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Coexpression cluster:C3277: Difference between revisions

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|full_id=C3277_Pericytes_kidney_Hepatocyte_endometrial_liver_Monocytederived_brain
|full_id=C3277_Pericytes_kidney_Hepatocyte_endometrial_liver_Monocytederived_brain
|id=C3277
|id=C3277
|ontology_enrichment_celltype=CL:0002009!3.06e-30!65;CL:0002194!2.68e-28!63;CL:0000576!2.68e-28!63;CL:0000040!2.68e-28!63;CL:0000559!2.68e-28!63;CL:0000557!2.36e-27!71;CL:0000766!8.70e-27!76;CL:0002057!2.95e-26!42;CL:0000860!6.34e-25!45;CL:0000839!6.50e-25!70;CL:0000763!1.94e-17!112;CL:0000049!1.94e-17!112;CL:0000738!5.18e-13!140;CL:0002087!1.92e-10!119;CL:0002031!4.09e-10!124;CL:0002393!4.65e-09!9;CL:0002397!4.65e-09!9;CL:0000990!5.07e-08!8;CL:0000037!1.34e-07!172;CL:0000566!1.34e-07!172;CL:0002032!1.43e-07!165;CL:0000837!1.43e-07!165;CL:0000988!1.88e-07!182;CL:0000453!9.29e-07!5
|ontology_enrichment_celltype=CL:0002009!2.78e-18!61;CL:0002194!3.25e-16!59;CL:0000576!3.25e-16!59;CL:0000040!3.25e-16!59;CL:0000559!3.25e-16!59;CL:0000557!7.70e-16!67;CL:0000766!6.53e-14!72;CL:0000473!1.21e-13!48;CL:0000234!1.21e-13!48;CL:0000839!1.27e-13!66;CL:0000860!1.18e-10!42;CL:0002057!1.18e-10!42;CL:0000990!2.25e-10!8;CL:0000763!3.33e-10!108;CL:0000049!3.33e-10!108;CL:0000453!1.50e-08!5;CL:0000451!3.33e-08!10;CL:0000738!6.75e-08!136
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!4.94e-36!115;UBERON:0001049!4.37e-35!57;UBERON:0005068!4.37e-35!57;UBERON:0006241!4.37e-35!57;UBERON:0007135!4.37e-35!57;UBERON:0002616!1.56e-31!59;UBERON:0005743!4.71e-31!86;UBERON:0000955!4.78e-30!69;UBERON:0006238!4.78e-30!69;UBERON:0001017!8.98e-30!82;UBERON:0000073!1.34e-27!94;UBERON:0001016!1.34e-27!94;UBERON:0003080!5.92e-27!42;UBERON:0002780!2.95e-26!41;UBERON:0001890!2.95e-26!41;UBERON:0006240!2.95e-26!41;UBERON:0002390!2.65e-25!102;UBERON:0003061!2.65e-25!102;UBERON:0003075!6.72e-23!86;UBERON:0007284!6.72e-23!86;UBERON:0002371!2.28e-22!80;UBERON:0001893!3.27e-22!34;UBERON:0002020!4.48e-22!34;UBERON:0003528!4.48e-22!34;UBERON:0002405!2.55e-21!115;UBERON:0002193!2.95e-21!112;UBERON:0002791!3.81e-21!33;UBERON:0002346!4.18e-21!90;UBERON:0001869!4.07e-20!32;UBERON:0001474!1.17e-19!86;UBERON:0003056!7.26e-18!61;UBERON:0002619!1.01e-16!22;UBERON:0004765!3.32e-16!101;UBERON:0001434!3.32e-16!101;UBERON:0000062!5.49e-15!511;UBERON:0001950!8.43e-15!20;UBERON:0000956!5.43e-14!25;UBERON:0000203!5.43e-14!25;UBERON:0000033!3.71e-13!123;UBERON:0000153!6.74e-13!129;UBERON:0007811!6.74e-13!129;UBERON:0002308!4.68e-10!9;UBERON:0000125!4.68e-10!9;UBERON:0000923!9.66e-10!604;UBERON:0005291!9.66e-10!604;UBERON:0006598!9.66e-10!604;UBERON:0002532!9.66e-10!604;UBERON:0002050!1.18e-09!605;UBERON:0005423!1.18e-09!605;UBERON:0003076!3.55e-09!15;UBERON:0003057!3.55e-09!15;UBERON:0000922!4.62e-09!612;UBERON:0000467!9.16e-09!625;UBERON:0000480!1.11e-08!626;UBERON:0004732!3.31e-08!13;UBERON:0004121!4.37e-08!169;UBERON:0000200!4.63e-08!6;UBERON:0009663!5.63e-08!7;UBERON:0002420!8.69e-08!9;UBERON:0007245!8.69e-08!9;UBERON:0010009!8.69e-08!9;UBERON:0010011!8.69e-08!9;UBERON:0000454!8.69e-08!9;UBERON:0000924!1.47e-07!173;UBERON:0006601!1.47e-07!173;UBERON:0002298!1.86e-07!8;UBERON:0004733!3.06e-07!12;UBERON:0002028!3.06e-07!12;UBERON:0007277!3.06e-07!12;UBERON:0001872!6.56e-07!5;UBERON:0000468!6.78e-07!659
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}}
}}

Revision as of 14:57, 19 October 2012


Full id: C3277_Pericytes_kidney_Hepatocyte_endometrial_liver_Monocytederived_brain



Phase1 CAGE Peaks

Hg19::chr12:323187..323209,-p3@SLC6A12
Hg19::chr12:323248..323263,-p4@SLC6A12
Hg19::chr12:323312..323329,-p2@SLC6A12


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 tube6.45e-3556
neural rod6.45e-3556
future spinal cord6.45e-3556
neural keel6.45e-3556
regional part of nervous system1.85e-3353
regional part of brain1.85e-3353
adult organism3.74e-29114
brain1.62e-2868
future brain1.62e-2868
central nervous system1.02e-2781
regional part of forebrain2.95e-2641
forebrain2.95e-2641
anterior neural tube2.95e-2641
future forebrain2.95e-2641
telencephalon5.74e-2634
brain grey matter8.05e-2634
gray matter8.05e-2634
nervous system3.50e-2589
regional part of telencephalon4.05e-2332
cerebral hemisphere4.64e-2332
neural plate7.21e-2382
presumptive neural plate7.21e-2382
regional part of cerebral cortex1.85e-2122
neurectoderm3.06e-2186
neocortex1.04e-1820
cerebral cortex2.53e-1825
pallium2.53e-1825
pre-chordal neural plate1.33e-1761
ecto-epithelium1.60e-15104
hematopoietic system7.90e-1598
blood island7.90e-1598
bone marrow6.30e-1376
hemolymphoid system1.81e-12108
structure with developmental contribution from neural crest3.53e-12132
organ system subdivision3.91e-12223
bone element2.33e-1182
organ1.31e-10503
immune system1.64e-1093
segmental subdivision of nervous system9.74e-1013
posterior neural tube1.09e-0915
chordal neural plate1.09e-0915
skeletal element1.28e-0990
skeletal system2.25e-09100
parietal lobe2.48e-095
germ layer3.24e-09560
germ layer / neural crest3.24e-09560
embryonic tissue3.24e-09560
presumptive structure3.24e-09560
germ layer / neural crest derived structure3.24e-09560
epiblast (generic)3.24e-09560
neural nucleus5.33e-099
nucleus of brain5.33e-099
developing anatomical structure5.41e-09581
embryonic structure5.79e-09564
segmental subdivision of hindbrain2.37e-0812
hindbrain2.37e-0812
presumptive hindbrain2.37e-0812
embryo2.51e-08592
ectoderm-derived structure5.38e-08171
ectoderm5.38e-08171
presumptive ectoderm5.38e-08171
tube9.61e-08192
brainstem9.75e-086
gyrus1.05e-076


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.