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Coexpression cluster:C1006: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0002049!3.19e-15!78;UBERON:0007798!3.19e-15!78;UBERON:0001637!4.97e-12!42;UBERON:0003509!4.97e-12!42;UBERON:0004572!4.97e-12!42;UBERON:0000055!6.88e-12!68;UBERON:0007500!3.10e-11!59;UBERON:0001981!3.10e-11!59;UBERON:0004537!3.10e-11!59;UBERON:0006965!3.10e-11!59;UBERON:0004535!9.69e-11!109;UBERON:0004872!1.29e-10!83;UBERON:0001009!3.96e-10!112;UBERON:0003914!1.09e-09!117;UBERON:0004573!3.66e-09!33;UBERON:0004571!3.66e-09!33;UBERON:0000490!1.86e-08!148;UBERON:0000475!4.03e-08!264;UBERON:0002100!3.54e-07!199;UBERON:0000477!6.37e-07!373
|ontology_enrichment_uberon=UBERON:0002049!3.19e-15!78;UBERON:0007798!3.19e-15!78;UBERON:0001637!4.97e-12!42;UBERON:0003509!4.97e-12!42;UBERON:0004572!4.97e-12!42;UBERON:0000055!6.88e-12!68;UBERON:0007500!3.10e-11!59;UBERON:0001981!3.10e-11!59;UBERON:0004537!3.10e-11!59;UBERON:0006965!3.10e-11!59;UBERON:0004535!9.69e-11!109;UBERON:0004872!1.29e-10!83;UBERON:0001009!3.96e-10!112;UBERON:0003914!1.09e-09!117;UBERON:0004573!3.66e-09!33;UBERON:0004571!3.66e-09!33;UBERON:0000490!1.86e-08!148;UBERON:0000475!4.03e-08!264;UBERON:0002100!3.54e-07!199;UBERON:0000477!6.37e-07!373
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|tfbs_overrepresentation_for_novel_motifs=0.348717,0.183537,0.341646,0.481684,0.816074,0.480078,1.36559,1.06773,1.05889,0.0394821,0.450635,0.597407,0.152895,1.34165,0.300614,0.863056,0.774423,0.698835,0.951811,0.264925,0.341703,0.180463,0.472508,0.29709,1.00212,0.619829,0.135503,0.470396,0.822672,0.122648,0.429397,0.810962,0.220667,0.469827,0.269459,0.0649851,0.266487,1.20926,1.96738,0.174436,0.268162,0.413601,0.444349,0.299183,0.198862,0.371118,0.555735,1.12076,0.416595,0.304949,0.63387,0.567337,0.0927889,0.887323,1.03948,0.546236,0.308962,1.27947,0.776738,0.513089,0.85167,0.558065,0.190442,0.746929,0.575742,0.712797,1.12756,1.49516,0.800646,1.33315,0.400869,0.573519,0.0911419,1.03748,0.149081,1.36791,0.127753,0.730167,0.797419,0.379656,0.96869,0.745864,0.575394,0.567311,0.986227,0.0220225,0.0757344,0.118789,0.659621,1.59442,1.22073,0.959334,0.827657,0.227232,0.302606,0.239285,0.488357,2.02056,0.664183,0.106284,0.246049,0.822041,0.864454,0.778061,0.701386,0.446229,0.762347,0.539961,0.385342,0.286892,0.352381,0.861701,0.336372,1.1633,1.17281,0.265019,0.0278613,0.428232,0.710479,0.229841,1.02923,0.657218,0.477387,0.586509,1.28328,1.73413,0.548418,0.83262,1.07171,0.240162,2.20459,0.432175,5.68027,0.583225,1.23359,1.20791,1.08503,0.470947,1.19123,2.04907,1.64679,1.15398,0.550118,0.866494,0.703126,0.505785,0.686615,1.88987,0.410382,0.637373,0.999704,0.0510299,0.960402,0.183004,0.557588,1.36372,0.643609,0.786331,0.385642,0.357927,1.15277,0.941964,0.796636,0.36101,0.71907,0.574616,0.611402,0.553354,0.00340764
}}
}}

Revision as of 14:37, 26 November 2012


Full id: C1006_Adipocyte_Olfactory_Preadipocyte_tenocyte_Hair_meningioma_Osteoblast



Phase1 CAGE Peaks

Hg19::chr11:86518734..86518759,+p5@PRSS23
Hg19::chr11:86518976..86519000,+p4@PRSS23
Hg19::chr11:86519101..86519122,+p7@PRSS23
Hg19::chr11:86519290..86519308,+p@chr11:86519290..86519308
+
Hg19::chr11:86519351..86519363,+p@chr11:86519351..86519363
+
Hg19::chr11:86519387..86519399,+p@chr11:86519387..86519399
+
Hg19::chr11:86519501..86519515,+p@chr11:86519501..86519515
+
Hg19::chr11:86519826..86519851,+p@chr11:86519826..86519851
+


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
mesodermal cell3.71e-16121
embryonic cell9.78e-13250
fibroblast2.25e-1176
animal cell1.05e-10679
eukaryotic cell1.05e-10679
lining cell1.38e-1058
barrier cell1.38e-1058
epithelial cell2.82e-10253
smooth muscle cell1.15e-0743
smooth muscle myoblast1.15e-0743
endothelial cell of vascular tree1.39e-0724
muscle precursor cell3.24e-0758
myoblast3.24e-0758
multi-potent skeletal muscle stem cell3.24e-0758
vascular associated smooth muscle cell7.61e-0732
stromal cell9.61e-0728
Uber Anatomy
Ontology termp-valuen
vasculature3.19e-1578
vascular system3.19e-1578
artery4.97e-1242
arterial blood vessel4.97e-1242
arterial system4.97e-1242
vessel6.88e-1268
epithelial tube open at both ends3.10e-1159
blood vessel3.10e-1159
blood vasculature3.10e-1159
vascular cord3.10e-1159
cardiovascular system9.69e-11109
splanchnic layer of lateral plate mesoderm1.29e-1083
circulatory system3.96e-10112
epithelial tube1.09e-09117
systemic artery3.66e-0933
systemic arterial system3.66e-0933
unilaminar epithelium1.86e-08148
organism subdivision4.03e-08264
trunk3.54e-07199
anatomical cluster6.37e-07373


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.