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Coexpression cluster:C2444: Difference between revisions

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{{Coexpression_clusters
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|full_id=C2444_Alveolar_Endothelial_Smooth_leiomyoma_Preadipocyte_Hair_Renal
|id=C2444
}}

Latest revision as of 12:06, 17 September 2013


Full id: C2444_Alveolar_Endothelial_Smooth_leiomyoma_Preadipocyte_Hair_Renal



Phase1 CAGE Peaks

Hg19::chr17:79826116..79826136,-p6@ARHGDIA
Hg19::chr17:79826202..79826231,-p3@ARHGDIA
Hg19::chr17:79826305..79826324,-p2@ARHGDIA
Hg19::chr17:79826336..79826347,-p16@ARHGDIA


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>

Cell Type
Ontology termp-valuen
somatic cell3.62e-22588
animal cell7.13e-20679
eukaryotic cell7.13e-20679
native cell3.37e-15722
embryonic cell2.50e-12250
mesodermal cell5.86e-12121
somatic stem cell2.63e-10433
stem cell1.36e-09441
fibroblast2.05e-0976
multi fate stem cell2.11e-09427
contractile cell2.17e-0759
electrically responsive cell2.68e-0761
electrically active cell2.68e-0761
muscle precursor cell8.19e-0758
myoblast8.19e-0758
multi-potent skeletal muscle stem cell8.19e-0758
Uber Anatomy
Ontology termp-valuen
mesoderm1.75e-11315
mesoderm-derived structure1.75e-11315
presumptive mesoderm1.75e-11315
epithelial vesicle6.35e-0978
epithelial tube open at both ends3.99e-0859
blood vessel3.99e-0859
blood vasculature3.99e-0859
vascular cord3.99e-0859
vessel6.06e-0868
vasculature1.06e-0778
vascular system1.06e-0778
splanchnic layer of lateral plate mesoderm1.07e-0783
artery1.49e-0742
arterial blood vessel1.49e-0742
arterial system1.49e-0742
surface structure2.00e-0799
lateral plate mesoderm2.38e-07203
epithelial tube2.67e-07117
dense mesenchyme tissue5.64e-0773
somite5.79e-0771
presomitic mesoderm5.79e-0771
presumptive segmental plate5.79e-0771
dermomyotome5.79e-0771
trunk paraxial mesoderm5.79e-0771
paraxial mesoderm6.22e-0772
presumptive paraxial mesoderm6.22e-0772
integument7.19e-0746
integumental system7.19e-0746


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
MA0004.11.69588
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.244769
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
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.709734
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.12.526
MA0056.10
MA0057.10.248209
MA0058.14.90963
MA0059.16.22663
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.12.36824
MA0074.11.91637
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.13.07281
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.11.32557
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
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.14.07269
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
MA0139.10.344952
MA0140.11.83481
MA0141.10.602484
MA0142.12.2938
MA0143.10.887001
MA0144.10.430413
MA0145.10.569905
MA0146.110.1665
MA0147.14.09671
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.22.01147
MA0138.20.928035
MA0002.20.98779
MA0137.20.558189
MA0104.23.68813
MA0047.20.856092
MA0112.20.551048
MA0065.20.577908
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.11.02191
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.12.03616
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.22.00408
MA0102.21.75932
MA0258.10.418966
MA0259.11.1888
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#602434.54710280373837.01262157705428e-073.1473622040652e-05
CCNT2#90546.336201576962630.0006203100587215640.0051213092666262
EGR1#195844.988179094810140.001615011500076050.0101419148611895
ETS1#211349.728760922202340.0001115955317418140.00154533621580261
FOSL2#2355416.93020060456171.2165416097647e-050.00030359471728128
GABPB1#255347.067683836182170.0004006876864423170.00390294919645114
GATA2#2624412.7449317335543.78864877853583e-050.000721653638120561
HEY1#2346244.040111043105710.00375304636917980.018601196362508
HMGN3#932448.178547723350590.0002234570284440470.00248087898306239
SIN3A#2594245.408884726815140.001168172384885160.0079620671999622
TAL1#6886429.86861667744021.25525650806991e-065.03834490569996e-05
YY1#752844.911170749853860.00171871838055440.0106839610110542
ZBTB7A#5134135.513931980906920.009038352821081090.0342397812862595
ZNF263#1012748.221841637010680.0002187871180958320.00248774173400224



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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