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Coexpression cluster:C742: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;0.0148593,MA0004.1;1.64978,MA0006.1;0.210781,MA0007.1;0.332734,MA0009.1;0.79061,MA0014.1;0.0481212,MA0017.1;0.682686,MA0019.1;1.21992,MA0024.1;0.688373,MA0025.1;0.921763,MA0027.1;2.39404,MA0028.1;0.637069,MA0029.1;0.707146,MA0030.1;0.696006,MA0031.1;0.633489,MA0038.1;0.443833,MA0040.1;0.712837,MA0041.1;0.959796,MA0042.1;0.895841,MA0043.1;0.790919,MA0046.1;0.779945,MA0048.1;0.0494179,MA0050.1;0.338274,MA0051.1;0.439895,MA0052.1;0.716602,MA0055.1;0.136684,MA0056.1;0,MA0057.1;0.703296,MA0058.1;3.784,MA0059.1;0.729981,MA0060.1;0.119532,MA0061.1;0.330174,MA0063.1;0,MA0066.1;0.444231,MA0067.1;1.1037,MA0068.1;0.0758327,MA0069.1;0.776171,MA0070.1;0.765217,MA0071.1;0.40788,MA0072.1;0.760818,MA0073.1;0.000309691,MA0074.1;1.95782,MA0076.1;0.764079,MA0077.1;0.753278,MA0078.1;0.533387,MA0081.1;0.26424,MA0083.1;0.79797,MA0084.1;1.28962,MA0087.1;0.758426,MA0088.1;1.10483,MA0089.1;0,MA0090.1;0.291627,MA0091.1;0.351901,MA0092.1;0.852371,MA0093.1;3.34956,MA0095.1;0,MA0098.1;0,MA0100.1;0.456802,MA0101.1;0.216017,MA0103.1;0.587485,MA0105.1;0.360248,MA0106.1;0.482519,MA0107.1;0.475157,MA0108.2;0.630531,MA0109.1;0,MA0111.1;0.303543,MA0113.1;0.498009,MA0114.1;0.465415,MA0115.1;1.02805,MA0116.1;0.935607,MA0117.1;0.827487,MA0119.1;0.250314,MA0122.1;0.852927,MA0124.1;0.98702,MA0125.1;0.904129,MA0130.1;0,MA0131.1;0.550695,MA0132.1;0,MA0133.1;0,MA0135.1;0.820382,MA0136.1;1.14308,MA0139.1;0.307853,MA0140.1;0.405425,MA0141.1;0.2626,MA0142.1;0.602852,MA0143.1;0.498176,MA0144.1;0.862195,MA0145.1;1.19384,MA0146.1;0.315774,MA0147.1;0.162359,MA0148.1;3.56607,MA0149.1;0.396509,MA0062.2;0.659456,MA0035.2;0.404774,MA0039.2;1.48374,MA0138.2;0.534556,MA0002.2;0.111226,MA0137.2;0.649788,MA0104.2;1.24411,MA0047.2;1.18756,MA0112.2;1.14277,MA0065.2;0.839576,MA0150.1;1.4246,MA0151.1;0,MA0152.1;0.411494,MA0153.1;0.887528,MA0154.1;0.153348,MA0155.1;0.0230394,MA0156.1;1.22,MA0157.1;0.576556,MA0158.1;0,MA0159.1;0.948902,MA0160.1;0.386031,MA0161.1;0,MA0162.1;0.00470038,MA0163.1;0.826158,MA0164.1;3.23562,MA0080.2;1.15057,MA0018.2;0.483823,MA0099.2;0.411824,MA0079.2;0.12952,MA0102.2;1.32663,MA0258.1;1.34618,MA0259.1;0.168926,MA0442.1;0
}}
}}

Revision as of 19:25, 22 January 2013


Full id: C742_lung_gastric_trachea_bile_esophagus_gall_neuroectodermal



Phase1 CAGE Peaks

Hg19::chr11:64976781..64976793,+p25@CAPN1
Hg19::chr11:64977490..64977525,+p13@CAPN1
Hg19::chr16:3041159..3041167,+p@chr16:3041159..3041167
+
Hg19::chr17:19651654..19651665,-p3@ALDH3A1
Hg19::chr17:19651668..19651682,-p2@ALDH3A1
Hg19::chr19:42259430..42259452,+p1@CEACAM6
Hg19::chr19:42259465..42259476,+p2@CEACAM6
Hg19::chr19:42259486..42259495,+p3@CEACAM6
Hg19::chr19:58838369..58838439,+p1@ZSCAN22
Hg19::chr20:44408556..44408563,-p5@WFDC3
Hg19::chr9:130913135..130913143,+p@chr9:130913135..130913143
+


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:0008106alcohol dehydrogenase (NADP+) activity0.0256078176098444
GO:0004029aldehyde dehydrogenase (NAD) activity0.0447820308772332
GO:0004033aldo-keto reductase activity0.0447820308772332
GO:0004030aldehyde dehydrogenase [NAD(P)+] activity0.0447820308772332



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>

Uber Anatomy
Ontology termp-valuen
endoderm-derived structure2.39e-31160
endoderm2.39e-31160
presumptive endoderm2.39e-31160
digestive system4.64e-29145
digestive tract4.64e-29145
primitive gut4.64e-29145
subdivision of digestive tract1.10e-26118
endo-epithelium3.73e-1682
respiratory system1.28e-1574
foregut5.77e-1487
respiratory tract1.29e-1354
thoracic cavity element1.65e-1234
thoracic cavity1.65e-1234
thoracic segment organ4.62e-1235
biliary system5.32e-129
biliary tree5.32e-129
biliary bud5.32e-129
immaterial anatomical entity8.57e-12117
gut epithelium1.28e-1154
anatomical space5.88e-1195
orifice8.29e-1136
hindgut1.68e-1019
gallbladder3.57e-103
gall bladder primordium3.57e-103
gastrointestinal system1.17e-0925
organ system subdivision1.89e-09223
tracheobronchial tree2.20e-0915
lower respiratory tract2.20e-0915
epithelial fold2.38e-0947
epithelium of mucosa3.29e-098
epithelial bud5.18e-0937
cloaca6.37e-0914
anal region6.37e-0914
embryonic cloaca6.37e-0914
terminal part of digestive tract6.37e-0914
primitive urogenital sinus6.37e-0914
proctodeum6.37e-0914
mucosa2.02e-0820
genitourinary system2.91e-0815
organism subdivision3.04e-08264
trunk region element7.83e-08101
respiratory primordium1.39e-0738
endoderm of foregut1.39e-0738
multi-tissue structure2.12e-07342
open tracheal system trachea2.23e-072
trachea2.26e-077
respiratory airway2.26e-077
intestine3.36e-0717
thoracic segment of trunk3.78e-0752
viscus5.22e-0718
segment of respiratory tract7.36e-0747
Disease
Ontology termp-valuen
carcinoma2.43e-12106
adenocarcinoma1.21e-1025
cell type cancer1.56e-07143
signet ring cell adenocarcinoma1.91e-072


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)
MA0003.10.0148593
MA0004.11.64978
MA0006.10.210781
MA0007.10.332734
MA0009.10.79061
MA0014.10.0481212
MA0017.10.682686
MA0019.11.21992
MA0024.10.688373
MA0025.10.921763
MA0027.12.39404
MA0028.10.637069
MA0029.10.707146
MA0030.10.696006
MA0031.10.633489
MA0038.10.443833
MA0040.10.712837
MA0041.10.959796
MA0042.10.895841
MA0043.10.790919
MA0046.10.779945
MA0048.10.0494179
MA0050.10.338274
MA0051.10.439895
MA0052.10.716602
MA0055.10.136684
MA0056.10
MA0057.10.703296
MA0058.13.784
MA0059.10.729981
MA0060.10.119532
MA0061.10.330174
MA0063.10
MA0066.10.444231
MA0067.11.1037
MA0068.10.0758327
MA0069.10.776171
MA0070.10.765217
MA0071.10.40788
MA0072.10.760818
MA0073.10.000309691
MA0074.11.95782
MA0076.10.764079
MA0077.10.753278
MA0078.10.533387
MA0081.10.26424
MA0083.10.79797
MA0084.11.28962
MA0087.10.758426
MA0088.11.10483
MA0089.10
MA0090.10.291627
MA0091.10.351901
MA0092.10.852371
MA0093.13.34956
MA0095.10
MA0098.10
MA0100.10.456802
MA0101.10.216017
MA0103.10.587485
MA0105.10.360248
MA0106.10.482519
MA0107.10.475157
MA0108.20.630531
MA0109.10
MA0111.10.303543
MA0113.10.498009
MA0114.10.465415
MA0115.11.02805
MA0116.10.935607
MA0117.10.827487
MA0119.10.250314
MA0122.10.852927
MA0124.10.98702
MA0125.10.904129
MA0130.10
MA0131.10.550695
MA0132.10
MA0133.10
MA0135.10.820382
MA0136.11.14308
MA0139.10.307853
MA0140.10.405425
MA0141.10.2626
MA0142.10.602852
MA0143.10.498176
MA0144.10.862195
MA0145.11.19384
MA0146.10.315774
MA0147.10.162359
MA0148.13.56607
MA0149.10.396509
MA0062.20.659456
MA0035.20.404774
MA0039.21.48374
MA0138.20.534556
MA0002.20.111226
MA0137.20.649788
MA0104.21.24411
MA0047.21.18756
MA0112.21.14277
MA0065.20.839576
MA0150.11.4246
MA0151.10
MA0152.10.411494
MA0153.10.887528
MA0154.10.153348
MA0155.10.0230394
MA0156.11.22
MA0157.10.576556
MA0158.10
MA0159.10.948902
MA0160.10.386031
MA0161.10
MA0162.10.00470038
MA0163.10.826158
MA0164.13.23562
MA0080.21.15057
MA0018.20.483823
MA0099.20.411824
MA0079.20.12952
MA0102.21.32663
MA0258.11.34618
MA0259.10.168926
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
FOXA2#317036.717399205272340.008635967022667360.0328944075232633



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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