21e-08!560;UBERON:0010316!1.21e-08!560;UBERON:0005291!1.21e-08!560;UBERON:0006598!1.21e-08!560;UBERON:0010317!1.21e-08!560;UBERON:0002532!1.21e-08!560;UBERON:0005423!1.54e-08!581;UBERON:0003296!1.69e-08!4;UBERON:0010133!1.69e-08!4;UBERON:0002784!2.41e-08!4;UBERON:0005383!6.96e-08!3;UBERON:0005382!6.96e-08!3;UBERON:0001870!2.31e-07!3;UBERON:0000988!6.89e-07!3;UBERON:0001896!6.89e-07!3;UBERON:0005290!6.89e-07!3;UBERON:0010096!6.89e-07!3
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}}
}}

Revision as of 15:01, 26 November 2012


Full id: C1646_peripheral_occipital_caudate_parietal_putamen_duodenum_temporal



Phase1 CAGE Peaks

Hg19::chr11:83393280..83393295,-p15@DLG2
Hg19::chr11:83393303..83393342,-p8@DLG2
Hg19::chr11:83393429..83393454,-p12@DLG2
Hg19::chr2:133015374..133015390,-p3@ANKRD30BL
Hg19::chrX:91034366..91034380,+p1@PCDH11X


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:0004385guanylate kinase activity0.018129910939371
GO:0019201nucleotide kinase activity0.0299614361024918
GO:0016776phosphotransferase activity, phosphate group as acceptor0.0299614361024918
GO:0044459plasma membrane part0.0299614361024918
GO:0019205nucleobase, nucleoside, nucleotide kinase activity0.0299614361024918
GO:0045211postsynaptic membrane0.0378242913176896
GO:0044456synapse part0.0378242913176896
GO:0007156homophilic cell adhesion0.0392454202050833
GO:0005886plasma membrane0.0392454202050833



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 tube2.64e-8456
neural rod2.64e-8456
future spinal cord2.64e-8456
neural keel2.64e-8456
regional part of nervous system3.60e-7953
regional part of brain3.60e-7953
central nervous system2.26e-7481
neurectoderm6.53e-7286
regional part of forebrain1.03e-7141
forebrain1.03e-7141
anterior neural tube1.03e-7141
future forebrain1.03e-7141
nervous system5.65e-6889
neural plate1.13e-6482
presumptive neural plate1.13e-6482
brain2.05e-6368
future brain2.05e-6368
brain grey matter3.89e-5934
gray matter3.89e-5934
telencephalon6.57e-5934
adult organism4.23e-58114
cerebral hemisphere6.87e-5632
regional part of telencephalon2.03e-5532
pre-chordal neural plate3.08e-5461
ecto-epithelium1.93e-51104
ectoderm-derived structure4.09e-44171
ectoderm4.09e-44171
presumptive ectoderm4.09e-44171
cerebral cortex6.64e-4225
pallium6.64e-4225
structure with developmental contribution from neural crest1.12e-41132
regional part of cerebral cortex3.49e-4122
neocortex3.34e-3720
organ system subdivision8.57e-28223
tube1.80e-19192
basal ganglion6.78e-199
nuclear complex of neuraxis6.78e-199
aggregate regional part of brain6.78e-199
collection of basal ganglia6.78e-199
cerebral subcortex6.78e-199
neural nucleus2.06e-189
nucleus of brain2.06e-189
anatomical cluster8.76e-17373
anatomical conduit2.30e-15240
telencephalic nucleus7.52e-157
posterior neural tube3.21e-1415
chordal neural plate3.21e-1415
diencephalon8.15e-147
future diencephalon8.15e-147
epithelium1.60e-13306
cell layer3.19e-13309
gyrus8.65e-136
brainstem3.93e-126
organ part6.88e-12218
limbic system1.03e-115
multi-tissue structure2.50e-11342
temporal lobe4.32e-116
parietal lobe4.58e-115
occipital lobe8.30e-115
corpus striatum6.08e-104
striatum6.08e-104
ventral part of telencephalon6.08e-104
future corpus striatum6.08e-104
segmental subdivision of hindbrain6.57e-1012
hindbrain6.57e-1012
presumptive hindbrain6.57e-1012
embryo4.69e-09592
segmental subdivision of nervous system5.05e-0913
embryonic structure5.63e-09564
germ layer1.21e-08560
germ layer / neural crest1.21e-08560
embryonic tissue1.21e-08560
presumptive structure1.21e-08560
germ layer / neural crest derived structure1.21e-08560
epiblast (generic)1.21e-08560
developing anatomical structure1.54e-08581
gland of diencephalon1.69e-084
neuroendocrine gland1.69e-084
regional part of diencephalon2.41e-084
caudate-putamen6.96e-083
dorsal striatum6.96e-083
frontal cortex2.31e-073
pons6.89e-073
medulla oblongata6.89e-073
myelencephalon6.89e-073
future myelencephalon6.89e-073


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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