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{{Coexpression_clusters
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|full_id=C2434_Renal_pancreas_Hepatocyte_Alveolar_gastric_kidney_nonsmall
|id=C2434
}}

Latest revision as of 12:05, 17 September 2013


Full id: C2434_Renal_pancreas_Hepatocyte_Alveolar_gastric_kidney_nonsmall



Phase1 CAGE Peaks

Hg19::chr17:72428185..72428199,+p4@GPRC5C
Hg19::chr17:72428218..72428264,+p1@GPRC5C
Hg19::chr17:72428266..72428277,+p6@GPRC5C
Hg19::chr17:72428301..72428329,+p@chr17:72428301..72428329
+


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 cell7.82e-27253
endodermal cell1.69e-1558
endo-epithelial cell1.44e-1042
kidney cell1.12e-0917
kidney epithelial cell1.12e-0917
kidney tubule cell4.52e-0910
nephron tubule epithelial cell4.52e-0910
epithelial cell of nephron1.53e-0815
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure3.38e-23160
endoderm3.38e-23160
presumptive endoderm3.38e-23160
subdivision of digestive tract5.46e-22118
digestive system1.96e-20145
digestive tract1.96e-20145
primitive gut1.96e-20145
trunk region element3.83e-19101
foregut1.03e-1787
organ system subdivision1.65e-17223
abdomen element2.50e-1654
abdominal segment element2.50e-1654
immaterial anatomical entity2.76e-16117
subdivision of trunk6.04e-15112
multi-tissue structure1.17e-14342
endo-epithelium3.68e-1482
abdominal segment of trunk6.27e-1460
abdomen6.27e-1460
anatomical cluster6.97e-14373
organ1.25e-13503
renal system1.82e-1248
primordium1.84e-12160
urinary system structure3.25e-1247
cavitated compound organ1.46e-1031
kidney4.72e-1026
kidney mesenchyme4.72e-1026
upper urinary tract4.72e-1026
kidney rudiment4.72e-1026
kidney field4.72e-1026
anatomical space5.34e-1095
epithelial sac8.08e-1025
sac8.29e-1026
epithelium of foregut-midgut junction1.41e-0925
anatomical boundary1.41e-0925
hepatobiliary system1.41e-0925
foregut-midgut junction1.41e-0925
septum transversum1.41e-0925
gut epithelium2.47e-0954
nephron tubule epithelium4.52e-0910
exocrine gland4.98e-0931
exocrine system4.98e-0931
excretory tube5.49e-0916
kidney epithelium5.49e-0916
embryo7.07e-09592
adult organism1.12e-08114
nephron epithelium1.53e-0815
renal tubule1.53e-0815
nephron tubule1.53e-0815
nephron1.53e-0815
uriniferous tubule1.53e-0815
nephrogenic mesenchyme1.53e-0815
hepatic diverticulum1.94e-0822
liver primordium1.94e-0822
digestive tract diverticulum1.95e-0823
organism subdivision3.38e-08264
gland6.61e-0859
respiratory system8.71e-0874
organ part9.74e-08218
gastrointestinal system9.86e-0825
compound organ1.47e-0768
liver2.22e-0719
digestive gland2.22e-0719
liver bud2.22e-0719
anatomical conduit3.39e-07240
multi-cellular organism3.46e-07656
anatomical cavity5.88e-0761
developing anatomical structure6.36e-07581
Disease
Ontology termp-valuen
carcinoma8.71e-22106
cell type cancer1.49e-15143
adenocarcinoma7.43e-0925
cancer4.75e-08235
disease of cellular proliferation1.05e-07239


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)
MA0003.11.45381
MA0004.10.71247
MA0006.12.26728
MA0007.10.6918
MA0009.11.20602
MA0014.11.86845
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.12.32784
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
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
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
MA0068.11.52107
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.599068
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
MA0106.12.01886
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
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
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.11.75643
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.21.5472
MA0138.20.928035
MA0002.20.98779
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.577908
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.12.80246
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.327251
MA0102.21.75932
MA0258.10.418966
MA0259.12.06681
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#186944.907389214879320.001724022357361790.0106484813401448
EGR1#195844.988179094810140.001615011500076050.0101413050779487
FOXA1#3169411.08141974938556.62943068949433e-050.00107045626434771
FOXA2#3170424.63046375266522.71504128667089e-069.42673527056585e-05
HDAC2#3066413.41562023662633.0859005065161e-050.000626532587480628
HEY1#2346244.040111043105710.00375304636917980.0185985485053746
HNF4A#3172423.13229036295373.48990320893214e-060.000115561826644789
MXI1#460149.96157162875930.0001015224754950450.00142320883466134
MYC#460945.22228187160940.001344309395272740.00887473634215483
NANOG#79923429.24477848101271.36586687657858e-065.3287176213295e-05
NRF1#4899412.21027944771094.49717228915276e-050.000793646800788823
SIN3A#2594245.408884726815140.001168172384885160.00796050865881644
SMARCB1#6598418.25271578115749.00423392720929e-060.00024137402133568
SP1#666745.69838137814090.0009482606065333980.00683946059984403
TAF1#687243.343046285745290.008005664898701650.0322098634854573
TBP#690843.706770687096390.005296377814784350.0244118629506272
TCF7L2#6934410.77017656313737.42969445082454e-050.00115417203443353
USF2#739239.74414803880220.001718341848410070.0107186229651854



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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