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Coexpression cluster:C405: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.0737355,0.435734,0.0704497,0.44898,1.16608,0.145481,0.193858,1.34275,0.201483,0.0567872,0.127781,0.635883,0.136369,0.18622,0.0527049,0.484254,0.359143,1.32472,0.154232,0.29811,0.528893,0.754158,0.14085,1.60804,0.0918928,0.239737,0.405008,0.139567,0.200446,0.195566,0.115556,0.389116,0.260815,0.487921,0.158665,0.282546,0.0397666,0.146177,0.567446,0.0657489,0.64612,0.106777,0.0999099,0.193557,0.0548432,0.0845678,0.194588,0.12165,0.0384572,0.200595,0.250009,0.585971,0.38667,0.453481,0.587358,0.188158,0.205541,0.166937,0.195328,0.498234,0.423157,0.196176,0.202296,0.336984,0.208359,0.309988,0.667509,1.01514,0.991173,0.859886,0.0999006,1.00174,0.00239942,0.585564,0.046819,0.0398214,0.209135,0.323653,0.37794,0.0888599,1.15577,0.336133,0.599262,0.665547,0.539768,3.60514e-05,0.00141773,0.0846612,0.269174,1.11136,0.753896,0.516018,0.402998,0.814489,0.0535122,0.125834,0.306601,0.438691,0.272612,0.284931,0.571588,0.398316,0.433978,0.362101,0.301097,0.125207,0.349366,0.18395,0.0917674,0.0472968,0.261459,0.431643,0.0680411,0.133204,0.70928,0.153662,0.0299643,1.21748,0.308176,0.826577,0.578146,1.35461,0.143829,0.215895,0.812657,0.866303,0.189628,0.407146,0.616494,0.0309871,0.516623,0.373998,0.629526,0.612237,0.765929,0.0774004,0.112299,0.432429,0.726382,1.55835,1.16239,0.691851,1.06196,0.43571,0.302448,0.486671,0.78843,1.40098,0.697322,0.0262058,0.197065,0.000449709,0.516957,0.0727688,0.19585,0.888975,0.257209,0.181063,0.0919218,0.0781127,0.690731,0.500787,0.377296,0.079602,0.314905,0.597974,0.24603,0.192969,0.000329526
|tfbs_overrepresentation_jaspar=MA0003.1;1.71169e-05,MA0004.1;0.130779,MA0006.1;0.0525289,MA0007.1;1.25112,MA0009.1;1.20783,MA0014.1;3.66985e-05,MA0017.1;0.242343,MA0019.1;0.644268,MA0024.1;0.391254,MA0025.1;0.599238,MA0027.1;2.03861,MA0028.1;0.0589063,MA0029.1;1.0498,MA0030.1;0.397801,MA0031.1;0.344829,MA0038.1;0.195728,MA0040.1;0.412311,MA0041.1;0.860371,MA0042.1;0.778983,MA0043.1;0.480818,MA0046.1;0.47108,MA0048.1;0.0169194,MA0050.1;0.123567,MA0051.1;0.562815,MA0052.1;0.41557,MA0055.1;0.121215,MA0056.1;0,MA0057.1;0.00240787,MA0058.1;0.0802423,MA0059.1;0.0796335,MA0060.1;0.2021,MA0061.1;0.0591371,MA0063.1;0,MA0066.1;0.196017,MA0067.1;0.769322,MA0068.1;0.105313,MA0069.1;0.467738,MA0070.1;0.458064,MA0071.1;1.55631,MA0072.1;0.454189,MA0073.1;0.00505094,MA0074.1;0.19236,MA0076.1;0.0879186,MA0077.1;0.44756,MA0078.1;0.263604,MA0081.1;0.27336,MA0083.1;0.487092,MA0084.1;0.947429,MA0087.1;0.452083,MA0088.1;0.0983632,MA0089.1;0,MA0090.1;0.315775,MA0091.1;0.132307,MA0092.1;0.110943,MA0093.1;0.053707,MA0095.1;0,MA0098.1;0,MA0100.1;0.592379,MA0101.1;0.202181,MA0103.1;0.411939,MA0105.1;0.00176673,MA0106.1;0.224407,MA0107.1;0.122976,MA0108.2;0.342362,MA0109.1;0,MA0111.1;0.102187,MA0113.1;2.69567,MA0114.1;0.524336,MA0115.1;0.697973,MA0116.1;0.299877,MA0117.1;0.513502,MA0119.1;0.537943,MA0122.1;0.53644,MA0124.1;0.659634,MA0125.1;1.42551,MA0130.1;0,MA0131.1;0.277285,MA0132.1;0,MA0133.1;0,MA0135.1;0.507125,MA0136.1;0.200538,MA0139.1;0.140093,MA0140.1;0.168354,MA0141.1;0.571374,MA0142.1;0.319458,MA0143.1;1.92252,MA0144.1;0.48115,MA0145.1;0.120776,MA0146.1;0.143735,MA0147.1;0.031895,MA0148.1;1.41112,MA0149.1;0.162171,MA0062.2;0.150391,MA0035.2;0.50217,MA0039.2;0.00119817,MA0138.2;0.264522,MA0002.2;0.182759,MA0137.2;0.221623,MA0104.2;0.0172311,MA0047.2;0.617535,MA0112.2;0.0185708,MA0065.2;0.126603,MA0150.1;0.307678,MA0151.1;0,MA0152.1;0.172601,MA0153.1;1.39352,MA0154.1;0.18484,MA0155.1;0.0961927,MA0156.1;1.27176,MA0157.1;0.298026,MA0158.1;0,MA0159.1;0.307966,MA0160.1;0.470272,MA0161.1;0,MA0162.1;0.000941791,MA0163.1;0.00408849,MA0164.1;0.245213,MA0080.2;0.766855,MA0018.2;0.225392,MA0099.2;0.514256,MA0079.2;2.39411e-07,MA0102.2;0.983247,MA0258.1;0.733928,MA0259.1;0.0344451,MA0442.1;0
}}
}}

Revision as of 19:08, 22 January 2013


Full id: C405_Keratinocyte_Mammary_Sebocyte_tongue_Corneal_Mallassezderived_Gingival



Phase1 CAGE Peaks

Hg19::chr10:105791095..105791110,-p@chr10:105791095..105791110
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Hg19::chr12:52818230..52818265,-p@chr12:52818230..52818265
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Hg19::chr12:52828147..52828164,-p1@KRT75
Hg19::chr12:52840461..52840467,-p@chr12:52840461..52840467
-
Hg19::chr12:52840473..52840479,-p@chr12:52840473..52840479
-
Hg19::chr12:52840487..52840511,-p@chr12:52840487..52840511
-
Hg19::chr12:52840896..52840905,-p@chr12:52840896..52840905
-
Hg19::chr12:52845923..52845938,-p1@KRT6B
Hg19::chr12:52880994..52881011,-p@chr12:52880994..52881011
-
Hg19::chr12:52908395..52908409,-p@chr12:52908395..52908409
-
Hg19::chr12:52908434..52908443,-p@chr12:52908434..52908443
-
Hg19::chr15:99637405..99637416,+p@chr15:99637405..99637416
+
Hg19::chr17:19702846..19702866,-p@chr17:19702846..19702866
-
Hg19::chr17:38632125..38632156,-p@chr17:38632125..38632156
-
Hg19::chr17:39775719..39775763,-p@chr17:39775719..39775763
-
Hg19::chr17:73753856..73753871,+p1@CU674593
Hg19::chr18:49762639..49762676,-p@chr18:49762639..49762676
-
Hg19::chr19:46627914..46627955,-p1@IGFL3
Hg19::chr1:153533849..153533860,-p@chr1:153533849..153533860
-
Hg19::chr1:153533861..153533893,-p@chr1:153533861..153533893
-
Hg19::chr1:209788292..209788321,-p@chr1:209788292..209788321
-
Hg19::chr5:134906504..134906518,-p@chr5:134906504..134906518
-
Hg19::chr5:64400723..64400730,-p@chr5:64400723..64400730
-
Hg19::chr9:108870138..108870152,+p1@uc004bcw.2
Hg19::chrY:7671750..7671771,-p@chrY:7671750..7671771
-


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

GO IDGO nameFDR corrected p-value
GO:0045111intermediate filament cytoskeleton0.00157857550617159
GO:0005882intermediate filament0.00157857550617159
GO:0044430cytoskeletal part0.0157589423587677
GO:0005856cytoskeleton0.0278905319402702
GO:0005200structural constituent of cytoskeleton0.0329455991167742
GO:0007398ectoderm development0.047072728176587



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>

Uber Anatomy
Ontology termp-valuen
gingival epithelium1.04e-263
mouth mucosa1.02e-1013
epithelium of mucosa2.27e-108
gingiva2.27e-108
surface structure3.18e-1099
mouth4.63e-1029
stomodeum4.63e-1029
oral opening1.35e-0922
mammalian vulva1.91e-091
external female genitalia1.91e-091
mammary gland2.00e-094
mammary bud2.00e-094
mammary ridge2.00e-094
mammary placode2.00e-094
head1.36e-0856
orifice4.77e-0836
respiratory system7.53e-0874
subdivision of head1.04e-0749
anterior region of body1.17e-0762
craniocervical region1.17e-0762
mucosa5.22e-0720


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)
MA0003.11.71169e-05
MA0004.10.130779
MA0006.10.0525289
MA0007.11.25112
MA0009.11.20783
MA0014.13.66985e-05
MA0017.10.242343
MA0019.10.644268
MA0024.10.391254
MA0025.10.599238
MA0027.12.03861
MA0028.10.0589063
MA0029.11.0498
MA0030.10.397801
MA0031.10.344829
MA0038.10.195728
MA0040.10.412311
MA0041.10.860371
MA0042.10.778983
MA0043.10.480818
MA0046.10.47108
MA0048.10.0169194
MA0050.10.123567
MA0051.10.562815
MA0052.10.41557
MA0055.10.121215
MA0056.10
MA0057.10.00240787
MA0058.10.0802423
MA0059.10.0796335
MA0060.10.2021
MA0061.10.0591371
MA0063.10
MA0066.10.196017
MA0067.10.769322
MA0068.10.105313
MA0069.10.467738
MA0070.10.458064
MA0071.11.55631
MA0072.10.454189
MA0073.10.00505094
MA0074.10.19236
MA0076.10.0879186
MA0077.10.44756
MA0078.10.263604
MA0081.10.27336
MA0083.10.487092
MA0084.10.947429
MA0087.10.452083
MA0088.10.0983632
MA0089.10
MA0090.10.315775
MA0091.10.132307
MA0092.10.110943
MA0093.10.053707
MA0095.10
MA0098.10
MA0100.10.592379
MA0101.10.202181
MA0103.10.411939
MA0105.10.00176673
MA0106.10.224407
MA0107.10.122976
MA0108.20.342362
MA0109.10
MA0111.10.102187
MA0113.12.69567
MA0114.10.524336
MA0115.10.697973
MA0116.10.299877
MA0117.10.513502
MA0119.10.537943
MA0122.10.53644
MA0124.10.659634
MA0125.11.42551
MA0130.10
MA0131.10.277285
MA0132.10
MA0133.10
MA0135.10.507125
MA0136.10.200538
MA0139.10.140093
MA0140.10.168354
MA0141.10.571374
MA0142.10.319458
MA0143.11.92252
MA0144.10.48115
MA0145.10.120776
MA0146.10.143735
MA0147.10.031895
MA0148.11.41112
MA0149.10.162171
MA0062.20.150391
MA0035.20.50217
MA0039.20.00119817
MA0138.20.264522
MA0002.20.182759
MA0137.20.221623
MA0104.20.0172311
MA0047.20.617535
MA0112.20.0185708
MA0065.20.126603
MA0150.10.307678
MA0151.10
MA0152.10.172601
MA0153.11.39352
MA0154.10.18484
MA0155.10.0961927
MA0156.11.27176
MA0157.10.298026
MA0158.10
MA0159.10.307966
MA0160.10.470272
MA0161.10
MA0162.10.000941791
MA0163.10.00408849
MA0164.10.245213
MA0080.20.766855
MA0018.20.225392
MA0099.20.514256
MA0079.22.39411e-07
MA0102.20.983247
MA0258.10.733928
MA0259.10.0344451
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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