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{{Coexpression_clusters
{
|full_id=C1824_Alveolar_nonsmall_brain_duodenum_Neurons_Renal_temporal
 

Latest revision as of 11:53, 17 September 2013


Full id: C1824_Alveolar_nonsmall_brain_duodenum_Neurons_Renal_temporal



Phase1 CAGE Peaks

Hg19::chr19:42806477..42806500,-p6@PAFAH1B3
Hg19::chr19:42806505..42806542,-p4@PAFAH1B3
Hg19::chr19:42806559..42806580,-p5@PAFAH1B3
Hg19::chr19:42806590..42806657,-p2@PAFAH1B3
Hg19::chr19:42806728..42806795,-p1@PAFAH1B3


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
anatomical cluster2.10e-17373
multi-tissue structure2.30e-12342
cell layer2.69e-12309
epithelium1.12e-11306
organ part7.58e-10218
organism subdivision1.59e-09264
organ segment2.54e-0998
organ system subdivision2.45e-08223
nephron epithelium2.85e-0815
renal tubule2.85e-0815
nephron tubule2.85e-0815
nephron2.85e-0815
uriniferous tubule2.85e-0815
nephrogenic mesenchyme2.85e-0815
segment of respiratory tract3.72e-0847
respiratory primordium4.04e-0838
endoderm of foregut4.04e-0838
trunk region element5.77e-08101
endoderm-derived structure1.04e-07160
endoderm1.04e-07160
presumptive endoderm1.04e-07160
kidney1.68e-0726
kidney mesenchyme1.68e-0726
upper urinary tract1.68e-0726
kidney rudiment1.68e-0726
kidney field1.68e-0726
urinary system structure1.93e-0747
excretory tube3.46e-0716
kidney epithelium3.46e-0716
renal system4.17e-0748
parenchyma4.33e-0715
respiratory tract4.62e-0754
cortex of kidney5.72e-0712
renal parenchyma5.72e-0712
Disease
Ontology termp-valuen
cancer6.19e-20235
disease of cellular proliferation1.73e-19239
cell type cancer2.06e-15143
carcinoma4.15e-13106
organ system cancer2.86e-10137


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)
MA0003.10.481059
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.10.660087
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.11.18667
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
MA0048.10.569896
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.603517
MA0056.10
MA0057.11.05691
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.11.98392
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.215829
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.412364
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.11.15584
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.10.175503
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.372523
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
MA0139.10.759606
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.868598
MA0146.10.946108
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.23.41529
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.425004
MA0065.20.449243
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.98952
MA0155.10.130813
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.12.67024
MA0160.10.669748
MA0161.10
MA0162.10.81299
MA0163.10.680296
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.211.1769
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
CCNT2#90556.336201576962639.78880505817628e-050.00139092926730731
CHD2#1106510.34402283411698.43981772346334e-060.000230202696061841
E2F1#186954.907389214879320.0003512818099256460.00352934304442756
E2F4#1874512.66806031528443.06319883889696e-060.000103466178375019
E2F6#187655.017155731697390.0003144978599297790.00322840986762396
EGR1#195854.988179094810140.0003237398000590710.00330864673435457
ELF1#199754.258097958807540.0007142416939776840.00573364245021794
EP300#203356.77394172622327.00901578206049e-050.00110860911595126
HEY1#2346254.040111043105710.0009288852205177990.00674442738776824
HMGN3#932458.178547723350592.73180911341838e-050.000582141220151606
IRF1#365957.63716375356393.84754333311872e-050.000724546660958504
JUND#372756.994663941871035.97069468343598e-050.000984330516248413
NR3C1#2908514.9730233311731.32777388277837e-065.24674145075634e-05
PAX5#507956.669565531177837.57493746384605e-050.0011701211267366
SIN3A#2594255.408884726815140.0002159522671657270.00248144337446599
SIX5#147912517.0867153554596.86007756253503e-073.1015568855134e-05
SP1#666755.69838137814090.000166391843712550.00204372548106492
STAT3#6774510.51946499715427.759040745861e-060.000220442452790255
TAF1#687253.343046285745290.002394600090870310.0135417824826946
TBP#690853.706770687096390.001428755106721120.00919111515804418
TCF7L2#6934510.77017656313736.89693748574565e-060.000199863832983848
USF1#739156.361499277207969.59569864925045e-050.0013687041398922
USF2#7392512.99219738506962.69963551658264e-069.42652068593696e-05
ZNF263#1012758.221841637010682.6606316672286e-050.00057128641178801



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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