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{{Coexpression_clusters
{
|full_id=C823_Fibroblast_Endothelial_hepatic_Pericytes_umbilical_Adipocyte_Lymphatic

Latest revision as of 11:31, 17 September 2013


Full id: C823_Fibroblast_Endothelial_hepatic_Pericytes_umbilical_Adipocyte_Lymphatic



Phase1 CAGE Peaks

Hg19::chr13:110827583..110827627,+p@chr13:110827583..110827627
+
Hg19::chr13:110829031..110829044,+p@chr13:110829031..110829044
+
Hg19::chr13:110830539..110830556,-p@chr13:110830539..110830556
-
Hg19::chr13:110845203..110845217,+p@chr13:110845203..110845217
+
Hg19::chr13:110847360..110847381,+p@chr13:110847360..110847381
+
Hg19::chr13:111077159..111077201,-p@chr13:111077159..111077201
-
Hg19::chr13:111086779..111086789,-p@chr13:111086779..111086789
-
Hg19::chr13:111118370..111118403,-p@chr13:111118370..111118403
-
Hg19::chr13:111137319..111137361,-p@chr13:111137319..111137361
-
Hg19::chr13:111164338..111164351,+p@chr13:111164338..111164351
+


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
vasculature3.52e-1378
vascular system3.52e-1378
mesenchyme6.18e-13160
entire embryonic mesenchyme6.18e-13160
epithelial tube1.02e-12117
circulatory system6.17e-12112
cardiovascular system1.28e-11109
epithelial vesicle3.25e-1078
excretory tube1.05e-0916
kidney epithelium1.05e-0916
nephron epithelium1.06e-0915
renal tubule1.06e-0915
nephron tubule1.06e-0915
nephron1.06e-0915
uriniferous tubule1.06e-0915
nephrogenic mesenchyme1.06e-0915
vessel2.44e-0968
splanchnic layer of lateral plate mesoderm4.01e-0983
muscle tissue7.48e-0964
musculature7.48e-0964
musculature of body7.48e-0964
skeletal muscle tissue7.64e-0962
striated muscle tissue7.64e-0962
myotome7.64e-0962
parenchyma8.27e-0915
trunk mesenchyme9.90e-09122
trunk1.59e-08199
cortex of kidney1.49e-0712
renal parenchyma1.49e-0712
compound organ1.65e-0768
organism subdivision2.15e-07264
dense mesenchyme tissue4.11e-0773
epithelial tube open at both ends4.66e-0759
blood vessel4.66e-0759
blood vasculature4.66e-0759
vascular cord4.66e-0759
somite4.98e-0771
presomitic mesoderm4.98e-0771
presumptive segmental plate4.98e-0771
dermomyotome4.98e-0771
trunk paraxial mesoderm4.98e-0771
unilaminar epithelium6.69e-07148
primitive nephron9.30e-077
renal glomerulus9.30e-077
renal corpuscle9.30e-077
glomerular capsule9.30e-077
metanephric mesenchyme9.30e-077
glomerular tuft9.30e-077
S-shaped body9.30e-077
renal vesicle9.30e-077
comma-shaped body9.30e-077
paraxial mesoderm9.36e-0772
presumptive paraxial mesoderm9.36e-0772


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)
MA0003.10.00834483
MA0004.10.990587
MA0006.10.665232
MA0007.10.363007
MA0009.10.828613
MA0014.10.0036779
MA0017.10.270554
MA0019.10.520264
MA0024.10.725404
MA0025.10.960689
MA0027.12.43535
MA0028.10.25013
MA0029.10.744375
MA0030.10.733118
MA0031.10.669876
MA0038.11.20033
MA0040.10.750125
MA0041.10.397617
MA0042.10.367902
MA0043.10.828925
MA0046.10.817858
MA0048.10.0613414
MA0050.10.368721
MA0051.10.473017
MA0052.10.753928
MA0055.10.0662377
MA0056.10
MA0057.10.0580131
MA0058.10.796055
MA0059.10.291897
MA0060.10.430116
MA0061.10.377096
MA0063.10
MA0066.11.2012
MA0067.11.1435
MA0068.10.304755
MA0069.10.814052
MA0070.10.803003
MA0071.10.440254
MA0072.10.798564
MA0073.10.000749839
MA0074.10.4723
MA0076.10.307383
MA0077.10.790956
MA0078.10.568317
MA0081.10.292043
MA0083.10.836033
MA0084.11.32998
MA0087.10.79615
MA0088.10.55119
MA0089.10
MA0090.10.857892
MA0091.10.382762
MA0092.10.347826
MA0093.10.671378
MA0095.10
MA0098.10
MA0100.10.49029
MA0101.10.241637
MA0103.10.646502
MA0105.10.422512
MA0106.10.516528
MA0107.10.179177
MA0108.20.666881
MA0109.10
MA0111.10.33284
MA0113.10.532314
MA0114.10.174997
MA0115.11.06753
MA0116.12.31128
MA0117.10.865782
MA0119.10.760742
MA0122.10.891407
MA0124.11.0263
MA0125.10.942948
MA0130.10
MA0131.10.585907
MA0132.10
MA0133.10
MA0135.10.858623
MA0136.10.483775
MA0139.11.1801
MA0140.10.437738
MA0141.10.290336
MA0142.10.638837
MA0143.10.532484
MA0144.13.68875
MA0145.10.14293
MA0146.10.0551603
MA0147.10.543675
MA0148.10.403564
MA0149.10.428597
MA0062.20.366815
MA0035.21.11424
MA0039.20.00259594
MA0138.20.569505
MA0002.20.129981
MA0137.21.31174
MA0104.20.428616
MA0047.20.504873
MA0112.22.25856
MA0065.20.147044
MA0150.10.315136
MA0151.10
MA0152.10.443956
MA0153.10.926242
MA0154.10.729959
MA0155.10.12484
MA0156.10.715501
MA0157.10.612166
MA0158.10
MA0159.10.544949
MA0160.10.417847
MA0161.10
MA0162.10.0377269
MA0163.10.484115
MA0164.10.544294
MA0080.20.238846
MA0018.20.517858
MA0099.20.444294
MA0079.20.000284498
MA0102.21.36707
MA0258.12.11165
MA0259.11.06648
MA0442.10



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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