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Coexpression cluster:C2015: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;1.04569,MA0004.1;0.626788,MA0006.1;0.452993,MA0007.1;0.606704,MA0009.1;1.11255,MA0014.1;5.83725,MA0017.1;0.496101,MA0019.1;0.784036,MA0024.1;1.00439,MA0025.1;1.24931,MA0027.1;2.73598,MA0028.1;1.18667,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;0.569896,MA0050.1;0.613347,MA0051.1;0.731787,MA0052.1;1.03442,MA0055.1;0.0853006,MA0056.1;0,MA0057.1;0.189508,MA0058.1;0.523638,MA0059.1;0.522232,MA0060.1;0.321781,MA0061.1;3.05948,MA0063.1;0,MA0066.1;0.736721,MA0067.1;1.43651,MA0068.1;0.247962,MA0069.1;1.09737,MA0070.1;1.08584,MA0071.1;0.695094,MA0072.1;1.0812,MA0073.1;0.00220137,MA0074.1;0.730989,MA0076.1;0.540943,MA0077.1;1.07324,MA0078.1;0.836493,MA0081.1;0.522409,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;2.02769,MA0103.1;1.12656,MA0105.1;3.01153,MA0106.1;5.8503,MA0107.1;2.62998,MA0108.2;0.94238,MA0109.1;0,MA0111.1;0.5713,MA0113.1;0.797251,MA0114.1;0.372523,MA0115.1;1.35895,MA0116.1;0.382106,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;0.743749,MA0139.1;0.277033,MA0140.1;0.692258,MA0141.1;0.520334,MA0142.1;0.912455,MA0143.1;0.797437,MA0144.1;0.356507,MA0145.1;1.39943,MA0146.1;0.0359558,MA0147.1;0.386018,MA0148.1;0.653474,MA0149.1;0.681935,MA0062.2;0.777733,MA0035.2;0.691506,MA0039.2;1.92202,MA0138.2;0.837782,MA0002.2;0.30855,MA0137.2;0.47779,MA0104.2;0.320919,MA0047.2;0.767096,MA0112.2;0.425004,MA0065.2;1.41695,MA0150.1;0.550239,MA0151.1;0,MA0152.1;0.69926,MA0153.1;1.21379,MA0154.1;7.52681,MA0155.1;0.409315,MA0156.1;3.10266,MA0157.1;0.883854,MA0158.1;0,MA0159.1;3.65431,MA0160.1;0.669748,MA0161.1;0,MA0162.1;0.0592265,MA0163.1;0.382496,MA0164.1;0.810347,MA0080.2;0.456437,MA0018.2;0.781393,MA0099.2;0.699641,MA0079.2;0.230892,MA0102.2;1.66336,MA0258.1;0.345771,MA0259.1;0.395396,MA0442.1;0
}}
}}

Revision as of 20:21, 22 January 2013


Full id: C2015_small_squamous_amniotic_rectal_malignant_maxillary_oral



Phase1 CAGE Peaks

Hg19::chr8:82644522..82644557,-p4@ZFAND1
Hg19::chr8:82644562..82644654,-p2@ZFAND1
Hg19::chr8:82644655..82644687,-p3@ZFAND1
Hg19::chr8:82644669..82644738,+p1@CHMP4C
Hg19::chr8:82644741..82644791,+p2@CHMP4C


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 cell5.87e-49253
endodermal cell3.76e-2258
endo-epithelial cell3.08e-2042
epithelial cell of alimentary canal4.98e-1120
respiratory epithelial cell7.94e-0813
epithelial cell of lung2.82e-0719
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure2.12e-30160
endoderm2.12e-30160
presumptive endoderm2.12e-30160
digestive system1.82e-24145
digestive tract1.82e-24145
primitive gut1.82e-24145
subdivision of digestive tract5.16e-23118
foregut1.41e-1887
respiratory system4.94e-1774
endo-epithelium1.66e-1682
trunk region element9.42e-15101
immaterial anatomical entity2.03e-14117
respiratory tract3.78e-1454
respiratory primordium9.31e-1338
endoderm of foregut9.31e-1338
anatomical space2.40e-1295
primordium1.19e-11160
epithelial bud1.57e-1037
segment of respiratory tract1.57e-1047
organ1.63e-09503
epithelial fold2.16e-0947
urinary system structure6.53e-0947
renal system1.68e-0848
lung2.24e-0822
respiratory tube2.24e-0822
respiration organ2.24e-0822
pair of lungs2.24e-0822
lung primordium2.24e-0822
lung bud2.24e-0822
thoracic cavity element3.20e-0834
thoracic cavity3.20e-0834
thoracic segment organ9.59e-0835
organ segment1.06e-0798
subdivision of trunk1.36e-07112
organ part1.85e-07218
organism subdivision2.57e-07264
respiratory tract epithelium2.82e-0719
lung epithelium2.82e-0719
gut epithelium3.25e-0754
gland3.25e-0759
respiratory system epithelium6.47e-0728
Disease
Ontology termp-valuen
carcinoma8.19e-40106
cell type cancer5.90e-33143
cancer2.50e-15235
disease of cellular proliferation6.29e-15239
adenocarcinoma1.26e-1025
squamous cell carcinoma1.58e-1014


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)
MA0003.11.04569
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.15.83725
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.11.18667
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
MA0048.10.569896
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.0853006
MA0056.10
MA0057.10.189508
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.13.05948
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.00220137
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
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
MA0101.12.02769
MA0103.11.12656
MA0105.13.01153
MA0106.15.8503
MA0107.12.62998
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.10.382106
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
MA0136.10.743749
MA0139.10.277033
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.11.39943
MA0146.10.0359558
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.777733
MA0035.20.691506
MA0039.21.92202
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.425004
MA0065.21.41695
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.17.52681
MA0155.10.409315
MA0156.13.10266
MA0157.10.883854
MA0158.10
MA0159.13.65431
MA0160.10.669748
MA0161.10
MA0162.10.0592265
MA0163.10.382496
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.20.230892
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#90556.336201576962639.78880505817628e-050.00139187612181194
E2F1#186954.907389214879320.0003512818099256460.00353580579672557
E2F6#187655.017155731697390.0003144978599297790.0032331766899504
EBF1#187958.9064668465691.78355672307702e-050.000406887026215467
ELF1#199754.258097958807540.0007142416939776840.00573893585761928
FOSL2#2355516.93020060456177.18315284751475e-073.21285353422524e-05
FOXA1#3169511.08141974938555.98116883436141e-060.00017934748546996
FOXA2#3170524.63046375266521.10174651693954e-076.41389657093916e-06
GABPB1#255357.067683836182175.6685482528729e-050.000949811504864098
HEY1#2346254.040111043105710.0009288852205177990.00675099815905765
HMGN3#932458.178547723350592.73180911341838e-050.000582973870037397
MXI1#460159.96157162875931.01894348670516e-050.000266844129408225
MYC#460955.22228187160940.0002573944848850610.00276848842501657
SIN3A#2594255.408884726815140.0002159522671657270.00248390295490323
TAF1#687253.343046285745290.002394600090870310.0135579333671476
TBP#690853.706770687096390.001428755106721120.00920529022768953
TCF7L2#6934510.77017656313736.89693748574565e-060.000200252781227075
USF1#739156.361499277207969.59569864925045e-050.00137113855688749
YY1#752854.911170749853860.00034993140821360.00353242667141118



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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