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Coexpression cluster:C2131: Difference between revisions

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{{Coexpression_clusters
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|full_id=C2131_Smooth_Fibroblast_gall_leiomyoma_bone_Chondrocyte_mesenchymal
|id=C2131
}}

Latest revision as of 11:59, 17 September 2013


Full id: C2131_Smooth_Fibroblast_gall_leiomyoma_bone_Chondrocyte_mesenchymal



Phase1 CAGE Peaks

Hg19::chr11:44117206..44117218,+p2@EXT2
Hg19::chr11:44117219..44117240,+p1@EXT2
Hg19::chr11:44117242..44117253,+p3@EXT2
Hg19::chr11:44117260..44117283,+p4@EXT2


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
vasculature5.07e-1778
vascular system5.07e-1778
multilaminar epithelium1.01e-1683
mesenchyme2.00e-16160
entire embryonic mesenchyme2.00e-16160
vessel8.39e-1668
organism subdivision8.71e-16264
epithelial tube9.30e-16117
splanchnic layer of lateral plate mesoderm3.04e-1583
epithelial tube open at both ends8.91e-1559
blood vessel8.91e-1559
blood vasculature8.91e-1559
vascular cord8.91e-1559
artery1.35e-1442
arterial blood vessel1.35e-1442
arterial system1.35e-1442
unilaminar epithelium2.01e-14148
trunk3.13e-14199
somite5.93e-1471
presomitic mesoderm5.93e-1471
presumptive segmental plate5.93e-1471
dermomyotome5.93e-1471
trunk paraxial mesoderm5.93e-1471
trunk mesenchyme6.21e-14122
dense mesenchyme tissue6.56e-1473
multi-cellular organism6.98e-14656
epithelial vesicle8.93e-1478
skeletal muscle tissue1.32e-1362
striated muscle tissue1.32e-1362
myotome1.32e-1362
anatomical system1.33e-13624
paraxial mesoderm2.08e-1372
presumptive paraxial mesoderm2.08e-1372
anatomical group2.82e-13625
muscle tissue2.93e-1364
musculature2.93e-1364
musculature of body2.93e-1364
systemic artery8.55e-1333
systemic arterial system8.55e-1333
cell layer2.61e-12309
epithelium3.44e-12306
surface structure1.56e-1199
anatomical cluster2.63e-11373
multi-tissue structure9.66e-11342
cardiovascular system1.70e-09109
circulatory system2.39e-09112
anatomical conduit6.41e-08240
integument1.09e-0746
integumental system1.09e-0746
skin of body3.27e-0741
organ component layer5.87e-0766


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)
MA0003.10.0938548
MA0004.10.71247
MA0006.11.31813
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.11.73823
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.791759
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.12.64938
MA0071.10.782546
MA0072.11.1744
MA0073.10.100363
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.11.57689
MA0113.12.05499
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.12.47057
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.8309
MA0147.10.46175
MA0148.11.75269
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.0247757
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.10.560797
MA0157.12.23474
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.000248021
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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
CCNT2#90546.336201576962630.0006203100587215640.00511241810470498
CTCF#1066445.360256373075030.001211145381643620.00815701376884493
CTCFL#140690419.74647435897446.5732084880439e-060.000192620460517064
ELF1#199744.258097958807540.003041525565781240.0160536659708206
ETS1#211349.728760922202340.0001115955317418140.00154308562684804
FOXA1#3169411.08141974938556.62943068949433e-050.00106913389712801
HEY1#2346244.040111043105710.00375304636917980.0185527717967894
HMGN3#932448.178547723350590.0002234570284440470.00247745526472058
NRF1#4899412.21027944771094.49717228915276e-050.000791773730119395
SIN3A#2594245.408884726815140.001168172384885160.00794185364568551
SMC3#9126415.04493284493281.95092670935632e-050.000437144034753196
SP2#6668426.15353049384462.13562021071447e-067.73914084617658e-05
TAF1#687243.343046285745290.008005664898701650.0321244721387598
TBP#690843.706770687096390.005296377814784350.0243484638875897
ZNF143#7702413.50087655222793.00867915035614e-050.000619525713296618



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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