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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:25, 17 September 2013


Full id: C543_Alveolar_Corneal_Urothelial_amniotic_Esophageal_Tracheal_esophagus



Phase1 CAGE Peaks

Hg19::chr15:41136499..41136552,-p@chr15:41136499..41136552
-
Hg19::chr15:41136586..41136725,+p1@SPINT1
Hg19::chr15:41136734..41136749,+p9@SPINT1
Hg19::chr16:67233007..67233061,+p1@ELMO3
Hg19::chr19:10697917..10697993,-p1@AP1M2
Hg19::chr19:4338783..4338834,-p1@STAP2
Hg19::chr19:50084561..50084603,+p1@PRRG2
Hg19::chr19:50084621..50084673,+p2@PRRG2
Hg19::chr1:156030937..156030983,+p1@RAB25
Hg19::chr1:156030987..156031007,+p2@RAB25
Hg19::chr1:201368707..201368760,-p3@LAD1
Hg19::chr1:26503974..26504025,+p1@CNKSR1
Hg19::chr1:27286862..27286885,-p2@C1orf172
Hg19::chr1:27286905..27286966,-p1@C1orf172
Hg19::chr20:821883..821934,+p@chr20:821883..821934
+
Hg19::chr6:42110342..42110365,-p1@C6orf132
Hg19::chrX:48916506..48916557,+p1@CCDC120


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
endoderm-derived structure1.52e-27160
endoderm1.52e-27160
presumptive endoderm1.52e-27160
digestive system1.96e-20145
digestive tract1.96e-20145
primitive gut1.96e-20145
subdivision of digestive tract8.78e-18118
respiratory system1.90e-1474
renal system8.91e-1348
endo-epithelium1.72e-1282
anatomical space2.23e-1295
urinary system structure2.30e-1247
immaterial anatomical entity9.83e-12117
foregut6.42e-1187
orifice1.00e-1036
trunk region element1.62e-10101
epithelial bud2.16e-1037
extraembryonic membrane4.03e-1014
membranous layer4.03e-1014
organ4.48e-10503
respiratory tract6.93e-1054
thoracic cavity element2.96e-0934
thoracic cavity2.96e-0934
reproductive structure6.20e-0959
reproductive system6.20e-0959
thoracic segment organ8.51e-0935
epithelial fold1.36e-0847
oral opening1.69e-0822
organism subdivision3.73e-08264
subdivision of trunk6.47e-08112
organ part7.75e-08218
multi-cellular organism9.45e-08656
reproductive organ1.18e-0748
nephron tubule epithelium1.23e-0710
chorion1.24e-077
internal genitalia1.92e-0725
thoracic segment of trunk2.24e-0752
gland5.69e-0759
respiratory primordium7.49e-0738
endoderm of foregut7.49e-0738
embryo8.26e-07592
Disease
Ontology termp-valuen
carcinoma9.72e-20106
cell type cancer2.73e-12143
squamous cell carcinoma5.48e-1214
adenocarcinoma8.26e-0925


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)
MA0003.11.63653
MA0004.10.221943
MA0006.10.731819
MA0007.10.208008
MA0009.10.621697
MA0014.15.32409
MA0017.10.840365
MA0019.10.340029
MA0024.10.525161
MA0025.10.747404
MA0027.12.20546
MA0028.11.26611
MA0029.10.542771
MA0030.10.532314
MA0031.10.474026
MA0038.10.302644
MA0040.10.548121
MA0041.10.236024
MA0042.10.211928
MA0043.10.621991
MA0046.10.611559
MA0048.12.04604
MA0050.10.212584
MA0051.10.299199
MA0052.10.551663
MA0055.10.429976
MA0056.10
MA0057.10.327175
MA0058.10.153757
MA0059.10.15289
MA0060.10.18988
MA0061.10.640118
MA0063.10
MA0066.10.818531
MA0067.10.924196
MA0068.10.502018
MA0069.10.607975
MA0070.10.597583
MA0071.10.27142
MA0072.10.593415
MA0073.10.0247836
MA0074.11.46857
MA0076.10.493997
MA0077.10.586275
MA0078.10.382364
MA0081.10.152999
MA0083.10.628701
MA0084.11.10674
MA0087.10.591148
MA0088.10.320704
MA0089.10
MA0090.10.518617
MA0091.10.223914
MA0092.10.570207
MA0093.10.114388
MA0095.10
MA0098.10
MA0100.10.314026
MA0101.11.22726
MA0103.11.70764
MA0105.11.83309
MA0106.11.60486
MA0107.11.40171
MA0108.20.471286
MA0109.10
MA0111.10.184188
MA0113.10.350573
MA0114.10.25223
MA0115.10.850405
MA0116.11.41998
MA0117.10.656858
MA0119.10.438293
MA0122.10.681203
MA0124.10.810546
MA0125.10.730403
MA0130.10
MA0131.10.398042
MA0132.10
MA0133.10
MA0135.10.650071
MA0136.11.50397
MA0139.10.140313
MA0140.10.269307
MA0141.10.151722
MA0142.10.445733
MA0143.10.925263
MA0144.10.5008
MA0145.11.88452
MA0146.10.603856
MA0147.10.269778
MA0148.10.240905
MA0149.10.261654
MA0062.21.38546
MA0035.20.268747
MA0039.21.3426
MA0138.20.997372
MA0002.20.174654
MA0137.20.398112
MA0104.20.420925
MA0047.20.326636
MA0112.21.0853
MA0065.20.593175
MA0150.10.170499
MA0151.10
MA0152.10.274535
MA0153.10.714423
MA0154.16.26214
MA0155.11.03039
MA0156.11.30109
MA0157.10.421609
MA0158.10
MA0159.10.0787617
MA0160.10.252705
MA0161.10
MA0162.11.00547
MA0163.10.55621
MA0164.10.361105
MA0080.21.77296
MA0018.20.89684
MA0099.20.27482
MA0079.22.37137
MA0102.21.14323
MA0258.10.476351
MA0259.10.28219
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
E2F1#186982.309359630531450.01224933189154410.04440808016596
MYC#460982.457544410169130.008361946486306990.032921677124568
POLR2A#5430172.147453176558072.27473247069268e-068.13320042816408e-05
TAF1#6872112.163147596658720.003152426505870830.0165503580076732
ZEB1#693587.947497420020642.25657064892169e-068.0710267809155e-05



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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