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Coexpression cluster:C1997: Difference between revisions

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{{Coexpression_clusters
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|full_id=C1997_Chondrocyte_vagina_aorta_mesodermal_heart_Fibroblast_tenocyte
|id=C1997
|ontology_enrichment_celltype=CL:0000055!7.45e-24!180;CL:0000057!5.25e-16!75;CL:0000183!1.01e-09!59;CL:0000187!2.36e-08!54;CL:0000680!7.97e-08!57;CL:0000056!7.97e-08!57;CL:0000355!7.97e-08!57;CL:0000192!8.37e-08!42;CL:0000514!8.37e-08!42;CL:0000393!2.34e-07!60;CL:0000211!2.34e-07!60;CL:0002620!3.02e-07!23;CL:0000359!3.75e-07!32
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.14e-15!115;UBERON:0000475!3.83e-14!365;UBERON:0000914!8.99e-13!83;UBERON:0002329!8.99e-13!83;UBERON:0003077!8.99e-13!83;UBERON:0003059!8.99e-13!83;UBERON:0007282!8.99e-13!83;UBERON:0009618!8.99e-13!83;UBERON:0007285!8.99e-13!83;UBERON:0000119!1.26e-10!312;UBERON:0004872!1.78e-10!84;UBERON:0004290!2.54e-10!70;UBERON:0000483!3.46e-10!309;UBERON:0000477!3.70e-10!286;UBERON:0001009!2.12e-09!113;UBERON:0004535!4.64e-09!110;UBERON:0002049!5.00e-09!79;UBERON:0007798!5.00e-09!79;UBERON:0002385!7.78e-09!63;UBERON:0001015!7.78e-09!63;UBERON:0000383!7.78e-09!63;UBERON:0000486!9.55e-09!82;UBERON:0004111!1.22e-08!241;UBERON:0000025!1.37e-08!194;UBERON:0005256!1.88e-08!143;UBERON:0001134!2.30e-08!61;UBERON:0002036!2.30e-08!61;UBERON:0003082!2.30e-08!61;UBERON:0000481!2.35e-08!347;UBERON:0002199!9.58e-08!45;UBERON:0002416!9.58e-08!45;UBERON:0001981!1.34e-07!60;UBERON:0007500!1.34e-07!60;UBERON:0004537!1.34e-07!60;UBERON:0006965!1.34e-07!60;UBERON:0007100!1.46e-07!27;UBERON:0003102!1.59e-07!95;UBERON:0003075!1.89e-07!86;UBERON:0007284!1.89e-07!86;UBERON:0003103!2.13e-07!69;UBERON:0000948!2.53e-07!24;UBERON:0005498!2.53e-07!24;UBERON:0004140!2.53e-07!24;UBERON:0009881!2.53e-07!24;UBERON:0004141!2.53e-07!24;UBERON:0003084!2.53e-07!24;UBERON:0007005!2.53e-07!24;UBERON:0004139!2.53e-07!24;UBERON:0004291!2.53e-07!24;UBERON:0002346!3.66e-07!90;UBERON:0000055!7.89e-07!69;UBERON:0002097!8.48e-07!40
}}

Latest revision as of 11:56, 17 September 2013


Full id: C1997_Chondrocyte_vagina_aorta_mesodermal_heart_Fibroblast_tenocyte



Phase1 CAGE Peaks

Hg19::chr7:44143738..44143760,+p4@AEBP1
Hg19::chr7:44143925..44143970,+p1@AEBP1
Hg19::chr7:44143978..44143989,+p2@AEBP1
Hg19::chr7:44143997..44144008,+p3@AEBP1
Hg19::chr7:44146212..44146234,+p@chr7:44146212..44146234
+


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
adult organism6.88e-15114
structure with developmental contribution from neural crest2.27e-14132
multi-tissue structure7.96e-13342
cell layer2.03e-11309
dense mesenchyme tissue3.02e-1173
epithelium5.10e-11306
paraxial mesoderm8.66e-1172
presumptive paraxial mesoderm8.66e-1172
anatomical cluster8.85e-11373
epithelial vesicle1.21e-1078
somite1.55e-1071
presomitic mesoderm1.55e-1071
presumptive segmental plate1.55e-1071
dermomyotome1.55e-1071
trunk paraxial mesoderm1.55e-1071
splanchnic layer of lateral plate mesoderm6.03e-1083
anatomical conduit3.11e-09240
muscle tissue3.45e-0964
musculature3.45e-0964
musculature of body3.45e-0964
tube5.77e-09192
mesenchyme8.23e-09160
entire embryonic mesenchyme8.23e-09160
skeletal muscle tissue1.07e-0862
striated muscle tissue1.07e-0862
myotome1.07e-0862
multilaminar epithelium1.15e-0883
primary circulatory organ1.56e-0827
compound organ2.71e-0868
integument3.54e-0846
integumental system3.54e-0846
heart5.18e-0824
primitive heart tube5.18e-0824
primary heart field5.18e-0824
anterior lateral plate mesoderm5.18e-0824
heart tube5.18e-0824
heart primordium5.18e-0824
cardiac mesoderm5.18e-0824
cardiogenic plate5.18e-0824
heart rudiment5.18e-0824
multi-cellular organism6.19e-08656
organism subdivision6.25e-08264
vasculature6.36e-0878
vascular system6.36e-0878
surface structure1.37e-0799
neural plate1.85e-0782
presumptive neural plate1.85e-0782
tissue1.95e-07773
trunk mesenchyme2.76e-07122
circulatory system3.87e-07112
neurectoderm3.99e-0786
skin of body4.31e-0741
epithelial tube open at both ends4.83e-0759
blood vessel4.83e-0759
blood vasculature4.83e-0759
vascular cord4.83e-0759
epithelial tube7.04e-07117
ecto-epithelium8.39e-07104


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)
MA0003.14.3611
MA0004.10.626788
MA0006.11.14863
MA0007.11.47524
MA0009.11.11255
MA0014.15.09469
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.12.0635
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
MA0048.10.195817
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.0853006
MA0056.10
MA0057.10.189508
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.146.1668
MA0074.10.730989
MA0076.11.33654
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.11.3271
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.11.16366
MA0103.10.442769
MA0105.11.00065
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.973423
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
MA0139.10.277033
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.442008
MA0146.10.143081
MA0147.11.00307
MA0148.10.653474
MA0149.10.681935
MA0062.22.17426
MA0035.20.691506
MA0039.211.0749
MA0138.24.65117
MA0002.20.30855
MA0137.20.47779
MA0104.21.54865
MA0047.20.767096
MA0112.20.839774
MA0065.24.30878
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.12.24205
MA0155.15.79564
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.11.00463
MA0160.10.669748
MA0161.10
MA0162.13.53221
MA0163.129.2681
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.233.5536
MA0102.21.66336
MA0258.10.345771
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

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

TF#promotersEnrichmentp-valueq-value
EGR1#195843.990543275848110.0067800983001440.0287766361754273



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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