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Coexpression cluster:C2550: Difference between revisions

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|full_id=C2550_Fibroblast_heart_Sebocyte_Mesenchymal_osteoclastoma_Mesothelial_Pericytes
|full_id=C2550_Fibroblast_heart_Sebocyte_Mesenchymal_osteoclastoma_Mesothelial_Pericytes
|id=C2550
|id=C2550
|ontology_enrichment_celltype=CL:0002321!6.78e-10!248;CL:0000220!1.11e-09!246;CL:0000359!6.60e-09!32;CL:0000222!1.52e-07!119
|ontology_enrichment_celltype=CL:0002321!1.74e-10!250;CL:0000359!9.72e-09!32;CL:0000222!7.99e-08!121
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000119!3.06e-25!312;UBERON:0000483!4.45e-24!309;UBERON:0000025!9.88e-22!194;UBERON:0004111!3.20e-20!241;UBERON:0000475!1.14e-19!365;UBERON:0000477!9.21e-18!286;UBERON:0003075!3.97e-16!86;UBERON:0007284!3.97e-16!86;UBERON:0002616!7.28e-16!59;UBERON:0004872!8.85e-15!84;UBERON:0002049!1.37e-14!79;UBERON:0007798!1.37e-14!79;UBERON:0001049!1.65e-14!57;UBERON:0005068!1.65e-14!57;UBERON:0006241!1.65e-14!57;UBERON:0007135!1.65e-14!57;UBERON:0002346!2.83e-14!90;UBERON:0004121!3.52e-14!169;UBERON:0000468!3.02e-13!659;UBERON:0000033!3.24e-13!123;UBERON:0000924!4.91e-13!173;UBERON:0006601!4.91e-13!173;UBERON:0005743!1.20e-12!86;UBERON:0001009!1.36e-12!113;UBERON:0000955!1.57e-12!69;UBERON:0006238!1.57e-12!69;UBERON:0000153!2.58e-12!129;UBERON:0007811!2.58e-12!129;UBERON:0001981!2.72e-12!60;UBERON:0007500!2.72e-12!60;UBERON:0004537!2.72e-12!60;UBERON:0006965!2.72e-12!60;UBERON:0001017!3.57e-12!82;UBERON:0000481!7.05e-12!347;UBERON:0003056!9.46e-12!61;UBERON:0001637!1.41e-11!42;UBERON:0003509!1.41e-11!42;UBERON:0004572!1.41e-11!42;UBERON:0004535!1.73e-11!110;UBERON:0007023!3.36e-11!115;UBERON:0000073!3.59e-11!94;UBERON:0001016!3.59e-11!94;UBERON:0003914!1.85e-10!118;UBERON:0003080!2.01e-10!42;UBERON:0000055!3.03e-10!69;UBERON:0002780!4.86e-10!41;UBERON:0001890!4.86e-10!41;UBERON:0006240!4.86e-10!41;UBERON:0002020!1.86e-09!34;UBERON:0003528!1.86e-09!34;UBERON:0001893!2.27e-09!34;UBERON:0002791!3.77e-09!33;UBERON:0000467!4.62e-09!625;UBERON:0000480!5.40e-09!626;UBERON:0004573!9.00e-09!33;UBERON:0004571!9.00e-09!33;UBERON:0001869!2.07e-08!32;UBERON:0007100!5.20e-08!27;UBERON:0000922!6.56e-08!612;UBERON:0000486!2.34e-07!82;UBERON:0000064!3.11e-07!219;UBERON:0002050!3.24e-07!605;UBERON:0005423!3.24e-07!605;UBERON:0000923!4.03e-07!604;UBERON:0005291!4.03e-07!604;UBERON:0006598!4.03e-07!604;UBERON:0002532!4.03e-07!604;UBERON:0003103!7.23e-07!69
|ontology_enrichment_uberon=UBERON:0000119!7.22e-25!309;UBERON:0000483!1.06e-23!306;UBERON:0000025!1.89e-21!192;UBERON:0010371!3.14e-19!104;UBERON:0004111!3.94e-19!240;UBERON:0000477!9.79e-18!373;UBERON:0003075!2.57e-16!82;UBERON:0007284!2.57e-16!82;UBERON:0010314!2.80e-15!132;UBERON:0004872!9.66e-15!83;UBERON:0002049!1.23e-14!78;UBERON:0007798!1.23e-14!78;UBERON:0002346!1.66e-14!86;UBERON:0000481!4.45e-14!342;UBERON:0001049!2.26e-13!56;UBERON:0005068!2.26e-13!56;UBERON:0006241!2.26e-13!56;UBERON:0007135!2.26e-13!56;UBERON:0000468!2.42e-13!656;UBERON:0000073!1.69e-12!53;UBERON:0002616!1.69e-12!53;UBERON:0004121!3.31e-12!171;UBERON:0000924!3.31e-12!171;UBERON:0006601!3.31e-12!171;UBERON:0007500!4.53e-12!59;UBERON:0001981!4.53e-12!59;UBERON:0004537!4.53e-12!59;UBERON:0006965!4.53e-12!59;UBERON:0001009!5.49e-12!112;UBERON:0003056!1.53e-11!61;UBERON:0000955!1.55e-11!68;UBERON:0006238!1.55e-11!68;UBERON:0001017!2.01e-11!81;UBERON:0001637!2.04e-11!42;UBERON:0003509!2.04e-11!42;UBERON:0004572!2.04e-11!42;UBERON:0004535!5.82e-11!109;UBERON:0003914!6.04e-11!117;UBERON:0000055!4.25e-10!68;UBERON:0001016!8.04e-10!89;UBERON:0002780!1.75e-09!41;UBERON:0001890!1.75e-09!41;UBERON:0003080!1.75e-09!41;UBERON:0006240!1.75e-09!41;UBERON:0007023!1.79e-09!114;UBERON:0000467!3.57e-09!624;UBERON:0000480!4.59e-09!625;UBERON:0003528!8.65e-09!34;UBERON:0002020!8.65e-09!34;UBERON:0001893!9.28e-09!34;UBERON:0004573!1.71e-08!33;UBERON:0004571!1.71e-08!33;UBERON:0000922!1.88e-08!592;UBERON:0007100!3.13e-08!27;UBERON:0002791!4.57e-08!32;UBERON:0001869!8.26e-08!32;UBERON:0002050!1.39e-07!564;UBERON:0005423!1.78e-07!581;UBERON:0000064!2.44e-07!218;UBERON:0003103!4.20e-07!68;UBERON:0000486!5.04e-07!83;UBERON:0000948!5.79e-07!24;UBERON:0005498!5.79e-07!24;UBERON:0004140!5.79e-07!24;UBERON:0009881!5.79e-07!24;UBERON:0004141!5.79e-07!24;UBERON:0003084!5.79e-07!24;UBERON:0007005!5.79e-07!24;UBERON:0004139!5.79e-07!24;UBERON:0004291!5.79e-07!24;UBERON:0000923!7.04e-07!560;UBERON:0010316!7.04e-07!560;UBERON:0005291!7.04e-07!560;UBERON:0006598!7.04e-07!560;UBERON:0010317!7.04e-07!560;UBERON:0002532!7.04e-07!560;UBERON:0000475!9.42e-07!264
|tf_chipseq_enrich=TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0322409145241778!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0244377469670096!TCF7L2#6934;4:10.7701765631373:7.42969445082454e-05:0.00115485914384531
|tf_chipseq_enrich=TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0322409145241778!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0244377469670096!TCF7L2#6934;4:10.7701765631373:7.42969445082454e-05:0.00115485914384531
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}}
}}

Revision as of 14:09, 19 October 2012


Full id: C2550_Fibroblast_heart_Sebocyte_Mesenchymal_osteoclastoma_Mesothelial_Pericytes



Phase1 CAGE Peaks

Hg19::chr1:201708992..201709011,+p6@NAV1
Hg19::chr1:201709014..201709019,+p16@NAV1
Hg19::chr1:201709020..201709035,+p1@NAV1
Hg19::chr1:201709054..201709065,+p5@NAV1


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>

Cell Type
Ontology termp-valuen
embryonic cell1.74e-10250
vascular associated smooth muscle cell9.72e-0932
mesodermal cell7.99e-08121
Uber Anatomy
Ontology termp-valuen
cell layer7.22e-25309
epithelium1.06e-23306
tube1.89e-21192
ecto-epithelium3.14e-19104
anatomical conduit3.94e-19240
anatomical cluster9.79e-18373
neural plate2.57e-1682
presumptive neural plate2.57e-1682
structure with developmental contribution from neural crest2.80e-15132
splanchnic layer of lateral plate mesoderm9.66e-1583
vasculature1.23e-1478
vascular system1.23e-1478
neurectoderm1.66e-1486
multi-tissue structure4.45e-14342
neural tube2.26e-1356
neural rod2.26e-1356
future spinal cord2.26e-1356
neural keel2.26e-1356
multi-cellular organism2.42e-13656
regional part of nervous system1.69e-1253
regional part of brain1.69e-1253
ectoderm-derived structure3.31e-12171
ectoderm3.31e-12171
presumptive ectoderm3.31e-12171
epithelial tube open at both ends4.53e-1259
blood vessel4.53e-1259
blood vasculature4.53e-1259
vascular cord4.53e-1259
circulatory system5.49e-12112
pre-chordal neural plate1.53e-1161
brain1.55e-1168
future brain1.55e-1168
central nervous system2.01e-1181
artery2.04e-1142
arterial blood vessel2.04e-1142
arterial system2.04e-1142
cardiovascular system5.82e-11109
epithelial tube6.04e-11117
vessel4.25e-1068
nervous system8.04e-1089
regional part of forebrain1.75e-0941
forebrain1.75e-0941
anterior neural tube1.75e-0941
future forebrain1.75e-0941
adult organism1.79e-09114
anatomical system3.57e-09624
anatomical group4.59e-09625
brain grey matter8.65e-0934
gray matter8.65e-0934
telencephalon9.28e-0934
systemic artery1.71e-0833
systemic arterial system1.71e-0833
embryo1.88e-08592
primary circulatory organ3.13e-0827
regional part of telencephalon4.57e-0832
cerebral hemisphere8.26e-0832
embryonic structure1.39e-07564
developing anatomical structure1.78e-07581
organ part2.44e-07218
compound organ4.20e-0768
multilaminar epithelium5.04e-0783
heart5.79e-0724
primitive heart tube5.79e-0724
primary heart field5.79e-0724
anterior lateral plate mesoderm5.79e-0724
heart tube5.79e-0724
heart primordium5.79e-0724
cardiac mesoderm5.79e-0724
cardiogenic plate5.79e-0724
heart rudiment5.79e-0724
germ layer7.04e-07560
germ layer / neural crest7.04e-07560
embryonic tissue7.04e-07560
presumptive structure7.04e-07560
germ layer / neural crest derived structure7.04e-07560
epiblast (generic)7.04e-07560
organism subdivision9.42e-07264


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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
TAF1#687243.343046285745290.008005664898701650.0322409145241778
TBP#690843.706770687096390.005296377814784350.0244377469670096
TCF7L2#6934410.77017656313737.42969445082454e-050.00115485914384531



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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