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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0,

Latest revision as of 11:20, 17 September 2013


Full id: C328_Endothelial_Lymphatic_Renal_Hepatic_chronic_extraskeletal_adipose



Phase1 CAGE Peaks

Hg19::chr10:3477893..3477912,-p@chr10:3477893..3477912
-
Hg19::chr12:105863737..105863745,+p@chr12:105863737..105863745
+
Hg19::chr12:105882068..105882076,+p@chr12:105882068..105882076
+
Hg19::chr12:105889859..105889862,+p@chr12:105889859..105889862
+
Hg19::chr12:10794718..10794741,+p@chr12:10794718..10794741
+
Hg19::chr12:6232421..6232447,-p8@VWF
Hg19::chr12:6233700..6233715,-p2@VWF
Hg19::chr12:6233743..6233756,-p3@VWF
Hg19::chr12:71031305..71031308,-p20@PTPRB
Hg19::chr16:77468905..77468944,-p1@ADAMTS18
Hg19::chr16:82029551..82029560,+p@chr16:82029551..82029560
+
Hg19::chr1:65344781..65344820,-p3@JAK1
Hg19::chr21:39875736..39875750,+p@chr21:39875736..39875750
+
Hg19::chr3:149051346..149051364,-p3@TM4SF18
Hg19::chr3:149051376..149051400,-p1@TM4SF18
Hg19::chr3:149051406..149051430,-p2@TM4SF18
Hg19::chr3:149051444..149051476,-p4@TM4SF18
Hg19::chr4:90815997..90816012,+p1@MMRN1
Hg19::chr4:90816021..90816032,+p3@MMRN1
Hg19::chr4:90816033..90816048,+p2@MMRN1
Hg19::chr4:90857427..90857438,+p@chr4:90857427..90857438
+
Hg19::chr6:136358591..136358656,+p@chr6:136358591..136358656
+
Hg19::chr6:136358786..136358809,+p12@PDE7B
Hg19::chr6:136359549..136359565,+p2@AB384352
Hg19::chr6:136359569..136359580,+p3@AB384352
Hg19::chr6:3753188..3753192,-p@chr6:3753188..3753192
-
Hg19::chr6:79315735..79315760,-p1@ENST00000449463
Hg19::chr7:47988045..47988072,-p1@PKD1L1
Hg19::chr8:6420647..6420659,-p3@ANGPT2
Hg19::chr8:6420759..6420775,-p1@ANGPT2
Hg19::chr8:6420777..6420779,-p5@ANGPT2
Hg19::chr8:6420791..6420805,-p2@ANGPT2
Hg19::chr8:6420948..6420957,-p4@ANGPT2
Hg19::chr8:6459787..6459796,+p@chr8:6459787..6459796
+
Hg19::chrX:20236970..20237027,-p4@RPS6KA3


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:0033093Weibel-Palade body0.015989329581669
GO:0007596blood coagulation0.015989329581669
GO:0050817coagulation0.015989329581669
GO:0007599hemostasis0.015989329581669
GO:0031091platelet alpha granule0.015989329581669
GO:0050878regulation of body fluid levels0.015989329581669
GO:0042060wound healing0.015989329581669
GO:0002020protease binding0.0224932504301092
GO:0005131growth hormone receptor binding0.0224932504301092
GO:0004718Janus kinase activity0.0253015549427426
GO:0001948glycoprotein binding0.0266751123096811
GO:0044421extracellular region part0.0266751123096811
GO:00041153',5'-cyclic-AMP phosphodiesterase activity0.0266751123096811
GO:0022610biological adhesion0.0266751123096811
GO:0007155cell adhesion0.0266751123096811
GO:0032501multicellular organismal process0.0293181393445014
GO:0005102receptor binding0.0293181393445014
GO:0004716receptor signaling protein tyrosine kinase activity0.0365079860188144
GO:0051087chaperone binding0.0404235519267515
GO:0019865immunoglobulin binding0.0404235519267515
GO:0019198transmembrane receptor protein phosphatase activity0.041725131879665
GO:0005001transmembrane receptor protein tyrosine phosphatase activity0.041725131879665
GO:0005518collagen binding0.041725131879665
GO:0005578proteinaceous extracellular matrix0.0448232066429677
GO:0009611response to wounding0.0448232066429677
GO:0030168platelet activation0.0485281336967221



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 organism4.98e-46114
blood vessel endothelium2.66e-3318
endothelium2.66e-3318
cardiovascular system endothelium2.66e-3318
anatomical conduit8.34e-28240
simple squamous epithelium4.04e-2622
tube3.86e-25192
anatomical cluster2.51e-22373
squamous epithelium2.96e-2225
neural tube1.97e-1956
neural rod1.97e-1956
future spinal cord1.97e-1956
neural keel1.97e-1956
vessel1.48e-1768
structure with developmental contribution from neural crest2.46e-17132
endothelial tube3.77e-179
arterial system endothelium3.77e-179
endothelium of artery3.77e-179
neural plate9.18e-1782
presumptive neural plate9.18e-1782
regional part of nervous system1.76e-1653
regional part of brain1.76e-1653
neurectoderm1.62e-1586
vasculature3.93e-1578
vascular system3.93e-1578
splanchnic layer of lateral plate mesoderm6.40e-1583
circulatory system1.70e-14112
epithelium2.41e-14306
cell layer5.20e-14309
regional part of forebrain1.64e-1341
forebrain1.64e-1341
anterior neural tube1.64e-1341
future forebrain1.64e-1341
cardiovascular system2.84e-13109
central nervous system1.50e-1281
epithelial tube open at both ends3.31e-1259
blood vessel3.31e-1259
blood vasculature3.31e-1259
vascular cord3.31e-1259
brain6.87e-1268
future brain6.87e-1268
brain grey matter3.12e-1134
gray matter3.12e-1134
ecto-epithelium3.68e-11104
telencephalon5.93e-1134
nervous system1.79e-1089
epithelial tube1.80e-10117
compound organ9.49e-1068
regional part of telencephalon2.25e-0932
multi-cellular organism2.42e-09656
lymphatic vessel2.96e-098
lymph vasculature2.96e-098
lymphatic part of lymphoid system2.96e-098
cerebral hemisphere3.14e-0932
lymphoid system4.12e-0910
pre-chordal neural plate5.40e-0961
anatomical system6.98e-09624
anatomical group7.98e-09625
neural nucleus2.88e-089
nucleus of brain2.88e-089
vein6.31e-089
venous blood vessel6.31e-089
venous system6.31e-089
posterior neural tube2.81e-0715
chordal neural plate2.81e-0715
organ system subdivision3.48e-07223
multi-tissue structure5.68e-07342
microcirculatory vessel6.01e-073
endothelium of capillary6.01e-073
capillary6.01e-073
regional part of cerebral cortex6.55e-0722
embryo8.26e-07592
brainstem9.46e-076


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)
MA0003.11.11216e-05
MA0004.10.0714537
MA0006.10.0212634
MA0007.10.0639049
MA0009.10.366503
MA0014.10.000100173
MA0017.10.2976
MA0019.10.145319
MA0024.10.285711
MA0025.10.47683
MA0027.11.89328
MA0028.10.0248137
MA0029.10.812088
MA0030.10.291553
MA0031.10.685216
MA0038.10.766443
MA0040.10.304553
MA0041.10.272403
MA0042.10.505489
MA0043.10.366755
MA0046.10.941017
MA0048.10.248488
MA0050.11.31325
MA0051.11.23775
MA0052.10.307481
MA0055.17.22271
MA0056.10
MA0057.10.0105621
MA0058.10.0375298
MA0059.10.0371511
MA0060.10.0266319
MA0061.10.412235
MA0063.10
MA0066.10.120471
MA0067.10.638784
MA0068.10.00128218
MA0069.12.51799
MA0070.10.345954
MA0071.11.64832
MA0072.10.906843
MA0073.18.44063e-05
MA0074.10.117607
MA0076.10.042375
MA0077.13.34668
MA0078.11.58632
MA0081.11.84812
MA0083.10.372513
MA0084.10.811454
MA0087.10.902582
MA0088.10.815219
MA0089.10
MA0090.11.54216
MA0091.10.539562
MA0092.10.460323
MA0093.10.0219094
MA0095.10
MA0098.10
MA0100.10.127731
MA0101.11.48755
MA0103.10.0863031
MA0105.10.60551
MA0106.10.865966
MA0107.11.04329
MA0108.20.680208
MA0109.10
MA0111.10.427313
MA0113.10.464394
MA0114.10.00922087
MA0115.10.570409
MA0116.10.0103227
MA0117.10.396851
MA0119.10.569091
MA0122.10.418111
MA0124.12.27269
MA0125.12.03325
MA0130.10
MA0131.10.186723
MA0132.10
MA0133.10
MA0135.11.0139
MA0136.11.27657
MA0139.10.557588
MA0140.11.11155
MA0141.11.8359
MA0142.10.222682
MA0143.14.39285
MA0144.10.0396877
MA0145.10.0266757
MA0146.14.53291e-05
MA0147.10.0107968
MA0148.10.280213
MA0149.10.0944562
MA0062.20.0161739
MA0035.22.88592
MA0039.27.94358e-06
MA0138.20.176028
MA0002.20.0224846
MA0137.20.0263382
MA0104.20.00463464
MA0047.20.422993
MA0112.20.0932543
MA0065.20.0111203
MA0150.10.690592
MA0151.10
MA0152.10.335052
MA0153.10.447419
MA0154.10.102576
MA0155.10.00685258
MA0156.10.81154
MA0157.10.590166
MA0158.10
MA0159.10.0108845
MA0160.11.54267
MA0161.10
MA0162.13.66444e-06
MA0163.10.00135834
MA0164.10.937239
MA0080.21.91556
MA0018.20.143876
MA0099.20.685753
MA0079.21.25941e-13
MA0102.20.846442
MA0258.10.387384
MA0259.10.0119921
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
FOS#235392.313759936572850.01234312400347420.044717064236119
GATA2#2624238.375240853478341.2167644793407e-172.60405052167752e-15
JUN#372593.217584649457910.001376091326126830.0089655397385752



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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