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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.

Latest revision as of 11:20, 17 September 2013


Full id: C332_Fibroblast_Smooth_Mesenchymal_mesenchymal_Chondrocyte_Skeletal_Pericytes



Phase1 CAGE Peaks

Hg19::chr2:238233052..238233077,-p@chr2:238233052..238233077
-
Hg19::chr2:238233102..238233125,-p@chr2:238233102..238233125
-
Hg19::chr2:238233169..238233193,-p@chr2:238233169..238233193
-
Hg19::chr2:238233200..238233214,-p@chr2:238233200..238233214
-
Hg19::chr2:238233221..238233252,-p@chr2:238233221..238233252
-
Hg19::chr2:238233270..238233287,-p@chr2:238233270..238233287
-
Hg19::chr2:238233328..238233343,-p@chr2:238233328..238233343
-
Hg19::chr2:238233367..238233381,-p@chr2:238233367..238233381
-
Hg19::chr2:238233399..238233412,-p@chr2:238233399..238233412
-
Hg19::chr2:238243426..238243476,-p5@COL6A3
Hg19::chr2:238245036..238245087,-p@chr2:238245036..238245087
-
Hg19::chr2:238245089..238245122,-p@chr2:238245089..238245122
-
Hg19::chr2:238245140..238245185,-p@chr2:238245140..238245185
-
Hg19::chr2:238247690..238247710,-p@chr2:238247690..238247710
-
Hg19::chr2:238249113..238249142,-p11@COL6A3
Hg19::chr2:238267705..238267736,-p@chr2:238267705..238267736
-
Hg19::chr2:238267881..238267893,-p@chr2:238267881..238267893
-
Hg19::chr2:238268028..238268038,-p25@COL6A3
Hg19::chr2:238269787..238269823,-p@chr2:238269787..238269823
-
Hg19::chr2:238270402..238270421,-p7@COL6A3
Hg19::chr2:238271931..238271942,-p@chr2:238271931..238271942
-
Hg19::chr2:238271947..238271972,-p@chr2:238271947..238271972
-
Hg19::chr2:238275490..238275526,-p@chr2:238275490..238275526
-
Hg19::chr2:238277500..238277511,-p17@COL6A3
Hg19::chr2:238277567..238277581,-p9@COL6A3
Hg19::chr2:238289803..238289845,-p@chr2:238289803..238289845
-
Hg19::chr2:238289886..238289905,-p@chr2:238289886..238289905
-
Hg19::chr2:238289901..238289937,+p@chr2:238289901..238289937
+
Hg19::chr2:238305397..238305434,-p10@COL6A3
Hg19::chr2:238322770..238322791,-p2@COL6A3
Hg19::chr2:238322800..238322824,-p1@COL6A3
Hg19::chr2:238322913..238322923,-p12@COL6A3
Hg19::chr2:238322924..238322940,-p6@COL6A3
Hg19::chr2:238322983..238323006,-p4@COL6A3
Hg19::chr2:238323007..238323038,-p3@COL6A3


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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
somite1.46e-2271
presomitic mesoderm1.46e-2271
presumptive segmental plate1.46e-2271
dermomyotome1.46e-2271
trunk paraxial mesoderm1.46e-2271
dense mesenchyme tissue1.84e-2273
paraxial mesoderm6.11e-2272
presumptive paraxial mesoderm6.11e-2272
muscle tissue7.30e-2064
musculature7.30e-2064
musculature of body7.30e-2064
skeletal muscle tissue2.22e-1962
striated muscle tissue2.22e-1962
myotome2.22e-1962
epithelial vesicle2.63e-1978
multilaminar epithelium4.57e-1883
trunk mesenchyme4.12e-14122
mesenchyme1.38e-13160
entire embryonic mesenchyme1.38e-13160
surface structure3.95e-1199
integument4.13e-1146
integumental system4.13e-1146
connective tissue1.31e-10371
mesoderm5.61e-10315
mesoderm-derived structure5.61e-10315
presumptive mesoderm5.61e-10315
skin of body2.06e-0941
unilaminar epithelium1.65e-08148
primary circulatory organ1.25e-0727
tissue1.54e-07773
organism subdivision2.04e-07264
trunk2.08e-07199
heart4.34e-0724
primitive heart tube4.34e-0724
primary heart field4.34e-0724
anterior lateral plate mesoderm4.34e-0724
heart tube4.34e-0724
heart primordium4.34e-0724
cardiac mesoderm4.34e-0724
cardiogenic plate4.34e-0724
heart rudiment4.34e-0724
musculoskeletal system7.41e-07167
Disease
Ontology termp-valuen
ovarian cancer2.43e-0714


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)
MA0003.10.000577223
MA0004.10.0714537
MA0006.10.0212634
MA0007.10.228407
MA0009.10.366503
MA0014.14.23681e-07
MA0017.10.547077
MA0019.12.02953
MA0024.10.285711
MA0025.10.47683
MA0027.11.89328
MA0028.10.0248137
MA0029.10.30014
MA0030.10.291553
MA0031.10.24472
MA0038.10.120244
MA0040.10.304553
MA0041.10.0793669
MA0042.10.505489
MA0043.10.960713
MA0046.10.357837
MA0048.10.0121508
MA0050.11.31325
MA0051.10.118004
MA0052.10.307481
MA0055.10.070867
MA0056.10
MA0057.10.354122
MA0058.10.148161
MA0059.10.0371511
MA0060.10.0046941
MA0061.11.15978
MA0063.10
MA0066.10.767457
MA0067.10.638784
MA0068.10.00882921
MA0069.10.354782
MA0070.10.914685
MA0071.10.100424
MA0072.10.906843
MA0073.10.47771
MA0074.11.80033
MA0076.10.042375
MA0077.10.336397
MA0078.10.175262
MA0081.10.340864
MA0083.10.372513
MA0084.10.811454
MA0087.10.340509
MA0088.10.00712764
MA0089.10
MA0090.10.178129
MA0091.10.253205
MA0092.10.209949
MA0093.10.0954868
MA0095.10
MA0098.10
MA0100.10.127731
MA0101.10.457879
MA0103.10.683065
MA0105.10.805926
MA0106.10.14308
MA0107.10.735552
MA0108.20.242565
MA0109.10
MA0111.10.192269
MA0113.12.08739
MA0114.10.46295
MA0115.10.570409
MA0116.10.0103227
MA0117.10.396851
MA0119.10.898554
MA0122.10.418111
MA0124.10.533912
MA0125.10.461632
MA0130.10
MA0131.10.186723
MA0132.10
MA0133.10
MA0135.11.0139
MA0136.10.124027
MA0139.10.0022589
MA0140.10.0991227
MA0141.10.0366436
MA0142.10.222682
MA0143.10.152737
MA0144.10.238059
MA0145.10.000603803
MA0146.10.000546743
MA0147.10.0533381
MA0148.10.280213
MA0149.10.0944562
MA0062.20.00260174
MA0035.20.0987789
MA0039.20.00021029
MA0138.21.00278
MA0002.20.157727
MA0137.20.50116
MA0104.20.0263481
MA0047.20.136179
MA0112.20.00240105
MA0065.20.0111203
MA0150.10.0451191
MA0151.10
MA0152.11.66583
MA0153.10.447419
MA0154.10.00704234
MA0155.13.4954e-05
MA0156.10.272778
MA0157.11.11527
MA0158.10
MA0159.10.0536962
MA0160.10.299258
MA0161.10
MA0162.10.0224645
MA0163.10.00135834
MA0164.12.86605
MA0080.20.095553
MA0018.20.869357
MA0099.20.102528
MA0079.21.24532e-05
MA0102.20.846442
MA0258.10.102628
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

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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