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

Latest revision as of 11:40, 17 September 2013


Full id: C1203_Endothelial_placenta_choriocarcinoma_Renal_Hair_Fibroblast_Myoblast



Phase1 CAGE Peaks

Hg19::chr14:75422292..75422308,-p1@PGF
Hg19::chr14:75469710..75469725,+p3@EIF2B2
Hg19::chr14:75469820..75469826,+p4@EIF2B2
Hg19::chr1:22264210..22264241,+p@chr1:22264210..22264241
+
Hg19::chr7:150329732..150329739,-p8@GIMAP6
Hg19::chr9:116716048..116716100,+p@chr9:116716048..116716100
+
Hg19::chrX:26933473..26933478,+p@chrX:26933473..26933478
+


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:0005851eukaryotic translation initiation factor 2B complex0.0142404022998594
GO:0014003oligodendrocyte development0.0142404022998594
GO:0009746response to hexose stimulus0.0142404022998594
GO:0009749response to glucose stimulus0.0142404022998594
GO:0048709oligodendrocyte differentiation0.0142404022998594
GO:0007267cell-cell signaling0.0142404022998594
GO:0009408response to heat0.0142404022998594
GO:0021782glial cell development0.0142404022998594
GO:0005525GTP binding0.0142404022998594
GO:0032561guanyl ribonucleotide binding0.0142404022998594
GO:0019001guanyl nucleotide binding0.0142404022998594
GO:0009743response to carbohydrate stimulus0.0142404022998594
GO:0001541ovarian follicle development0.0142404022998594
GO:0043434response to peptide hormone stimulus0.0142404022998594
GO:0051716cellular response to stimulus0.0142404022998594
GO:0022601menstrual cycle phase0.0142404022998594
GO:0022602menstrual cycle process0.0142404022998594
GO:0042552myelination0.0142404022998594
GO:0008585female gonad development0.0142404022998594
GO:0009266response to temperature stimulus0.0142404022998594
GO:0046545development of primary female sexual characteristics0.0142404022998594
GO:0010001glial cell differentiation0.0142404022998594
GO:0046660female sex differentiation0.0142404022998594
GO:0007272ensheathment of neurons0.0143331463710477
GO:0008366axon ensheathment0.0143331463710477
GO:0042698menstrual cycle0.0143331463710477
GO:0042063gliogenesis0.0150557125642903
GO:0048513organ development0.0151118031882626
GO:0001508regulation of action potential0.0155730405882961
GO:0008406gonad development0.0189321349448705
GO:0048608reproductive structure development0.0189321349448705
GO:0006446regulation of translational initiation0.0194320767044059
GO:0045137development of primary sexual characteristics0.0194320767044059
GO:0048609reproductive process in a multicellular organism0.0194320767044059
GO:0032504multicellular organism reproduction0.0194320767044059
GO:0010033response to organic substance0.0194320767044059
GO:0048731system development0.0219785942562387
GO:0008201heparin binding0.0219785942562387
GO:0009725response to hormone stimulus0.0219785942562387
GO:0007548sex differentiation0.0228355766681232
GO:0003006reproductive developmental process0.0239246494356034
GO:0048869cellular developmental process0.0244377192355441
GO:0030154cell differentiation0.0244377192355441
GO:0006413translational initiation0.0253594105001998
GO:0005539glycosaminoglycan binding0.0275420356370652
GO:0048856anatomical structure development0.0278034830529979
GO:0030247polysaccharide binding0.0278034830529979
GO:0003743translation initiation factor activity0.0281596910833609
GO:0001871pattern binding0.0290530936829223
GO:0001525angiogenesis0.0290530936829223
GO:0022618protein-RNA complex assembly0.030682397488284
GO:0048514blood vessel morphogenesis0.0316725005081661
GO:0007275multicellular organismal development0.0316725005081661
GO:0048646anatomical structure formation0.0318832880281242
GO:0001568blood vessel development0.0327591185942815
GO:0009628response to abiotic stimulus0.0327591185942815
GO:0001944vasculature development0.0327591185942815
GO:0006417regulation of translation0.0356663193063391
GO:0031326regulation of cellular biosynthetic process0.0376439794609047
GO:0008135translation factor activity, nucleic acid binding0.0376439794609047
GO:0009889regulation of biosynthetic process0.0399554155439376
GO:0008284positive regulation of cell proliferation0.0418738061862045
GO:0007417central nervous system development0.0418738061862045
GO:0022613ribonucleoprotein complex biogenesis and assembly0.0431349501067882
GO:0008083growth factor activity0.0436708477324468
GO:0022008neurogenesis0.0445273105530129



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
blood vessel endothelium1.03e-5718
endothelium1.03e-5718
cardiovascular system endothelium1.03e-5718
simple squamous epithelium2.79e-4622
squamous epithelium4.13e-4025
vessel6.10e-3168
endothelial tube6.55e-309
arterial system endothelium6.55e-309
endothelium of artery6.55e-309
vasculature5.65e-2678
vascular system5.65e-2678
epithelial tube open at both ends1.33e-2159
blood vessel1.33e-2159
blood vasculature1.33e-2159
vascular cord1.33e-2159
cardiovascular system6.92e-21109
circulatory system4.19e-20112
splanchnic layer of lateral plate mesoderm7.49e-2083
epithelial tube1.13e-14117
lymphatic vessel2.99e-148
lymph vasculature2.99e-148
lymphatic part of lymphoid system2.99e-148
vein2.93e-139
venous blood vessel2.93e-139
venous system2.93e-139
unilaminar epithelium8.39e-13148
lymphoid system3.00e-1110
microcirculatory vessel1.08e-103
endothelium of capillary1.08e-103
capillary1.08e-103
artery2.75e-1042
arterial blood vessel2.75e-1042
arterial system2.75e-1042
anatomical conduit4.25e-09240
tube3.18e-08192
segment of aorta6.05e-082
thoracic aorta6.05e-082
aorta5.13e-0721
aortic system5.13e-0721
epithelium9.64e-07306
lateral plate mesoderm9.67e-07203


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)
MA0003.10.213534
MA0004.10.502801
MA0006.10.341337
MA0007.10.483857
MA0009.10.973289
MA0014.10.610358
MA0017.10.380797
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.940207
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.11.25271
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.10.362619
MA0056.10
MA0057.10.369442
MA0058.10.406232
MA0059.10.404929
MA0060.10.224688
MA0061.10.198335
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.162298
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.10.0022316
MA0074.10.60198
MA0076.11.90063
MA0077.10.934645
MA0078.11.67751
MA0081.11.04478
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.917255
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.11.17914
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.347695
MA0103.10.88373
MA0105.10.104569
MA0106.10.648997
MA0107.10.274127
MA0108.21.8902
MA0109.10
MA0111.10.45062
MA0113.10.665691
MA0114.10.269076
MA0115.11.21667
MA0116.10.760835
MA0117.11.01134
MA0119.10.388712
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.10.186511
MA0140.10.564957
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.10.708913
MA0145.10.581146
MA0146.10.324987
MA0147.10.281049
MA0148.10.528066
MA0149.10.555119
MA0062.22.39331
MA0035.20.564239
MA0039.20.403603
MA0138.20.704862
MA0002.20.611548
MA0137.20.36398
MA0104.20.223944
MA0047.20.636643
MA0112.20.556641
MA0065.20.0828768
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.102476
MA0155.10.910701
MA0156.10.959643
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.10.485816
MA0163.10.19677
MA0164.10.678332
MA0080.20.344472
MA0018.20.650405
MA0099.20.572
MA0079.20.361922
MA0102.21.51913
MA0258.10.245543
MA0259.10.787775
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
CTBP2#1488217.91914295409380.005060297063777310.0235660556962382
FOS#235356.427110934924580.0002931195965424140.00310793071505515
IRF3#3661213.42341491756850.00885816023056540.0336156897031365



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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