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Coexpression cluster:C1673: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.508327,1.20042,0.500341,0.654974,1.15291,0.653236,0.733342,0.324142,0.321368,0.106358,0.621241,0.778743,0.274093,0.721271,0.453496,0.478935,0.963929,0.395009,0.784337,1.54297,0.500405,0.384437,0.645033,1.14094,0.549618,0.802434,1.29435,0.642741,1.16016,1.90917,0.598009,1.00172,0.359091,0.27659,1.0713,0.432883,0.413782,0.654459,0.388123,0.301779,1.06799,0.580638,0.132849,0.451846,0.824538,0.533483,0.734485,0.609718,0.785708,0.458489,0.817229,0.746838,0.191745,1.08035,1.2359,0.724351,0.4631,0.689906,0.659455,0.688844,1.04369,0.736968,0.321912,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,0.330474,0.189341,1.23387,0.269111,0.255232,0.240727,0.917983,0.987729,0.543014,0.796279,0.934302,0.755403,0.327263,1.18161,0.0719601,0.166306,2.64291,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,0.455791,0.381528,0.28626,1.06255,0.849074,0.211081,1.01093,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,0.549347,0.437618,0.512457,1.05402,0.494368,0.631235,1.37132,0.412056,0.084145,0.596731,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.995523,1.15483,0.601055,1.28328,0.763715,1.43285,0.221105,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,2.0258,2.09294,0.577088,0.363423,0.526389,0.126633,1.15522,0.312599,0.736459,1.56426,0.827475,0.439798,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,0.731946,0.233587
|tfbs_overrepresentation_jaspar=MA0003.1;0.136928,MA0004.1;0.626788,MA0006.1;0.452993,MA0007.1;0.606704,MA0009.1;1.11255,MA0014.1;0.0418333,MA0017.1;0.496101,MA0019.1;1.84387,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;0.195817,MA0050.1;0.613347,MA0051.1;0.731787,MA0052.1;1.03442,MA0055.1;1.5062,MA0056.1;0,MA0057.1;0.189508,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;0.247962,MA0069.1;1.09737,MA0070.1;1.08584,MA0071.1;0.695094,MA0072.1;1.0812,MA0073.1;0.0469445,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;0.132006,MA0089.1;0,MA0090.1;0.556637,MA0091.1;1.52322,MA0092.1;0.588959,MA0093.1;0.456342,MA0095.1;0,MA0098.1;0,MA0100.1;0.750974,MA0101.1;0.459973,MA0103.1;0.442769,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;0.372523,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;0.442008,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;0.0118463,MA0138.2;0.837782,MA0002.2;0.30855,MA0137.2;0.47779,MA0104.2;0.320919,MA0047.2;0.767096,MA0112.2;0.136971,MA0065.2;0.146576,MA0150.1;0.550239,MA0151.1;0,MA0152.1;0.69926,MA0153.1;1.21379,MA0154.1;0.514087,MA0155.1;0.409315,MA0156.1;0.480289,MA0157.1;0.883854,MA0158.1;0,MA0159.1;0.386729,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;0.00207114,MA0102.2;1.66336,MA0258.1;0.345771,MA0259.1;0.395396,MA0442.1;0
}}
}}

Revision as of 20:05, 22 January 2013


Full id: C1673_salivary_Corneal_Keratinocyte_Sebocyte_Small_Bronchial_tongue



Phase1 CAGE Peaks

Hg19::chr12:52908631..52908640,-p@chr12:52908631..52908640
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Hg19::chr12:52908986..52908996,-p@chr12:52908986..52908996
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Hg19::chr12:52909007..52909012,-p@chr12:52909007..52909012
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Hg19::chr17:39740615..39740628,-p7@KRT14
Hg19::chr17:39741249..39741272,-p@chr17:39741249..39741272
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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
endo-epithelial cell2.34e-3642
endodermal cell6.91e-2758
respiratory epithelial cell3.06e-2413
epithelial cell of alimentary canal4.09e-1820
epithelial cell8.37e-18253
general ecto-epithelial cell7.66e-1514
epithelial cell of tracheobronchial tree2.69e-139
epithelial cell of lower respiratory tract2.69e-139
acinar cell8.74e-125
bronchial epithelial cell2.06e-113
acinar cell of salivary gland2.21e-113
gingival epithelial cell8.46e-113
duct epithelial cell1.22e-103
branched duct epithelial cell1.22e-103
tracheal epithelial cell1.22e-103
tracheoblast1.22e-103
protein secreting cell8.19e-106
stratified squamous epithelial cell1.25e-096
keratin accumulating cell1.25e-096
stratified epithelial cell1.25e-096
keratinizing barrier epithelial cell1.25e-096
epithelial fate stem cell1.25e-096
stratified epithelial stem cell1.25e-096
surface ectodermal cell1.25e-096
corneal epithelial cell2.34e-082
squamous epithelial cell2.91e-0863
transitional epithelial cell3.94e-084
urothelial cell3.94e-084
mammary gland epithelial cell7.91e-084
keratinocyte5.46e-075
embryonic cell6.90e-07250
Uber Anatomy
Ontology termp-valuen
oral opening2.79e-2222
respiratory system3.04e-2174
mouth6.18e-1929
stomodeum6.18e-1929
orifice8.48e-1736
endoderm-derived structure4.56e-16160
endoderm4.56e-16160
presumptive endoderm4.56e-16160
head1.25e-1456
surface structure1.45e-1499
anterior region of body2.39e-1462
craniocervical region2.39e-1462
subdivision of head1.88e-1349
tracheobronchial tree6.93e-1315
lower respiratory tract6.93e-1315
respiratory tract1.68e-1154
mouth mucosa1.95e-1113
lower respiratory tract epithelium2.06e-113
epithelium of bronchus2.06e-113
trachea3.61e-117
respiratory airway3.61e-117
gingival epithelium8.46e-113
tongue4.57e-103
gustatory system4.57e-103
future tongue4.57e-103
saliva-secreting gland2.15e-096
gland of oral region2.15e-096
gland of foregut2.15e-096
oral gland2.15e-096
oral cavity2.15e-096
mucosa4.71e-0920
digestive system1.41e-08145
digestive tract1.41e-08145
primitive gut1.41e-08145
mammary gland7.91e-084
mammary bud7.91e-084
mammary ridge7.91e-084
mammary placode7.91e-084
foregut8.41e-0887
thoracic cavity element8.66e-0834
thoracic cavity8.66e-0834
mucosa of oral region1.24e-074
respiratory system mucosa1.24e-074
thoracic segment organ1.64e-0735
segment of respiratory tract2.63e-0747
bronchus5.57e-075
open tracheal system trachea8.19e-072
Disease
Ontology termp-valuen
squamous cell carcinoma6.03e-1314


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)
MA0003.10.136928
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.10.0418333
MA0017.10.496101
MA0019.11.84387
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
MA0048.10.195817
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.11.5062
MA0056.10
MA0057.10.189508
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.0469445
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.132006
MA0089.10
MA0090.10.556637
MA0091.11.52322
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.10.175503
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.11.40074
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
MA0145.10.442008
MA0146.10.0359558
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.777733
MA0035.20.691506
MA0039.20.0118463
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.136971
MA0065.20.146576
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.514087
MA0155.10.409315
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.0592265
MA0163.10.382496
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.20.00207114
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

No analysis results for this cluster

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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