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Coexpression cluster:C564: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.157827,1.0879,0.464859,0.718081,0.789854,0.25764,0.318839,0.470337,1.71171,5.40049,0.234283,0.355038,0.0400361,0.832947,1.28063,0.431887,0.511522,0.0927064,0.388593,0.306606,0.152859,1.75461,0.701134,1.26563,0.18461,0.374311,2.79055,0.249905,1.29855,0.274385,3.38816,0.544857,1.4042,0.15896,0.104423,0.266293,0.33558,0.258546,0.299553,0.0503272,0.103604,0.205653,0.373399,0.123709,1.78486,0.173971,0.319738,0.226038,0.541305,1.29907,0.386472,0.329494,0.625622,0.615394,0.758742,0.311792,0.407898,0.778218,0.509529,0.284391,0.582323,1.55141,2.26328,0.48664,0.893874,0.456015,0.843028,1.20113,0.535417,1.04233,1.08274,0.0621482,0.0732084,0.756844,0.0383048,0.913924,0.532449,0.471562,0.532468,0.18023,0.0470011,0.48568,0.336303,0.219253,0.70821,0.14461,0.0552506,1.15199,0.408949,1.29895,0.932961,0.68283,0.560183,0.571383,1.2891,0.60642,0.0444202,0.599297,0.412954,0.229879,0.0899484,0.555021,0.594155,0.514828,0.445845,0.230832,0.500571,0.826592,1.63868,0.370056,0.160439,0.591605,4.34355,0.241506,0.886618,0.681552,0.186245,0.216858,2.00748,0.0803321,0.748992,1.0486,0.255485,0.914205,0.993708,0.472239,0.313614,0.564749,0.78949,0.608973,0.683478,0.219902,0.803201,0.342946,0.945426,1.5144,0.611533,0.250344,0.904406,1.74999,1.35069,0.868456,0.315034,0.596045,0.447394,0.278424,1.10486,1.59165,0.203207,1.96638,0.063941,0.193567,0.683836,0.201134,0.859679,1.07219,0.394947,0.373254,0.184652,2.17867,0.867287,0.66649,0.531753,0.499061,0.46162,0.335644,0.0708512,0.317742,3.32302
|tfbs_overrepresentation_for_novel_motifs=0.157827,1.0879,0.464859,0.718081,0.789854,0.25764,0.318839,0.470337,1.71171,5.40049,0.234283,0.355038,0.0400361,0.832947,1.28063,0.431887,0.511522,0.0927064,0.388593,0.306606,0.152859,1.75461,0.701134,1.26563,0.18461,0.374311,2.79055,0.249905,1.29855,0.274385,3.38816,0.544857,1.4042,0.15896,0.104423,0.266293,0.33558,0.258546,0.299553,0.0503272,0.103604,0.205653,0.373399,0.123709,1.78486,0.173971,0.319738,0.226038,0.541305,1.29907,0.386472,0.329494,0.625622,0.615394,0.758742,0.311792,0.407898,0.778218,0.509529,0.284391,0.582323,1.55141,2.26328,0.48664,0.893874,0.456015,0.843028,1.20113,0.535417,1.04233,1.08274,0.0621482,0.0732084,0.756844,0.0383048,0.913924,0.532449,0.471562,0.532468,0.18023,0.0470011,0.48568,0.336303,0.219253,0.70821,0.14461,0.0552506,1.15199,0.408949,1.29895,0.932961,0.68283,0.560183,0.571383,1.2891,0.60642,0.0444202,0.599297,0.412954,0.229879,0.0899484,0.555021,0.594155,0.514828,0.445845,0.230832,0.500571,0.826592,1.63868,0.370056,0.160439,0.591605,4.34355,0.241506,0.886618,0.681552,0.186245,0.216858,2.00748,0.0803321,0.748992,1.0486,0.255485,0.914205,0.993708,0.472239,0.313614,0.564749,0.78949,0.608973,0.683478,0.219902,0.803201,0.342946,0.945426,1.5144,0.611533,0.250344,0.904406,1.74999,1.35069,0.868456,0.315034,0.596045,0.447394,0.278424,1.10486,1.59165,0.203207,1.96638,0.063941,0.193567,0.683836,0.201134,0.859679,1.07219,0.394947,0.373254,0.184652,2.17867,0.867287,0.66649,0.531753,0.499061,0.46162,0.335644,0.0708512,0.317742,3.32302
|tfbs_overrepresentation_jaspar=MA0003.1;0.257142,MA0004.1;0.238283,MA0006.1;0.392773,MA0007.1;1.85633,MA0009.1;0.644692,MA0014.1;0.00796524,MA0017.1;0.45828,MA0019.1;0.359322,MA0024.1;0.547222,MA0025.1;0.771296,MA0027.1;2.23171,MA0028.1;0.419336,MA0029.1;0.565022,MA0030.1;0.554453,MA0031.1;0.495474,MA0038.1;0.321141,MA0040.1;0.570428,MA0041.1;0.252793,MA0042.1;0.646075,MA0043.1;0.644989,MA0046.1;0.634468,MA0048.1;0.0172925,MA0050.1;0.228625,MA0051.1;0.317617,MA0052.1;0.574006,MA0055.1;0.715233,MA0056.1;0,MA0057.1;0.0158853,MA0058.1;0.167587,MA0059.1;0.166682,MA0060.1;0.0584466,MA0061.1;1.52826,MA0063.1;0,MA0066.1;0.321498,MA0067.1;0.948938,MA0068.1;0.128042,MA0069.1;0.630852,MA0070.1;0.620368,MA0071.1;0.289163,MA0072.1;0.616162,MA0073.1;1.88779e-05,MA0074.1;0.316991,MA0076.1;0.528959,MA0077.1;0.608956,MA0078.1;0.402443,MA0081.1;0.166796,MA0083.1;0.651755,MA0084.1;1.13204,MA0087.1;0.613875,MA0088.1;0.583662,MA0089.1;0,MA0090.1;0.189305,MA0091.1;0.240316,MA0092.1;1.14306,MA0093.1;0.12631,MA0095.1;0,MA0098.1;0,MA0100.1;0.885358,MA0101.1;0.403202,MA0103.1;0.118522,MA0105.1;1.1728,MA0106.1;20.2925,MA0107.1;1.0064,MA0108.2;0.492699,MA0109.1;0,MA0111.1;0.199239,MA0113.1;0.370073,MA0114.1;0.985949,MA0115.1;0.874839,MA0116.1;0.607827,MA0117.1;0.680135,MA0119.1;1.47085,MA0122.1;0.70466,MA0124.1;0.834787,MA0125.1;0.75419,MA0130.1;0,MA0131.1;1.07372,MA0132.1;0,MA0133.1;0,MA0135.1;0.673296,MA0136.1;0.87256,MA0139.1;0.364861,MA0140.1;0.286995,MA0141.1;0.165463,MA0142.1;0.4668,MA0143.1;0.370225,MA0144.1;0.25687,MA0145.1;0.650967,MA0146.1;2.03552,MA0147.1;0.0881384,MA0148.1;0.257816,MA0149.1;0.279141,MA0062.2;0.67985,MA0035.2;0.286421,MA0039.2;0.0506563,MA0138.2;0.403517,MA0002.2;0.0530127,MA0137.2;0.430142,MA0104.2;0.0580852,MA0047.2;0.345656,MA0112.2;1.56287,MA0065.2;0.0080232,MA0150.1;0.185024,MA0151.1;0,MA0152.1;0.292357,MA0153.1;0.738108,MA0154.1;0.542249,MA0155.1;0.576832,MA0156.1;0.854962,MA0157.1;0.442323,MA0158.1;0,MA0159.1;0.29763,MA0160.1;0.743405,MA0161.1;0,MA0162.1;0.0485277,MA0163.1;0.864319,MA0164.1;0.380804,MA0080.2;0.793571,MA0018.2;1.67652,MA0099.2;0.292649,MA0079.2;3.01277e-05,MA0102.2;1.16862,MA0258.1;0.890751,MA0259.1;2.16017,MA0442.1;0
}}
}}

Revision as of 19:16, 22 January 2013


Full id: C564_Small_salivary_Corneal_Bronchial_Urothelial_Keratinocyte_Tracheal



Phase1 CAGE Peaks

Hg19::chr11:72432903..72432945,-p7@ARAP1
Hg19::chr17:4762391..4762450,+p@chr17:4762391..4762450
+
Hg19::chr17:4762451..4762477,+p@chr17:4762451..4762477
+
Hg19::chr1:2359091..2359102,+p@chr1:2359091..2359102
+
Hg19::chr1:2359111..2359148,+p@chr1:2359111..2359148
+
Hg19::chr1:2359155..2359168,+p@chr1:2359155..2359168
+
Hg19::chr1:2360057..2360066,+p@chr1:2360057..2360066
+
Hg19::chr1:2360073..2360082,+p@chr1:2360073..2360082
+
Hg19::chr1:2360084..2360095,+p@chr1:2360084..2360095
+
Hg19::chr1:2360109..2360129,+p@chr1:2360109..2360129
+
Hg19::chr1:2360132..2360167,+p@chr1:2360132..2360167
+
Hg19::chr2:131669765..131669776,+p@chr2:131669765..131669776
+
Hg19::chr2:131669791..131669801,+p@chr2:131669791..131669801
+
Hg19::chr2:131669803..131669810,+p@chr2:131669803..131669810
+
Hg19::chr2:131669820..131669838,+p@chr2:131669820..131669838
+
Hg19::chr4:159092554..159092575,+p2@ENST00000505532


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><br>

Cell Type
Ontology termp-valuen
endo-epithelial cell1.85e-3342
respiratory epithelial cell2.80e-2513
general ecto-epithelial cell4.55e-2314
endodermal cell1.40e-2258
acinar cell4.06e-175
epithelial cell4.00e-16253
epithelial cell of alimentary canal1.75e-1420
protein secreting cell3.31e-146
transitional epithelial cell3.53e-144
urothelial cell3.53e-144
epithelial cell of tracheobronchial tree1.13e-139
epithelial cell of lower respiratory tract1.13e-139
ecto-epithelial cell6.62e-1234
duct epithelial cell2.28e-113
branched duct epithelial cell2.28e-113
tracheal epithelial cell2.28e-113
tracheoblast2.28e-113
bronchial epithelial cell2.90e-113
gingival epithelial cell8.74e-113
acinar cell of salivary gland9.98e-113
epithelial cell of Malassez1.92e-103
epidermal cell9.04e-109
stratified squamous epithelial cell1.19e-096
keratin accumulating cell1.19e-096
stratified epithelial cell1.19e-096
keratinizing barrier epithelial cell1.19e-096
epithelial fate stem cell1.19e-096
stratified epithelial stem cell1.19e-096
surface ectodermal cell1.19e-096
glandular epithelial cell2.41e-099
corneal epithelial cell2.79e-082
sebum secreting cell4.22e-082
epithelial cell of sweat gland4.22e-082
epithelial cell of skin gland4.22e-082
acinar cell of sebaceous gland4.22e-082
mammary gland epithelial cell5.40e-084
embryonic cell1.08e-07250
keratinocyte4.75e-075
Uber Anatomy
Ontology termp-valuen
respiratory system2.13e-1974
surface structure8.36e-1699
endoderm-derived structure4.96e-15160
endoderm4.96e-15160
presumptive endoderm4.96e-15160
anterior region of body5.00e-1462
craniocervical region5.00e-1462
oral opening8.90e-1322
orifice3.28e-1236
respiratory tract8.51e-1254
urothelium2.41e-115
lower respiratory tract epithelium2.90e-113
epithelium of bronchus2.90e-113
mouth3.05e-1129
stomodeum3.05e-1129
head4.01e-1156
gingival epithelium8.74e-113
tracheobronchial tree2.18e-1015
lower respiratory tract2.18e-1015
transitional epithelium1.89e-096
digestive system1.85e-08145
digestive tract1.85e-08145
primitive gut1.85e-08145
subdivision of head2.00e-0849
mouth mucosa2.05e-0813
skin gland4.22e-082
epidermis gland4.22e-082
gland of integumental system4.22e-082
sebaceous gland4.22e-082
skin sebaceous gland4.22e-082
sweat gland4.22e-082
sweat gland placode4.22e-082
sebaceous gland placode4.22e-082
trachea5.23e-087
respiratory airway5.23e-087
mammary gland5.40e-084
mammary bud5.40e-084
mammary ridge5.40e-084
mammary placode5.40e-084
jaw skeleton6.23e-084
splanchnocranium6.23e-084
thoracic cavity element6.53e-0834
thoracic cavity6.53e-0834
skin epidermis9.37e-0815
outer epithelium9.37e-0815
enveloping layer of ectoderm9.37e-0815
gland of gut9.63e-0810
thoracic segment organ1.25e-0735
epithelial fold1.31e-0747
neck2.70e-0710
mucosa5.84e-0720
epithelial bud6.17e-0737
bronchus6.79e-075
foregut9.06e-0787


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)
MA0003.10.257142
MA0004.10.238283
MA0006.10.392773
MA0007.11.85633
MA0009.10.644692
MA0014.10.00796524
MA0017.10.45828
MA0019.10.359322
MA0024.10.547222
MA0025.10.771296
MA0027.12.23171
MA0028.10.419336
MA0029.10.565022
MA0030.10.554453
MA0031.10.495474
MA0038.10.321141
MA0040.10.570428
MA0041.10.252793
MA0042.10.646075
MA0043.10.644989
MA0046.10.634468
MA0048.10.0172925
MA0050.10.228625
MA0051.10.317617
MA0052.10.574006
MA0055.10.715233
MA0056.10
MA0057.10.0158853
MA0058.10.167587
MA0059.10.166682
MA0060.10.0584466
MA0061.11.52826
MA0063.10
MA0066.10.321498
MA0067.10.948938
MA0068.10.128042
MA0069.10.630852
MA0070.10.620368
MA0071.10.289163
MA0072.10.616162
MA0073.11.88779e-05
MA0074.10.316991
MA0076.10.528959
MA0077.10.608956
MA0078.10.402443
MA0081.10.166796
MA0083.10.651755
MA0084.11.13204
MA0087.10.613875
MA0088.10.583662
MA0089.10
MA0090.10.189305
MA0091.10.240316
MA0092.11.14306
MA0093.10.12631
MA0095.10
MA0098.10
MA0100.10.885358
MA0101.10.403202
MA0103.10.118522
MA0105.11.1728
MA0106.120.2925
MA0107.11.0064
MA0108.20.492699
MA0109.10
MA0111.10.199239
MA0113.10.370073
MA0114.10.985949
MA0115.10.874839
MA0116.10.607827
MA0117.10.680135
MA0119.11.47085
MA0122.10.70466
MA0124.10.834787
MA0125.10.75419
MA0130.10
MA0131.11.07372
MA0132.10
MA0133.10
MA0135.10.673296
MA0136.10.87256
MA0139.10.364861
MA0140.10.286995
MA0141.10.165463
MA0142.10.4668
MA0143.10.370225
MA0144.10.25687
MA0145.10.650967
MA0146.12.03552
MA0147.10.0881384
MA0148.10.257816
MA0149.10.279141
MA0062.20.67985
MA0035.20.286421
MA0039.20.0506563
MA0138.20.403517
MA0002.20.0530127
MA0137.20.430142
MA0104.20.0580852
MA0047.20.345656
MA0112.21.56287
MA0065.20.0080232
MA0150.10.185024
MA0151.10
MA0152.10.292357
MA0153.10.738108
MA0154.10.542249
MA0155.10.576832
MA0156.10.854962
MA0157.10.442323
MA0158.10
MA0159.10.29763
MA0160.10.743405
MA0161.10
MA0162.10.0485277
MA0163.10.864319
MA0164.10.380804
MA0080.20.793571
MA0018.21.67652
MA0099.20.292649
MA0079.23.01277e-05
MA0102.21.16862
MA0258.10.890751
MA0259.12.16017
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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