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Coexpression cluster:C1415: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0002204!6.51e-23!167;UBERON:0000926!7.58e-23!315;UBERON:0004120!7.58e-23!315;UBERON:0006603!7.58e-23!315;UBERON:0002384!4.93e-17!371;UBERON:0002329!2.28e-16!71;UBERON:0003059!2.28e-16!71;UBERON:0007282!2.28e-16!71;UBERON:0004290!2.28e-16!71;UBERON:0009618!2.28e-16!71;UBERON:0007524!3.91e-16!73;UBERON:0003077!7.68e-16!72;UBERON:0007285!7.68e-16!72;UBERON:0007503!2.95e-15!78;UBERON:0000486!8.93e-13!83;UBERON:0003081!4.71e-12!203;UBERON:0002385!7.14e-12!64;UBERON:0001015!7.14e-12!64;UBERON:0000383!7.14e-12!64;UBERON:0001134!1.03e-11!62;UBERON:0002036!1.03e-11!62;UBERON:0003082!1.03e-11!62;UBERON:0005256!4.61e-11!122;UBERON:0000490!3.05e-10!148;UBERON:0001434!1.00e-09!100;UBERON:0004535!1.14e-09!109;UBERON:0003104!3.13e-09!160;UBERON:0009142!3.13e-09!160;UBERON:0002049!5.46e-09!78;UBERON:0007798!5.46e-09!78;UBERON:0002371!5.52e-09!76;UBERON:0002199!5.84e-09!46;UBERON:0002416!5.84e-09!46;UBERON:0001009!7.17e-09!112;UBERON:0004765!1.06e-08!90;UBERON:0002390!3.99e-08!98;UBERON:0003061!3.99e-08!98;UBERON:0000467!4.38e-08!624;UBERON:0000480!5.84e-08!625;UBERON:0001474!1.02e-07!82;UBERON:0002193!1.05e-07!108;UBERON:0004573!1.07e-07!33;UBERON:0004571!1.07e-07!33;UBERON:0007500!1.11e-07!59;UBERON:0001981!1.11e-07!59;UBERON:0004537!1.11e-07!59;UBERON:0006965!1.11e-07!59;UBERON:0001637!1.13e-07!42;UBERON:0003509!1.13e-07!42;UBERON:0004572!1.13e-07!42;UBERON:0000479!1.58e-07!773;UBERON:0000055!2.85e-07!68;UBERON:0002097!2.93e-07!41;UBERON:0002067!3.87e-07!9;UBERON:0004016!3.87e-07!9;UBERON:0010083!3.87e-07!9;UBERON:0002405!4.14e-07!93;UBERON:0000468!4.50e-07!656
|ontology_enrichment_uberon=UBERON:0002204!6.51e-23!167;UBERON:0000926!7.58e-23!315;UBERON:0004120!7.58e-23!315;UBERON:0006603!7.58e-23!315;UBERON:0002384!4.93e-17!371;UBERON:0002329!2.28e-16!71;UBERON:0003059!2.28e-16!71;UBERON:0007282!2.28e-16!71;UBERON:0004290!2.28e-16!71;UBERON:0009618!2.28e-16!71;UBERON:0007524!3.91e-16!73;UBERON:0003077!7.68e-16!72;UBERON:0007285!7.68e-16!72;UBERON:0007503!2.95e-15!78;UBERON:0000486!8.93e-13!83;UBERON:0003081!4.71e-12!203;UBERON:0002385!7.14e-12!64;UBERON:0001015!7.14e-12!64;UBERON:0000383!7.14e-12!64;UBERON:0001134!1.03e-11!62;UBERON:0002036!1.03e-11!62;UBERON:0003082!1.03e-11!62;UBERON:0005256!4.61e-11!122;UBERON:0000490!3.05e-10!148;UBERON:0001434!1.00e-09!100;UBERON:0004535!1.14e-09!109;UBERON:0003104!3.13e-09!160;UBERON:0009142!3.13e-09!160;UBERON:0002049!5.46e-09!78;UBERON:0007798!5.46e-09!78;UBERON:0002371!5.52e-09!76;UBERON:0002199!5.84e-09!46;UBERON:0002416!5.84e-09!46;UBERON:0001009!7.17e-09!112;UBERON:0004765!1.06e-08!90;UBERON:0002390!3.99e-08!98;UBERON:0003061!3.99e-08!98;UBERON:0000467!4.38e-08!624;UBERON:0000480!5.84e-08!625;UBERON:0001474!1.02e-07!82;UBERON:0002193!1.05e-07!108;UBERON:0004573!1.07e-07!33;UBERON:0004571!1.07e-07!33;UBERON:0007500!1.11e-07!59;UBERON:0001981!1.11e-07!59;UBERON:0004537!1.11e-07!59;UBERON:0006965!1.11e-07!59;UBERON:0001637!1.13e-07!42;UBERON:0003509!1.13e-07!42;UBERON:0004572!1.13e-07!42;UBERON:0000479!1.58e-07!773;UBERON:0000055!2.85e-07!68;UBERON:0002097!2.93e-07!41;UBERON:0002067!3.87e-07!9;UBERON:0004016!3.87e-07!9;UBERON:0010083!3.87e-07!9;UBERON:0002405!4.14e-07!93;UBERON:0000468!4.50e-07!656
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|tfbs_overrepresentation_for_novel_motifs=0.44418,0.946942,1.94876,0.58616,0.393082,0.584466,0.662701,0.742622,0.736703,0.262261,0.553339,0.707204,0.635275,2.6514,0.391663,0.415981,0.889639,0.336106,1.23744,0.800617,0.436569,0.29639,0.576478,0.387783,0.483957,0.730467,0.585619,0.574247,0.396295,1.04549,0.530785,0.92701,0.302275,0.225641,0.35719,0.909936,0.35388,0.585658,0.329602,0.248856,0.936389,0.513952,2.87385,0.390088,0.0393783,0.468392,0.66382,0.542147,1.56014,0.396429,0.745008,0.675919,0.891214,1.00488,1.15929,0.653901,0.400834,0.62023,0.547548,0.619193,0.968558,0.666252,0.737866,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.275507,0.146905,1.15727,0.218784,0.206105,1.07049,0.84426,0.913168,0.477584,0.240887,0.86037,0.684313,0.272514,1.10535,0.406668,0.126687,0.181871,0.771626,1.71797,1.34233,1.07807,0.94406,0.30974,0.393853,0.32338,0.234532,0.987239,0.776336,0.166235,2.40275,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,0.647343,0.483695,0.376529,0.44815,0.978783,0.430775,0.563054,1.29401,0.928633,0.0577227,0.529546,0.824029,0.840396,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,0.866571,1.07876,0.53374,1.20639,0.692462,1.35529,0.175219,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,0.306342,0.8388,0.0926553,1.07915,0.258882,0.665754,1.48627,0.755083,0.378604,0.484017,4.05264,1.27379,1.06043,0.912368,0.457485,0.83286,0.683502,1.45122,0.661335,0.307168
}}
}}

Revision as of 14:52, 26 November 2012


Full id: C1415_small_Hair_Mesenchymal_Preadipocyte_Fibroblast_duodenum_colon



Phase1 CAGE Peaks

Hg19::chr15:90347724..90347746,+p@chr15:90347724..90347746
+
Hg19::chr15:90348362..90348394,+p@chr15:90348362..90348394
+
Hg19::chr15:90348572..90348598,+p@chr15:90348572..90348598
+
Hg19::chr15:90349575..90349613,+p@chr15:90349575..90349613
+
Hg19::chr15:90349614..90349663,+p@chr15:90349614..90349663
+
Hg19::chr15:90349664..90349706,+p@chr15:90349664..90349706
+


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
multi fate stem cell2.60e-27427
somatic stem cell8.10e-26433
stem cell6.54e-24441
somatic cell7.32e-22588
connective tissue cell1.23e-17361
fibroblast2.45e-1776
mesenchymal cell3.91e-15354
muscle precursor cell3.48e-1358
myoblast3.48e-1358
multi-potent skeletal muscle stem cell3.48e-1358
motile cell3.09e-12386
contractile cell6.47e-1259
muscle cell1.68e-1155
monopoietic cell3.52e-1159
monocyte3.52e-1159
monoblast3.52e-1159
promonocyte3.52e-1159
skin fibroblast6.82e-1123
macrophage dendritic cell progenitor2.58e-1061
mesodermal cell4.86e-10121
animal cell5.91e-10679
eukaryotic cell5.91e-10679
myeloid leukocyte1.01e-0972
defensive cell1.65e-0948
phagocyte1.65e-0948
smooth muscle cell3.76e-0943
smooth muscle myoblast3.76e-0943
electrically responsive cell6.30e-0961
electrically active cell6.30e-0961
myeloid lineage restricted progenitor cell8.27e-0966
granulocyte monocyte progenitor cell1.82e-0867
classical monocyte2.99e-0742
CD14-positive, CD16-negative classical monocyte2.99e-0742
vascular associated smooth muscle cell3.18e-0732
native cell3.44e-07722
mesenchymal stem cell of adipose7.53e-078
Uber Anatomy
Ontology termp-valuen
musculoskeletal system6.51e-23167
mesoderm7.58e-23315
mesoderm-derived structure7.58e-23315
presumptive mesoderm7.58e-23315
connective tissue4.93e-17371
somite2.28e-1671
presomitic mesoderm2.28e-1671
presumptive segmental plate2.28e-1671
dermomyotome2.28e-1671
trunk paraxial mesoderm2.28e-1671
dense mesenchyme tissue3.91e-1673
paraxial mesoderm7.68e-1672
presumptive paraxial mesoderm7.68e-1672
epithelial vesicle2.95e-1578
multilaminar epithelium8.93e-1383
lateral plate mesoderm4.71e-12203
muscle tissue7.14e-1264
musculature7.14e-1264
musculature of body7.14e-1264
skeletal muscle tissue1.03e-1162
striated muscle tissue1.03e-1162
myotome1.03e-1162
trunk mesenchyme4.61e-11122
unilaminar epithelium3.05e-10148
skeletal system1.00e-09100
cardiovascular system1.14e-09109
mesenchyme3.13e-09160
entire embryonic mesenchyme3.13e-09160
vasculature5.46e-0978
vascular system5.46e-0978
bone marrow5.52e-0976
integument5.84e-0946
integumental system5.84e-0946
circulatory system7.17e-09112
skeletal element1.06e-0890
hematopoietic system3.99e-0898
blood island3.99e-0898
anatomical system4.38e-08624
anatomical group5.84e-08625
bone element1.02e-0782
hemolymphoid system1.05e-07108
systemic artery1.07e-0733
systemic arterial system1.07e-0733
epithelial tube open at both ends1.11e-0759
blood vessel1.11e-0759
blood vasculature1.11e-0759
vascular cord1.11e-0759
artery1.13e-0742
arterial blood vessel1.13e-0742
arterial system1.13e-0742
tissue1.58e-07773
vessel2.85e-0768
skin of body2.93e-0741
dermis3.87e-079
dermatome3.87e-079
future dermis3.87e-079
immune system4.14e-0793
multi-cellular organism4.50e-07656


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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