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{{Coexpression_clusters
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|full_id=C1765_Renal_Hepatic_Endothelial_placenta_Lymphatic_breast_lung
|id=C1765
}}

Latest revision as of 11:51, 17 September 2013


Full id: C1765_Renal_Hepatic_Endothelial_placenta_Lymphatic_breast_lung



Phase1 CAGE Peaks

Hg19::chr16:67224002..67224047,-p1@EXOC3L1
Hg19::chr19:17375527..17375538,-p2@USHBP1
Hg19::chr5:180076580..180076605,-p1@FLT4
Hg19::chr5:180076613..180076634,-p2@FLT4
Hg19::chr9:80263579..80263618,-p2@GNA14


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

GO IDGO nameFDR corrected p-value
GO:0048010vascular endothelial growth factor receptor signaling pathway0.0435920646625478
GO:0030165PDZ domain binding0.0435920646625478
GO:0005021vascular endothelial growth factor receptor activity0.0435920646625478
GO:0006471protein amino acid ADP-ribosylation0.0435920646625478
GO:0005834heterotrimeric G-protein complex0.0496118168482225



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
adult organism4.14e-56114
anatomical conduit8.33e-23240
anatomical cluster7.12e-21373
tube1.00e-19192
neural tube5.61e-1856
neural rod5.61e-1856
future spinal cord5.61e-1856
neural keel5.61e-1856
blood vessel endothelium1.83e-1618
endothelium1.83e-1618
cardiovascular system endothelium1.83e-1618
regional part of nervous system7.37e-1653
regional part of brain7.37e-1653
regional part of forebrain9.05e-1541
forebrain9.05e-1541
anterior neural tube9.05e-1541
future forebrain9.05e-1541
brain grey matter4.01e-1434
gray matter4.01e-1434
telencephalon5.42e-1434
central nervous system1.44e-1381
cerebral hemisphere1.01e-1232
regional part of telencephalon1.06e-1232
neural plate1.47e-1282
presumptive neural plate1.47e-1282
simple squamous epithelium1.65e-1222
neurectoderm1.87e-1186
multi-cellular organism3.42e-11656
regional part of cerebral cortex3.90e-1122
nervous system4.39e-1189
organ system subdivision5.00e-11223
neocortex6.26e-1120
brain9.61e-1168
future brain9.61e-1168
structure with developmental contribution from neural crest1.00e-10132
squamous epithelium2.11e-1025
cell layer1.01e-09309
epithelium1.29e-09306
vessel2.46e-0968
cerebral cortex2.69e-0925
pallium2.69e-0925
anatomical system8.46e-09624
anatomical group1.01e-08625
lymphoid system1.01e-0810
ecto-epithelium2.77e-08104
pre-chordal neural plate2.89e-0861
embryo1.08e-07592
splanchnic layer of lateral plate mesoderm1.67e-0783
multi-tissue structure1.80e-07342
vein2.59e-079
venous blood vessel2.59e-079
venous system2.59e-079
vasculature4.46e-0778
vascular system4.46e-0778
lymphatic vessel7.83e-078
lymph vasculature7.83e-078
lymphatic part of lymphoid system7.83e-078
circulatory system1.00e-06112


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)
MA0003.11.80249
MA0004.10.626788
MA0006.11.14863
MA0007.10.606704
MA0009.11.11255
MA0014.12.48957
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.569896
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.288856
MA0056.10
MA0057.10.554727
MA0058.11.29981
MA0059.10.522232
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.11.98392
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.14.40502
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.11.92154
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.11.15584
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.11.16366
MA0103.10.442769
MA0105.10.175503
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.759606
MA0140.10.692258
MA0141.11.29278
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.13.46016
MA0146.11.82062
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.25.20522
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.858845
MA0047.20.767096
MA0112.21.35805
MA0065.21.41695
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.514087
MA0155.10.130813
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.469165
MA0163.13.1409
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.211.1769
MA0102.21.66336
MA0258.11.63655
MA0259.10.395396
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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