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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.67869215418404,

Latest revision as of 14:16, 17 September 2013


Full id: C4626_salivary_amniotic_choriocarcinoma_Keratinocyte_maxillary_cervical_esophagus



Phase1 CAGE Peaks

Hg19::chr6:7541814..7541825,+p7@DSP
Hg19::chr6:7541832..7541844,+p3@DSP
Hg19::chr6:7541845..7541878,+p2@DSP


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>

Cell Type
Ontology termp-valuen
epithelial cell4.25e-35253
endodermal cell5.51e-1958
endo-epithelial cell5.35e-1742
epithelial cell of alimentary canal1.39e-0920
respiratory epithelial cell6.92e-0713
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure5.35e-22160
endoderm5.35e-22160
presumptive endoderm5.35e-22160
digestive system1.58e-17145
digestive tract1.58e-17145
primitive gut1.58e-17145
subdivision of digestive tract2.05e-16118
foregut2.34e-1387
organ4.98e-12503
respiratory system7.36e-1274
subdivision of trunk8.75e-11112
immaterial anatomical entity1.24e-10117
multi-cellular organism1.67e-10656
organ part2.13e-10218
organism subdivision2.32e-10264
endo-epithelium1.10e-0982
respiratory tract5.83e-0954
trunk region element9.36e-09101
anatomical space1.15e-0895
primordium1.38e-08160
multi-tissue structure2.34e-08342
extraembryonic membrane1.36e-0714
membranous layer1.36e-0714
renal system4.19e-0748
respiratory primordium5.38e-0738
endoderm of foregut5.38e-0738
anatomical system5.72e-07624
urinary system structure7.20e-0747
anatomical group8.21e-07625
gland8.73e-0759
Disease
Ontology termp-valuen
carcinoma9.02e-22106
cell type cancer6.67e-15143
adenocarcinoma2.88e-0725


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)
MA0003.11.54338
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.11.80735
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.13.37768
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.13.5636
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.15.87909
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.11.52002
MA0105.11.5295
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.12.29491
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.11.12079
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.13.00132
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.211.588
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.22.88736
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.13.52399
MA0163.10.387745
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.28.15771
MA0102.21.88331
MA0258.12.22591
MA0259.10.575594
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
BHLHE40#8553344.87181354697741.10603738662898e-050.000285712190507406
CHD2#1106310.34402283411690.0009033701102746880.00662596186157583
E2F1#186934.907389214879320.008460985347239390.0327522923899309
ELF1#199734.258097958807540.01295179875054610.0464756196429577
EP300#203336.77394172622320.003216880500103790.0168354270670645
FOSL2#2355316.93020060456170.0002060162053171620.0024403001550549
FOXA1#3169311.08141974938550.000734755275698670.00583996242303602
FOXA2#3170324.63046375266526.68983856509345e-050.0010768804714855
HDAC2#3066313.41562023662630.0004140761399857210.00393357267454691
HNF4A#3172323.13229036295378.07584663437677e-050.00123363075420166
HNF4G#3174328.75342252644684.20470658818262e-050.000760144281397273
MYC#460935.22228187160940.007020843755740150.0295927799259725
RXRA#6256320.07461713913330.0001235730348432220.00165948877279045
SIN3A#2594235.408884726815140.006318961977991520.0278176559610292
SP1#666735.69838137814090.005403962701712170.0247808764260864
TCF7L2#6934310.77017656313730.0008003181298398380.00617178063666417
TFAP2A#7020316.5186343730450.0002218033880766340.00249407020320151
TFAP2C#7022310.80922860986020.0007916746575753130.00618736133821059
ZNF263#1012738.221841637010680.001799043925565870.011008340083324



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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