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{{Coexpression_clusters
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182559,0.164471,0.177664,0.313891,0.292462,0.026492,0.137165,0.467981,0.191837,0.0912568,0.320916,0.289812,0.384881,0.441686,0.369492,0.592234|tfbs_overrepresentation_for_novel_motifs=0.44418,0.333388,0.436508,0.58616,0.393082,0.584466,0.662701,0.269608,0.736703,0.94331,0.553339,0.707204,0.223349,0.650887,0.391663,0.415981,0.889639,3.34487,0.236034,0.402028,0.436569,0.0880431,0.576478,0.387783,0.483957,0.730467,0.585619,0.574247,0.396295,0.547818,0.530785,0.92701,0.302275,0.225641,0.35719,0.0334022,0.35388,0.585658,0.329602,0.248856,0.355745,0.513952,0.664116,0.390088,0.154075,0.468392,0.66382,0.542147,1.05432,0.396429,0.745008,0.675919,0.455399,1.00488,1.15929,0.653901,4.81797,0.62023,0.186533,0.619193,0.968558,0.666252,0.267534,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.275507,0.146905,1.15727,0.218784,3.28695,1.07049,0.84426,0.913168,0.477584,1.94676,0.86037,0.684313,0.272514,1.10535,0.181326,0.126687,0.181871,0.771626,1.71797,1.34233,1.07807,0.94406,0.30974,0.393853,2.36544,1.23175,0.987239,0.776336,0.166235,0.330999,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,0.647343,0.483695,0.376529,0.44815,0.978783,0.430775,0.563054,1.29401,0.352243,1.21803,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,0.324369,1.07876,0.53374,1.20639,0.692462,1.35529,0.999497,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,1.49651,0.424432,0.0926553,1.07915,0.717973,0.665754,1.48627,0.755083,0.378604,0.484017,0.454152,1.27379,1.06043,0.912368,0.457485,0.83286,0.683502,0.79772,2.6848,0.521461|tfbs_overrepresentation_jaspar=MA0003.1;0.026277,MA0004.1;0.558729,MA0006.1;0.391183,MA0007.1;0.539222,MA0009.1;1.03681,MA0014.1;0.262822,MA0017.1;1.10421,MA0019.1;0.7124,MA0024.1;0.929647,MA0025.1;1.17262,MA0027.1;2.65688,MA0028.1;0.408079,MA0029.1;0.949428,MA0030.1;0.937696,MA0031.1;0.871496,MA0038.1;0.665566,MA0040.1;0.955415,MA0041.1;0.578072,MA0042.1;0.544748,MA0043.1;1.03713,MA0046.1;1.02569,MA0048.1;2.08744,MA0050.1;0.545671,MA0051.1;0.661179,MA0052.1;0.959373,MA0055.1;0.465994,MA0056.1;0,MA0057.1;0.147053,MA0058.1;0.458909,MA0059.1;0.457555,MA0060.1;0.267412,MA0061.1;1.93637,MA0063.1;0,MA0066.1;0.66601,MA0067.1;1.35893,MA0068.1;0.199491,MA0069.1;1.02175,MA0070.1;1.01032,MA0071.1;0.625297,MA0072.1;1.00572,MA0073.1;0.00563817,MA0074.1;0.660398,MA0076.1;0.475586,MA0077.1;0.997832,MA0078.1;0.763954,MA0081.1;0.457725,MA0083.1;1.04447,MA0084.1;1.5477,MA0087.1;1.00322,MA0088.1;0.660742,MA0089.1;0,MA0090.1;2.13027,MA0091.1;0.561458,MA0092.1;0.522012,MA0093.1;0.394379,MA0095.1;0,MA0098.1;0,MA0100.1;0.679972,MA0101.1;0.397846,MA0103.1;0.381434,MA0105.1;0.830067,MA0106.1;1.68738,MA0107.1;0.320267,MA0108.2;0.868347,MA0109.1;0,MA0111.1;0.504913,MA0113.1;0.725375,MA0114.1;0.314898,MA0115.1;1.28169,MA0116.1;0.865577,MA0117.1;1.07516,MA0119.1;0.440684,MA0122.1;1.10154,MA0124.1;1.23968,MA0125.1;1.15445,MA0130.1;0,MA0131.1;0.782708,MA0132.1;0,MA0133.1;0,MA0135.1;1.06778,MA0136.1;0.672893,MA0139.1;0.226048,MA0140.1;0.622527,MA0141.1;0.455728,MA0142.1;0.838805,MA0143.1;1.72302,MA0144.1;0.299851,MA0145.1;1.16614,MA0146.1;0.232472,MA0147.1;0.327615,MA0148.1;0.584698,MA0149.1;0.612449,MA0062.2;0.23336,MA0035.2;0.621793,MA0039.2;0.35955,MA0138.2;0.765223,MA0002.2;0.255126,MA0137.2;0.414885,MA0104.2;0.26661,MA0047.2;0.695777,MA0112.2;0.680553,MA0065.2;0.718489,MA0150.1;0.484557,MA0151.1;0,MA0152.1;0.629368,MA0153.1;1.13732,MA0154.1;0.132326,MA0155.1;0.65596,MA0156.1;0.417278,MA0157.1;0.810597,MA0158.1;0,MA0159.1;0.328286,MA0160.1;0.600559,MA0161.1;0,MA0162.1;0.62636,MA0163.1;0.113377,MA0164.1;0.738243,MA0080.2;0.394469,MA0018.2;0.709805,MA0099.2;1.52352,MA0079.2;5.9246e-06,MA0102.2;1.58513,MA0258.1;0.788656,MA0259.1;0.336472,MA0442.1;0}}
|full_id=C1302_keratoacanthoma_cervical_immature_salivary_malignant_oral_Keratinocyte
|id=C1302
}}

Latest revision as of 11:42, 17 September 2013


Full id: C1302_keratoacanthoma_cervical_immature_salivary_malignant_oral_Keratinocyte



Phase1 CAGE Peaks

Hg19::chr10:123845246..123845261,+p@chr10:123845246..123845261
+
Hg19::chr10:123845267..123845279,+p@chr10:123845267..123845279
+
Hg19::chr10:123845284..123845296,+p@chr10:123845284..123845296
+
Hg19::chr18:28622680..28622694,-p5@DSC3
Hg19::chr1:204885187..204885205,+p@chr1:204885187..204885205
+
Hg19::chr6:113971282..113971295,-p1@ENST00000427157


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 cell2.88e-4042
endodermal cell2.27e-2958
epithelial cell of alimentary canal4.78e-2620
respiratory epithelial cell3.41e-2013
epithelial cell3.02e-19253
acinar cell2.04e-155
general ecto-epithelial cell2.33e-1514
protein secreting cell8.95e-136
transitional epithelial cell5.29e-124
urothelial cell5.29e-124
epithelial cell of tracheobronchial tree7.67e-119
epithelial cell of lower respiratory tract7.67e-119
squamous epithelial cell1.39e-1063
acinar cell of salivary gland3.82e-103
gingival epithelial cell1.31e-093
bronchial epithelial cell3.46e-093
duct epithelial cell3.88e-093
branched duct epithelial cell3.88e-093
tracheal epithelial cell3.88e-093
tracheoblast3.88e-093
glandular epithelial cell2.30e-089
stratified squamous epithelial cell3.46e-086
keratin accumulating cell3.46e-086
stratified epithelial cell3.46e-086
keratinizing barrier epithelial cell3.46e-086
epithelial fate stem cell3.46e-086
stratified epithelial stem cell3.46e-086
surface ectodermal cell3.46e-086
epidermal cell4.94e-089
ecto-epithelial cell4.95e-0834
embryonic cell1.74e-07250
sebum secreting cell5.83e-072
epithelial cell of sweat gland5.83e-072
epithelial cell of skin gland5.83e-072
acinar cell of sebaceous gland5.83e-072
Uber Anatomy
Ontology termp-valuen
orifice3.05e-2136
respiratory system9.41e-2174
oral opening9.36e-2022
endoderm-derived structure6.47e-19160
endoderm6.47e-19160
presumptive endoderm6.47e-19160
surface structure3.33e-1899
mouth1.04e-1629
stomodeum1.04e-1629
anterior region of body6.68e-1562
craniocervical region6.68e-1562
urothelium3.10e-145
mouth mucosa1.65e-1313
neck1.10e-1210
mucosa1.28e-1220
head2.23e-1256
digestive system2.87e-12145
digestive tract2.87e-12145
primitive gut2.87e-12145
mucosa of oral region3.07e-124
respiratory system mucosa3.07e-124
respiratory tract6.33e-1254
transitional epithelium8.39e-126
subdivision of head2.27e-1149
pharynx4.63e-1111
tracheobronchial tree1.70e-1015
lower respiratory tract1.70e-1015
gingival epithelium1.31e-093
trachea1.66e-097
respiratory airway1.66e-097
lower respiratory tract epithelium3.46e-093
epithelium of bronchus3.46e-093
chordate pharynx5.11e-0910
pharyngeal region of foregut5.11e-0910
tongue5.89e-093
gustatory system5.89e-093
future tongue5.89e-093
subdivision of digestive tract6.41e-09118
segment of respiratory tract4.93e-0847
foregut9.86e-0887
skin gland5.83e-072
epidermis gland5.83e-072
gland of integumental system5.83e-072
sebaceous gland5.83e-072
skin sebaceous gland5.83e-072
sweat gland5.83e-072
sweat gland placode5.83e-072
sebaceous gland placode5.83e-072
gland of gut5.97e-0710
Disease
Ontology termp-valuen
squamous cell carcinoma1.78e-1914


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)
MA0003.10.026277
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.10.262822
MA0017.11.10421
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.12.08744
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.465994
MA0056.10
MA0057.10.147053
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.11.93637
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.00563817
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.660742
MA0089.10
MA0090.12.13027
MA0091.10.561458
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.10.830067
MA0106.11.68738
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.10.865577
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.10.226048
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.11.72302
MA0144.10.299851
MA0145.11.16614
MA0146.10.232472
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.20.35955
MA0138.20.765223
MA0002.20.255126
MA0137.20.414885
MA0104.20.26661
MA0047.20.695777
MA0112.20.680553
MA0065.20.718489
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.132326
MA0155.10.65596
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.10.62636
MA0163.10.113377
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.21.52352
MA0079.25.9246e-06
MA0102.21.58513
MA0258.10.788656
MA0259.10.336472
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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