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Coexpression cluster:C435: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.086801,0.0156627,0.0831821,0.165202,1.79318,0.492946,0.616006,0.100075,0.241904,0.0364691,0.145297,0.246281,0.168902,0.596995,0.2271,0.546223,0.386278,0.667244,0.369861,0.798491,0.0832107,0.10998,0.159229,0.061867,0.346469,0.263074,0.48237,0.928223,0.232674,0.943132,0.819121,0.416977,0.0319501,0.0654381,0.734627,0.268021,0.0488212,0.16489,0.157401,0.0184362,0.0494993,0.122756,0.239836,0.488521,0.0834249,0.3252,0.617815,0.138738,0.341215,0.863323,0.273745,0.224271,0.697402,0.482679,0.61862,0.209199,0.238182,0.186863,0.657353,0.546719,0.451758,0.217609,0.458777,0.363534,0.230363,0.33576,0.699678,1.04962,0.408258,0.893579,0.11533,0.482045,0.0215101,0.616804,0.0606565,0.0522785,0.984849,0.349828,0.405538,0.337709,0.943285,0.362659,0.230109,0.102596,0.570388,7.64563e-05,0.014259,0.405719,0.293613,1.14619,0.786844,0.546282,0.43117,0.0341616,0.229729,0.979731,0.365749,0.467605,0.297172,0.030006,0.0408868,0.426385,0.462798,0.389311,0.326595,0.142545,0.376249,0.204779,0.106511,0.057369,0.0887009,1.16461,3.2875,0.151086,1.75675,0.718696,0.0189649,0.411067,0.333893,0.14017,0.60929,0.291743,5.41614,0.238235,0.846043,0.350442,0.605496,0.435409,0.648109,0.350382,0.546896,0.417172,0.66129,1.92,0.798972,0.215,0.128702,0.15822,0.759101,1.59408,1.19737,0.724259,1.14509,0.464565,0.327989,1.62053,0.314828,1.43649,0.120862,0.0331453,0.0570933,0.000779656,0.547236,2.88523,0.217268,0.922839,0.281215,0.211649,0.106679,0.0916077,0.723128,0.530809,0.404879,0.0932398,0.340824,0.229543,0.536442,0.6138,0.133367
|tfbs_overrepresentation_for_novel_motifs=0.086801,0.0156627,0.0831821,0.165202,1.79318,0.492946,0.616006,0.100075,0.241904,0.0364691,0.145297,0.246281,0.168902,0.596995,0.2271,0.546223,0.386278,0.667244,0.369861,0.798491,0.0832107,0.10998,0.159229,0.061867,0.346469,0.263074,0.48237,0.928223,0.232674,0.943132,0.819121,0.416977,0.0319501,0.0654381,0.734627,0.268021,0.0488212,0.16489,0.157401,0.0184362,0.0494993,0.122756,0.239836,0.488521,0.0834249,0.3252,0.617815,0.138738,0.341215,0.863323,0.273745,0.224271,0.697402,0.482679,0.61862,0.209199,0.238182,0.186863,0.657353,0.546719,0.451758,0.217609,0.458777,0.363534,0.230363,0.33576,0.699678,1.04962,0.408258,0.893579,0.11533,0.482045,0.0215101,0.616804,0.0606565,0.0522785,0.984849,0.349828,0.405538,0.337709,0.943285,0.362659,0.230109,0.102596,0.570388,7.64563e-05,0.014259,0.405719,0.293613,1.14619,0.786844,0.546282,0.43117,0.0341616,0.229729,0.979731,0.365749,0.467605,0.297172,0.030006,0.0408868,0.426385,0.462798,0.389311,0.326595,0.142545,0.376249,0.204779,0.106511,0.057369,0.0887009,1.16461,3.2875,0.151086,1.75675,0.718696,0.0189649,0.411067,0.333893,0.14017,0.60929,0.291743,5.41614,0.238235,0.846043,0.350442,0.605496,0.435409,0.648109,0.350382,0.546896,0.417172,0.66129,1.92,0.798972,0.215,0.128702,0.15822,0.759101,1.59408,1.19737,0.724259,1.14509,0.464565,0.327989,1.62053,0.314828,1.43649,0.120862,0.0331453,0.0570933,0.000779656,0.547236,2.88523,0.217268,0.922839,0.281215,0.211649,0.106679,0.0916077,0.723128,0.530809,0.404879,0.0932398,0.340824,0.229543,0.536442,0.6138,0.133367
|tfbs_overrepresentation_jaspar=MA0003.1;0.000667077,MA0004.1;0.454064,MA0006.1;0.490927,MA0007.1;0.137043,MA0009.1;0.510226,MA0014.1;0.00216637,MA0017.1;1.46691,MA0019.1;0.250001,MA0024.1;0.419164,MA0025.1;0.630648,MA0027.1;2.07466,MA0028.1;0.90227,MA0029.1;0.435662,MA0030.1;0.425859,MA0031.1;0.371592,MA0038.1;0.21714,MA0040.1;0.440685,MA0041.1;0.160207,MA0042.1;0.140252,MA0043.1;0.510506,MA0046.1;1.25073,MA0048.1;0.0737273,MA0050.1;0.856183,MA0051.1;0.613549,MA0052.1;0.444013,MA0055.1;0.0197225,MA0056.1;0,MA0057.1;0.0676588,MA0058.1;0.645288,MA0059.1;0.642105,MA0060.1;0.0226691,MA0061.1;0.193842,MA0063.1;0,MA0066.1;0.217443,MA0067.1;0.802392,MA0068.1;7.57832,MA0069.1;3.17907,MA0070.1;0.487346,MA0071.1;0.556315,MA0072.1;0.483399,MA0073.1;3.01149e-10,MA0074.1;0.213609,MA0076.1;0.334977,MA0077.1;0.476645,MA0078.1;0.287843,MA0081.1;0.0933581,MA0083.1;3.2675,MA0084.1;0.981601,MA0087.1;0.481255,MA0088.1;1.30486,MA0089.1;0,MA0090.1;0.355863,MA0091.1;0.15013,MA0092.1;0.127244,MA0093.1;0.230362,MA0095.1;0,MA0098.1;0,MA0100.1;0.227084,MA0101.1;0.0660267,MA0103.1;1.23596,MA0105.1;0.243344,MA0106.1;1.27923,MA0107.1;0.0374129,MA0108.2;2.58637,MA0109.1;0,MA0111.1;2.4397,MA0113.1;2.04327,MA0114.1;0.600893,MA0115.1;0.730438,MA0116.1;0.151524,MA0117.1;0.543727,MA0119.1;0.288423,MA0122.1;0.567011,MA0124.1;0.691722,MA0125.1;0.614264,MA0130.1;0,MA0131.1;0.816303,MA0132.1;0,MA0133.1;0,MA0135.1;0.537249,MA0136.1;0.632521,MA0139.1;0.0139039,MA0140.1;0.188358,MA0141.1;1.06456,MA0142.1;0.345512,MA0143.1;0.259501,MA0144.1;0.302438,MA0145.1;0.160384,MA0146.1;0.302934,MA0147.1;0.0397742,MA0148.1;0.164295,MA0149.1;5.70261,MA0062.2;0.184791,MA0035.2;1.05042,MA0039.2;2.40025e-05,MA0138.2;0.288795,MA0002.2;1.02031,MA0137.2;0.073361,MA0104.2;0.022476,MA0047.2;0.238164,MA0112.2;0.588343,MA0065.2;0.451301,MA0150.1;0.10696,MA0151.1;0,MA0152.1;0.192836,MA0153.1;0.598889,MA0154.1;0.591248,MA0155.1;0.00641934,MA0156.1;0.549156,MA0157.1;0.323429,MA0158.1;0,MA0159.1;0.358237,MA0160.1;0.174237,MA0161.1;0,MA0162.1;0.000349302,MA0163.1;0.00776052,MA0164.1;0.268764,MA0080.2;0.498167,MA0018.2;0.248141,MA0099.2;0.193081,MA0079.2;3.49978e-07,MA0102.2;1.01759,MA0258.1;1.21055,MA0259.1;1.96503,MA0442.1;0
}}
}}

Revision as of 19:10, 22 January 2013


Full id: C435_submaxillary_salivary_parotid_small_colon_gall_trachea



Phase1 CAGE Peaks

Hg19::chr16:67470830..67470840,+p@chr16:67470830..67470840
+
Hg19::chr17:4463856..4463896,-p1@GGT6
Hg19::chr19:5838734..5838762,-p2@FUT6
Hg19::chr19:5838768..5838808,-p1@FUT6
Hg19::chr1:207102409..207102415,-p2@AK026320
Hg19::chr1:207102584..207102587,-p5@AK026320
Hg19::chr1:207102614..207102619,-p8@AK026320
Hg19::chr1:207102939..207103053,-p1@AK026320
Hg19::chr1:207103060..207103088,-p4@AK026320
Hg19::chr1:207103091..207103112,-p6@AK026320
Hg19::chr1:207103113..207103134,-p7@AK026320
Hg19::chr1:207103165..207103180,-p9@AK026320
Hg19::chr1:207103182..207103214,-p3@AK026320
Hg19::chr1:207103233..207103243,-p19@PIGR
Hg19::chr1:207103254..207103271,-p15@PIGR
Hg19::chr1:207103317..207103348,-p7@PIGR
Hg19::chr1:207103645..207103668,-p9@PIGR
Hg19::chr1:207104842..207104869,+p@chr1:207104842..207104869
+
Hg19::chr1:207105823..207105837,-p@chr1:207105823..207105837
-
Hg19::chr1:207109152..207109165,-p@chr1:207109152..207109165
-
Hg19::chr1:207112600..207112616,-p10@PIGR
Hg19::chr1:207112651..207112664,-p14@PIGR
Hg19::chr1:207119738..207119839,-p1@PIGR


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:00170603-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity0.0143723137587088
GO:0046920alpha(1,3)-fucosyltransferase activity0.0143723137587088
GO:0019317fucose catabolic process0.0143723137587088
GO:0042355L-fucose catabolic process0.0143723137587088
GO:0042354L-fucose metabolic process0.0143723137587088
GO:0006004fucose metabolic process0.0163302515211526
GO:0008417fucosyltransferase activity0.0167953466229545
GO:0003840gamma-glutamyltransferase activity0.0195911098353632
GO:0016755transferase activity, transferring amino-acyl groups0.0297345746328789
GO:0009306protein secretion0.0371869527356907



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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism2.94e-16114
major salivary gland1.82e-142
open tracheal system trachea7.61e-142
subdivision of digestive tract1.23e-13118
intestine1.62e-1217
digestive system7.24e-12145
digestive tract7.24e-12145
primitive gut7.24e-12145
colon8.99e-129
saliva-secreting gland1.31e-106
gland of oral region1.31e-106
gland of foregut1.31e-106
oral gland1.31e-106
oral cavity1.31e-106
endoderm-derived structure2.13e-10160
endoderm2.13e-10160
presumptive endoderm2.13e-10160
oral opening6.13e-1022
large intestine1.19e-0911
pharynx3.59e-0911
tongue4.01e-093
gustatory system4.01e-093
future tongue4.01e-093
gastrointestinal system1.73e-0825
submandibular gland4.28e-081
submandibular gland primordium4.28e-081
parotid gland4.57e-081
cheek4.57e-081
parotid gland primordium4.57e-081
vermiform appendix7.26e-081
caecum7.26e-081
midgut7.26e-081
lower lobe of right lung8.28e-081
right lung lobe8.28e-081
lower lobe of lung8.28e-081
lobe of lung8.28e-081
right lung8.28e-081
orifice9.33e-0836
penis1.48e-071
intromittent organ1.48e-071
lateral plate mesenchyme1.48e-071
undifferentiated genital tubercle1.48e-071
somatopleure1.48e-071
mouth2.11e-0729
stomodeum2.11e-0729
tonsil2.17e-071
mucosa-associated lymphoid tissue2.17e-071
lymphoid tissue2.17e-071
tonsillar ring2.17e-071
respiratory system7.19e-0774


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)
MA0003.10.000667077
MA0004.10.454064
MA0006.10.490927
MA0007.10.137043
MA0009.10.510226
MA0014.10.00216637
MA0017.11.46691
MA0019.10.250001
MA0024.10.419164
MA0025.10.630648
MA0027.12.07466
MA0028.10.90227
MA0029.10.435662
MA0030.10.425859
MA0031.10.371592
MA0038.10.21714
MA0040.10.440685
MA0041.10.160207
MA0042.10.140252
MA0043.10.510506
MA0046.11.25073
MA0048.10.0737273
MA0050.10.856183
MA0051.10.613549
MA0052.10.444013
MA0055.10.0197225
MA0056.10
MA0057.10.0676588
MA0058.10.645288
MA0059.10.642105
MA0060.10.0226691
MA0061.10.193842
MA0063.10
MA0066.10.217443
MA0067.10.802392
MA0068.17.57832
MA0069.13.17907
MA0070.10.487346
MA0071.10.556315
MA0072.10.483399
MA0073.13.01149e-10
MA0074.10.213609
MA0076.10.334977
MA0077.10.476645
MA0078.10.287843
MA0081.10.0933581
MA0083.13.2675
MA0084.10.981601
MA0087.10.481255
MA0088.11.30486
MA0089.10
MA0090.10.355863
MA0091.10.15013
MA0092.10.127244
MA0093.10.230362
MA0095.10
MA0098.10
MA0100.10.227084
MA0101.10.0660267
MA0103.11.23596
MA0105.10.243344
MA0106.11.27923
MA0107.10.0374129
MA0108.22.58637
MA0109.10
MA0111.12.4397
MA0113.12.04327
MA0114.10.600893
MA0115.10.730438
MA0116.10.151524
MA0117.10.543727
MA0119.10.288423
MA0122.10.567011
MA0124.10.691722
MA0125.10.614264
MA0130.10
MA0131.10.816303
MA0132.10
MA0133.10
MA0135.10.537249
MA0136.10.632521
MA0139.10.0139039
MA0140.10.188358
MA0141.11.06456
MA0142.10.345512
MA0143.10.259501
MA0144.10.302438
MA0145.10.160384
MA0146.10.302934
MA0147.10.0397742
MA0148.10.164295
MA0149.15.70261
MA0062.20.184791
MA0035.21.05042
MA0039.22.40025e-05
MA0138.20.288795
MA0002.21.02031
MA0137.20.073361
MA0104.20.022476
MA0047.20.238164
MA0112.20.588343
MA0065.20.451301
MA0150.10.10696
MA0151.10
MA0152.10.192836
MA0153.10.598889
MA0154.10.591248
MA0155.10.00641934
MA0156.10.549156
MA0157.10.323429
MA0158.10
MA0159.10.358237
MA0160.10.174237
MA0161.10
MA0162.10.000349302
MA0163.10.00776052
MA0164.10.268764
MA0080.20.498167
MA0018.20.248141
MA0099.20.193081
MA0079.23.49978e-07
MA0102.21.01759
MA0258.11.21055
MA0259.11.96503
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
CTCF#10664112.563600874079360.001385286952948610.00901645170628193



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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