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Coexpression cluster:C1817: Difference between revisions

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{{Coexpression_clusters
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50943,MA0009.1;1.11255,MA0014.1;2.48957,MA0017.1;0.496101,MA0019.1;0.784036,MA0024.1;1.00439,MA0025.1;1.24931,MA0027.1;2.73598,MA0028.1;3.05902,MA0029.1;1.02437,MA0030.1;1.01252,MA0031.1;0.945567,MA0038.1;0.736268,MA0040.1;1.03042,MA0041.1;0.64667,MA0042.1;0.612397,MA0043.1;1.11288,MA0046.1;1.10134,MA0048.1;1.7027,MA0050.1;0.613347,MA0051.1;0.731787,MA0052.1;1.03442,MA0055.1;0.0853006,MA0056.1;0,MA0057.1;0.554727,MA0058.1;0.523638,MA0059.1;0.522232,MA0060.1;0.321781,MA0061.1;0.291022,MA0063.1;0,MA0066.1;0.736721,MA0067.1;1.43651,MA0068.1;0.692739,MA0069.1;1.09737,MA0070.1;1.08584,MA0071.1;0.695094,MA0072.1;1.0812,MA0073.1;0.551452,MA0074.1;0.730989,MA0076.1;2.29573,MA0077.1;1.07324,MA0078.1;0.836493,MA0081.1;1.2972,MA0083.1;1.12028,MA0084.1;1.62584,MA0087.1;1.07867,MA0088.1;0.818263,MA0089.1;0,MA0090.1;2.34702,MA0091.1;0.629594,MA0092.1;0.588959,MA0093.1;0.456342,MA0095.1;0,MA0098.1;0,MA0100.1;0.750974,MA0101.1;0.459973,MA0103.1;1.96988,MA0105.1;0.175503,MA0106.1;0.779931,MA0107.1;0.378225,MA0108.2;0.94238,MA0109.1;0,MA0111.1;1.40074,MA0113.1;0.797251,MA0114.1;0.973423,MA0115.1;1.35895,MA0116.1;0.994489,MA0117.1;1.1512,MA0119.1;0.504689,MA0122.1;1.17777,MA0124.1;1.31673,MA0125.1;1.23103,MA0130.1;0,MA0131.1;0.855546,MA0132.1;0,MA0133.1;0,MA0135.1;1.14377,MA0136.1;1.76068,MA0139.1;0.277033,MA0140.1;0.692258,MA0141.1;0.520334,MA0142.1;0.912455,MA0143.1;0.797437,MA0144.1;0.938075,MA0145.1;0.868598,MA0146.1;0.143081,MA0147.1;0.386018,MA0148.1;0.653474,MA0149.1;0.681935,MA0062.2;4.92942,MA0035.2;0.691506,MA0039.2;1.12758,MA0138.2;0.837782,MA0002.2;0.30855,MA0137.2;1.20193,MA0104.2;0.320919,MA0047.2;0.767096,MA0112.2;0.136971,MA0065.2;3.49428,MA0150.1;0.550239,MA0151.1;0,MA0152.1;0.69926,MA0153.1;1.21379,MA0154.1;0.514087,MA0155.1;0.130813,MA0156.1;1.20729,MA0157.1;0.883854,MA0158.1;0,MA0159.1;0.386729,MA0160.1;0.669748,MA0161.1;0,MA0162.1;0.0592265,MA0163.1;1.05321,MA0164.1;0.810347,MA0080.2;0.456437,MA0018.2;0.781393,MA0099.2;0.699641,MA0079.2;3.15891,MA0102.2;1.66336,MA0258.1;0.345771,MA0259.1;0.395396,MA0442.1;0}}
|full_id=C1817_Alveolar_smallcell_acantholytic_Hepatocyte_squamous_liver_mesothelioma
|id=C1817
}}

Latest revision as of 11:52, 17 September 2013


Full id: C1817_Alveolar_smallcell_acantholytic_Hepatocyte_squamous_liver_mesothelioma



Phase1 CAGE Peaks

Hg19::chr19:35739597..35739627,+p4@LSR
Hg19::chr19:35739631..35739674,+p2@LSR
Hg19::chr19:35739679..35739690,+p6@LSR
Hg19::chr19:35739871..35739882,+p3@LSR
Hg19::chr19:35739897..35739920,+p1@LSR


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 cell1.65e-24253
endodermal cell1.05e-1258
endo-epithelial cell1.37e-1242
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure1.22e-14160
endoderm1.22e-14160
presumptive endoderm1.22e-14160
trunk region element1.89e-13101
subdivision of digestive tract1.21e-11118
renal system2.08e-1148
digestive system3.59e-11145
digestive tract3.59e-11145
primitive gut3.59e-11145
urinary system structure3.71e-1147
adult organism5.50e-11114
foregut2.02e-0987
abdomen element5.12e-0954
abdominal segment element5.12e-0954
endo-epithelium1.24e-0882
organ part3.66e-08218
cavitated compound organ4.20e-0831
kidney5.86e-0826
kidney mesenchyme5.86e-0826
upper urinary tract5.86e-0826
kidney rudiment5.86e-0826
kidney field5.86e-0826
subdivision of trunk1.37e-07112
respiratory system3.00e-0774
immaterial anatomical entity6.41e-07117
organ6.54e-07503
Disease
Ontology termp-valuen
carcinoma6.90e-21106
cell type cancer2.27e-12143
squamous cell carcinoma5.93e-0814
adenocarcinoma2.66e-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)
MA0003.11.80249
MA0004.10.626788
MA0006.10.452993
MA0007.12.50943
MA0009.11.11255
MA0014.12.48957
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.13.05902
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
MA0048.11.7027
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.0853006
MA0056.10
MA0057.10.554727
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.692739
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.551452
MA0074.10.730989
MA0076.12.29573
MA0077.11.07324
MA0078.10.836493
MA0081.11.2972
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.818263
MA0089.10
MA0090.12.34702
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.11.96988
MA0105.10.175503
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.11.40074
MA0113.10.797251
MA0114.10.973423
MA0115.11.35895
MA0116.10.994489
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
MA0136.11.76068
MA0139.10.277033
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.938075
MA0145.10.868598
MA0146.10.143081
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.24.92942
MA0035.20.691506
MA0039.21.12758
MA0138.20.837782
MA0002.20.30855
MA0137.21.20193
MA0104.20.320919
MA0047.20.767096
MA0112.20.136971
MA0065.23.49428
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.514087
MA0155.10.130813
MA0156.11.20729
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.0592265
MA0163.11.05321
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.23.15891
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#90545.068961261570110.002709998091280770.0148978571773488
CTCF#1066444.288205098460020.005152015588243280.0239366233382508
E2F1#186954.907389214879320.0003512818099256460.00352900355394618
E2F4#1874410.13444825222760.0001818201509632970.00220342477911996
ELF1#199754.258097958807540.0007142416939776840.0057327611648736
ELK4#2005516.2356816584688.85705446514576e-073.8239847510763e-05
EP300#203356.77394172622327.00901578206049e-050.00110844124661208
FOXA1#3169511.08141974938555.98116883436141e-060.000178987762719734
FOXA2#3170524.63046375266521.10174651693954e-076.40318889719803e-06
GABPB1#255357.067683836182175.6685482528729e-050.00094844202336077
HMGN3#932458.178547723350592.73180911341838e-050.000582022464292742
IRF1#365957.63716375356393.84754333311872e-050.00072441604140542
IRF4#3662521.91451268674411.97628413609567e-071.07054532619137e-05
JUND#372756.994663941871035.97069468343598e-050.000984175161053298
NANOG#79923211.69791139240510.01091164951956080.0402273911600625
RDBP#7936261.455361596010.0004178191022410310.00391009043180565
SIN3A#2594255.408884726815140.0002159522671657270.00248117038839619
SIX5#147912517.0867153554596.86007756253503e-073.10021480118389e-05
SMARCC2#6601594.15537442689761.34457127652426e-101.43731504144234e-08
SP1#666755.69838137814090.000166391843712550.00204348515586724
SPI1#668858.204323508522732.68916109982495e-050.000574577119690298
TAF1#687253.343046285745290.002394600090870310.0135403161283381
TBP#690853.706770687096390.001428755106721120.00918998303817499
TFAP2C#7022510.80922860986026.77323239348459e-060.000197264254864232
ZEB1#6935516.88843201754397.27243686732534e-073.23065093146147e-05
ZNF263#1012758.221841637010682.6606316672286e-050.000571051604384891



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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