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Coexpression cluster:C1346: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;0.176622,MA0004.1;0.558729,MA0006.1;0.391183,MA0007.1;0.539222,MA0009.1;1.03681,MA0014.1;0.0254709,MA0017.1;1.10421,MA0019.1;0.7124,MA0024.1;0.929647,MA0025.1;1.17262,MA0027.1;2.65688,MA0028.1;0.408079,MA0029.1;0.949428,MA0030.1;0.937696,MA0031.1;0.871496,MA0038.1;0.665566,MA0040.1;0.955415,MA0041.1;0.578072,MA0042.1;0.544748,MA0043.1;1.03713,MA0046.1;1.02569,MA0048.1;2.08744,MA0050.1;1.34656,MA0051.1;0.661179,MA0052.1;0.959373,MA0055.1;0.808182,MA0056.1;0,MA0057.1;0.147053,MA0058.1;0.458909,MA0059.1;0.457555,MA0060.1;0.267412,MA0061.1;0.23892,MA0063.1;0,MA0066.1;0.66601,MA0067.1;1.35893,MA0068.1;1.09642,MA0069.1;1.02175,MA0070.1;1.01032,MA0071.1;0.625297,MA0072.1;1.00572,MA0073.1;0.347876,MA0074.1;0.660398,MA0076.1;0.475586,MA0077.1;0.997832,MA0078.1;0.763954,MA0081.1;2.02016,MA0083.1;1.04447,MA0084.1;1.5477,MA0087.1;1.00322,MA0088.1;0.660742,MA0089.1;0,MA0090.1;1.22966,MA0091.1;0.561458,MA0092.1;0.522012,MA0093.1;0.394379,MA0095.1;0,MA0098.1;0,MA0100.1;0.679972,MA0101.1;0.397846,MA0103.1;0.381434,MA0105.1;0.134725,MA0106.1;0.70837,MA0107.1;0.320267,MA0108.2;0.868347,MA0109.1;0,MA0111.1;0.504913,MA0113.1;0.725375,MA0114.1;0.845337,MA0115.1;1.28169,MA0116.1;0.323925,MA0117.1;1.07516,MA0119.1;0.440684,MA0122.1;2.49233,MA0124.1;1.23968,MA0125.1;1.15445,MA0130.1;0,MA0131.1;0.782708,MA0132.1;0,MA0133.1;0,MA0135.1;1.06778,MA0136.1;0.672893,MA0139.1;0.226048,MA0140.1;2.5604,MA0141.1;0.455728,MA0142.1;0.838805,MA0143.1;0.725558,MA0144.1;3.11622,MA0145.1;3.00011,MA0146.1;0.441872,MA0147.1;0.327615,MA0148.1;0.584698,MA0149.1;0.612449,MA0062.2;0.23336,MA0035.2;1.50688,MA0039.2;0.569061,MA0138.2;0.765223,MA0002.2;0.255126,MA0137.2;1.06611,MA0104.2;0.26661,MA0047.2;0.695777,MA0112.2;0.332548,MA0065.2;0.718489,MA0150.1;1.21643,MA0151.1;0,MA0152.1;0.629368,MA0153.1;1.13732,MA0154.1;0.132326,MA0155.1;0.318517,MA0156.1;0.417278,MA0157.1;0.810597,MA0158.1;0,MA0159.1;0.328286,MA0160.1;0.600559,MA0161.1;0,MA0162.1;0.0383129,MA0163.1;0.113377,MA0164.1;0.738243,MA0080.2;1.02158,MA0018.2;0.709805,MA0099.2;0.629739,MA0079.2;0.0607789,MA0102.2;1.58513,MA0258.1;0.289793,MA0259.1;0.336472,MA0442.1;0
}}
}}

Revision as of 19:52, 22 January 2013


Full id: C1346_Endothelial_Renal_Hepatic_Lymphatic_heart_breast_adipose



Phase1 CAGE Peaks

Hg19::chr11:62344721..62344758,-p2@TUT1
Hg19::chr12:120687909..120687930,-p13@PXN
Hg19::chr12:120687948..120687971,-p6@PXN
Hg19::chrX:45060073..45060131,-p1@CXorf36
Hg19::chrX:45060135..45060149,-p2@CXorf36
Hg19::chrX:45060204..45060209,-p5@CXorf36


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:0050265RNA uridylyltransferase activity0.00512186506534793
GO:0017166vinculin binding0.0128031549908582
GO:0007172signal complex assembly0.0273045536036868



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 organism1.17e-61114
anatomical conduit3.60e-28240
blood vessel endothelium1.55e-2418
endothelium1.55e-2418
cardiovascular system endothelium1.55e-2418
anatomical cluster2.51e-24373
tube2.66e-24192
neural tube9.22e-2456
neural rod9.22e-2456
future spinal cord9.22e-2456
neural keel9.22e-2456
regional part of nervous system1.46e-2153
regional part of brain1.46e-2153
regional part of forebrain1.40e-1941
forebrain1.40e-1941
anterior neural tube1.40e-1941
future forebrain1.40e-1941
simple squamous epithelium7.67e-1922
neural plate1.77e-1882
presumptive neural plate1.77e-1882
brain grey matter1.48e-1734
gray matter1.48e-1734
telencephalon3.36e-1734
neurectoderm5.58e-1786
regional part of telencephalon6.67e-1632
cerebral hemisphere8.50e-1632
squamous epithelium8.56e-1625
structure with developmental contribution from neural crest2.08e-15132
epithelium2.20e-15306
central nervous system4.19e-1581
cell layer5.73e-15309
regional part of cerebral cortex6.14e-1522
brain6.69e-1568
future brain6.69e-1568
nervous system2.48e-1389
neocortex3.26e-1320
pre-chordal neural plate5.23e-1361
endothelial tube1.39e-129
arterial system endothelium1.39e-129
endothelium of artery1.39e-129
cerebral cortex1.52e-1225
pallium1.52e-1225
ecto-epithelium1.53e-12104
vessel2.07e-1268
multi-cellular organism5.69e-12656
anatomical system3.92e-11624
anatomical group4.74e-11625
organ system subdivision6.48e-11223
splanchnic layer of lateral plate mesoderm9.33e-1183
organ part2.09e-10218
vasculature3.32e-1078
vascular system3.32e-1078
multi-tissue structure4.31e-10342
circulatory system1.63e-09112
epithelial tube open at both ends9.42e-0959
blood vessel9.42e-0959
blood vasculature9.42e-0959
vascular cord9.42e-0959
lymphoid system1.35e-0810
embryonic structure1.55e-08564
germ layer2.08e-08560
germ layer / neural crest2.08e-08560
embryonic tissue2.08e-08560
presumptive structure2.08e-08560
germ layer / neural crest derived structure2.08e-08560
epiblast (generic)2.08e-08560
embryo3.12e-08592
developing anatomical structure3.90e-08581
cardiovascular system5.54e-08109
vein7.31e-089
venous blood vessel7.31e-089
venous system7.31e-089
compound organ2.42e-0768
epithelial tube2.83e-07117
lymphatic vessel5.79e-078
lymph vasculature5.79e-078
lymphatic part of lymphoid system5.79e-078


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)
MA0003.10.176622
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.10.0254709
MA0017.11.10421
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.12.08744
MA0050.11.34656
MA0051.10.661179
MA0052.10.959373
MA0055.10.808182
MA0056.10
MA0057.10.147053
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.11.09642
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.347876
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.12.02016
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.660742
MA0089.10
MA0090.11.22966
MA0091.10.561458
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.10.134725
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.845337
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.10.440684
MA0122.12.49233
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.10.226048
MA0140.12.5604
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.13.11622
MA0145.13.00011
MA0146.10.441872
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.21.50688
MA0039.20.569061
MA0138.20.765223
MA0002.20.255126
MA0137.21.06611
MA0104.20.26661
MA0047.20.695777
MA0112.20.332548
MA0065.20.718489
MA0150.11.21643
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.132326
MA0155.10.318517
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.10.0383129
MA0163.10.113377
MA0164.10.738243
MA0080.21.02158
MA0018.20.709805
MA0099.20.629739
MA0079.20.0607789
MA0102.21.58513
MA0258.10.289793
MA0259.10.336472
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

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

TF#promotersEnrichmentp-valueq-value
GATA2#262436.3724658667770.008058821308742550.0318845034914484



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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