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Coexpression cluster:C2933: Difference between revisions

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{{Coexpression_clusters
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|full_id=C2933_testicular_rectal_squamous_malignant_nasal_small_large
|id=C2933
}}

Latest revision as of 12:15, 17 September 2013


Full id: C2933_testicular_rectal_squamous_malignant_nasal_small_large



Phase1 CAGE Peaks

Hg19::chr8:95653327..95653364,+p3@ESRP1
Hg19::chr8:95653373..95653415,+p1@ESRP1
Hg19::chr8:95653432..95653460,+p2@ESRP1
Hg19::chr8:95653478..95653491,+p4@ESRP1


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 structure2.82e-25160
endoderm2.82e-25160
presumptive endoderm2.82e-25160
digestive system7.82e-19145
digestive tract7.82e-19145
primitive gut7.82e-19145
subdivision of digestive tract1.55e-16118
respiratory system1.56e-1574
epithelial bud1.02e-1337
anatomical space1.37e-1395
endo-epithelium1.44e-1282
thoracic cavity element2.12e-1134
thoracic cavity2.12e-1134
immaterial anatomical entity3.97e-11117
epithelial fold6.20e-1147
thoracic segment organ7.32e-1135
respiratory tract7.52e-1154
orifice8.47e-1136
reproductive structure3.78e-1059
reproductive system3.78e-1059
lung5.69e-1022
respiratory tube5.69e-1022
respiration organ5.69e-1022
pair of lungs5.69e-1022
lung primordium5.69e-1022
lung bud5.69e-1022
foregut1.55e-0987
thoracic segment of trunk4.85e-0952
respiratory system epithelium7.24e-0928
reproductive organ1.18e-0848
respiratory tract epithelium2.77e-0819
lung epithelium2.77e-0819
oral opening4.58e-0822
male organism1.46e-0722
male reproductive system1.46e-0722
respiratory primordium1.91e-0738
endoderm of foregut1.91e-0738
renal system2.40e-0748
trunk region element3.35e-07101
urinary system structure5.05e-0747
extraembryonic membrane5.79e-0714
membranous layer5.79e-0714
segment of respiratory tract6.28e-0747
internal genitalia6.74e-0725
mucosa7.07e-0720
male reproductive organ9.39e-0711
Disease
Ontology termp-valuen
carcinoma7.59e-26106
cell type cancer3.00e-18143
squamous cell carcinoma4.75e-1514
adenocarcinoma2.93e-0825


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)
MA0003.11.05935
MA0004.11.69588
MA0006.11.31813
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
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
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.13.6449
MA0058.12.50688
MA0059.12.50216
MA0060.11.01899
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.16.27432
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.13.86888
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.12.31225
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.14.51906
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.11.29536
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
MA0116.11.15856
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
MA0146.10.061409
MA0147.12.03364
MA0148.10.739888
MA0149.11.813
MA0062.20.931615
MA0035.20.778873
MA0039.20.777367
MA0138.20.928035
MA0002.20.98779
MA0137.20.558189
MA0104.21.79838
MA0047.20.856092
MA0112.20.551048
MA0065.24.98884
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.11.21162
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.13.02177
MA0160.10.756582
MA0161.10
MA0162.10.309472
MA0163.10.539587
MA0164.12.08227
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.216.1395
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
ATF3#467422.46317452600873.92475754624726e-060.000127654236490974
CTCF#1066445.360256373075030.001211145381643620.00820516427824846
EP300#203346.77394172622320.0004748459821442640.00435671084328954
GATA3#2625427.2365163572061.81561517799785e-066.80132832047766e-05
HDAC2#3066413.41562023662633.0859005065161e-050.00062897806986736
JUND#372746.994663941871030.000417684217818580.00392854124862704
MAX#414946.452555509007120.0005767613195645490.00486837270298245
MYC#460945.22228187160940.001344309395272740.00890230986829556
NANOG#79923429.24477848101271.36586687657858e-065.35271184701653e-05
SIN3A#2594245.408884726815140.001168172384885160.00798499611918456
SP1#666745.69838137814090.0009482606065333980.0068607820911494
TAF1#687243.343046285745290.008005664898701650.0323519438305023
TBP#690843.706770687096390.005296377814784350.0245179026904066
TCF12#6938410.63446490218647.8163066689251e-050.00120331257693967
TCF7L2#6934410.77017656313737.42969445082454e-050.00115865291735055
USF1#739146.361499277207960.0006105011399140830.00509388260377782
USF2#7392412.99219738506963.50833029870167e-050.000683594231466611
YY1#752844.911170749853860.00171871838055440.0107132932824065
ZEB1#6935416.88843201754391.22862303393937e-050.000305441944874063



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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