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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.685063979246177,0

Latest revision as of 11:21, 17 September 2013


Full id: C353_tenocyte_Nucleus_Chondrocyte_Anulus_Fibroblast_Synoviocyte_tridermal



Phase1 CAGE Peaks

Hg19::chr17:38599693..38599708,+p1@IGFBP4
Hg19::chr17:38599805..38599839,-p@chr17:38599805..38599839
-
Hg19::chr17:38609237..38609305,+p@chr17:38609237..38609305
+
Hg19::chr17:38609262..38609296,-p@chr17:38609262..38609296
-
Hg19::chr17:38609342..38609354,+p@chr17:38609342..38609354
+
Hg19::chr17:38609343..38609359,-p@chr17:38609343..38609359
-
Hg19::chr17:38610202..38610277,+p@chr17:38610202..38610277
+
Hg19::chr17:38610240..38610307,-p@chr17:38610240..38610307
-
Hg19::chr17:38610311..38610321,-p@chr17:38610311..38610321
-
Hg19::chr17:38612787..38612806,+p@chr17:38612787..38612806
+
Hg19::chr17:38612812..38612823,+p@chr17:38612812..38612823
+
Hg19::chr17:38612826..38612905,+p@chr17:38612826..38612905
+
Hg19::chr17:38612907..38612937,+p@chr17:38612907..38612937
+
Hg19::chr17:38612942..38613067,+p@chr17:38612942..38613067
+
Hg19::chr17:38613046..38613073,-p@chr17:38613046..38613073
-
Hg19::chr17:38613071..38613097,+p@chr17:38613071..38613097
+
Hg19::chr17:38613104..38613148,+p@chr17:38613104..38613148
+
Hg19::chr17:38613168..38613230,-p@chr17:38613168..38613230
-
Hg19::chr17:38613229..38613250,+p@chr17:38613229..38613250
+
Hg19::chr17:38613261..38613276,+p@chr17:38613261..38613276
+
Hg19::chr17:38613285..38613298,-p@chr17:38613285..38613298
-
Hg19::chr17:38613290..38613313,+p@chr17:38613290..38613313
+
Hg19::chr17:38613300..38613311,-p@chr17:38613300..38613311
-
Hg19::chr17:38613329..38613352,+p@chr17:38613329..38613352
+
Hg19::chr17:38613379..38613443,+p@chr17:38613379..38613443
+
Hg19::chr17:38613501..38613547,+p@chr17:38613501..38613547
+
Hg19::chr17:38613568..38613587,+p@chr17:38613568..38613587
+
Hg19::chr17:38613595..38613628,+p@chr17:38613595..38613628
+
Hg19::chr17:38613674..38613696,-p@chr17:38613674..38613696
-
Hg19::chr17:38613694..38613726,+p@chr17:38613694..38613726
+
Hg19::chr17:38613757..38613870,+p@chr17:38613757..38613870
+
Hg19::chr17:38613830..38613904,-p@chr17:38613830..38613904
-


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
mesenchyme1.67e-22160
entire embryonic mesenchyme1.67e-22160
trunk mesenchyme2.70e-21122
epithelial vesicle1.61e-1878
muscle tissue1.78e-1764
musculature1.78e-1764
musculature of body1.78e-1764
skeletal muscle tissue2.44e-1762
striated muscle tissue2.44e-1762
myotome2.44e-1762
trunk4.50e-17199
vasculature1.57e-1678
vascular system1.57e-1678
unilaminar epithelium1.62e-16148
dense mesenchyme tissue2.81e-1673
somite3.38e-1671
presomitic mesoderm3.38e-1671
presumptive segmental plate3.38e-1671
dermomyotome3.38e-1671
trunk paraxial mesoderm3.38e-1671
epithelial tube5.19e-16117
paraxial mesoderm1.20e-1572
presumptive paraxial mesoderm1.20e-1572
splanchnic layer of lateral plate mesoderm1.42e-1583
organism subdivision6.80e-15264
multilaminar epithelium5.32e-1483
circulatory system6.31e-13112
epithelial tube open at both ends1.17e-1259
blood vessel1.17e-1259
blood vasculature1.17e-1259
vascular cord1.17e-1259
cardiovascular system1.37e-12109
vessel1.71e-1268
artery3.97e-1142
arterial blood vessel3.97e-1142
arterial system3.97e-1142
mesoderm6.41e-11315
mesoderm-derived structure6.41e-11315
presumptive mesoderm6.41e-11315
systemic artery1.81e-0933
systemic arterial system1.81e-0933
multi-tissue structure2.42e-07342
multi-cellular organism3.45e-07656
subdivision of trunk6.15e-07112


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)
MA0003.10.0794203
MA0004.12.693
MA0006.13.20331
MA0007.11.42296
MA0009.10.395891
MA0014.10.336518
MA0017.11.88293
MA0019.10.165418
MA0024.10.312615
MA0025.10.508683
MA0027.11.93196
MA0028.13.37058
MA0029.10.327543
MA0030.10.318663
MA0031.10.270046
MA0038.10.429002
MA0040.10.332103
MA0041.10.0940493
MA0042.10.0792314
MA0043.10.39615
MA0046.10.386991
MA0048.10.110797
MA0050.10.0796249
MA0051.10.422881
MA0052.10.335128
MA0055.10.828339
MA0056.10
MA0057.10.046597
MA0058.11.54054
MA0059.10.703386
MA0060.10.00694078
MA0061.10.314844
MA0063.10
MA0066.14.20051
MA0067.10.673046
MA0068.11.68482
MA0069.10.383853
MA0070.10.374777
MA0071.11.79596
MA0072.10.371146
MA0073.11.90095
MA0074.11.95193
MA0076.14.04105
MA0077.10.364942
MA0078.10.197204
MA0081.12.60322
MA0083.10.40206
MA0084.10.847335
MA0087.10.369175
MA0088.11.26589
MA0089.10
MA0090.10.802046
MA0091.19.31059
MA0092.11.87188
MA0093.12.13055
MA0095.10
MA0098.10
MA0100.10.146599
MA0101.10.121552
MA0103.10.108135
MA0105.10.0801977
MA0106.10.490178
MA0107.10.17155
MA0108.20.267801
MA0109.10
MA0111.11.27881
MA0113.10.173209
MA0114.10.0617658
MA0115.10.603788
MA0116.10.348601
MA0117.10.427006
MA0119.19.94343
MA0122.11.1395
MA0124.10.566745
MA0125.10.493194
MA0130.10
MA0131.10.2093
MA0132.10
MA0133.10
MA0135.10.420972
MA0136.10.142619
MA0139.11.24856
MA0140.10.115685
MA0141.12.58819
MA0142.10.247045
MA0143.10.173319
MA0144.10.0107485
MA0145.13.9484
MA0146.10.443429
MA0147.11.24352
MA0148.10.0971411
MA0149.10.110599
MA0062.22.05637
MA0035.20.11531
MA0039.20.00178466
MA0138.20.198014
MA0002.20.0316769
MA0137.20.0338658
MA0104.20.620363
MA0047.20.155654
MA0112.20.136984
MA0065.20.163186
MA0150.10.783414
MA0151.10
MA0152.10.119196
MA0153.10.478697
MA0154.10.37603
MA0155.10.0311639
MA0156.10.323801
MA0157.10.227782
MA0158.10
MA0159.10.015016
MA0160.10.104733
MA0161.10
MA0162.10.59729
MA0163.11.96038
MA0164.10.181076
MA0080.21.64687
MA0018.20.163878
MA0099.20.379875
MA0079.20.00076384
MA0102.20.88257
MA0258.10.72089
MA0259.15.01658
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
BCL3#6021314.03476051401872.04780743999384e-122.78840888168862e-10
POLR2A#5430322.147453176558072.38288969218142e-112.83447171482614e-09



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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