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Coexpression cluster:C394: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.0627807,0.450316,1.73364,0.130193,5.94735,0.129262,0.175095,4.77061,0.560943,0.884646,0.112658,0.203538,1.61093,0.167821,3.77857,0.75352,0.33472,0.0277321,0.125731,0.379818,0.0598255,3.01999,0.124907,0.042611,0.27241,0.219025,1.08603,2.50238,0.69312,1.63568,0.101256,0.363981,0.0198904,2.04441,0.0333798,0.296331,0.0324544,0.809149,0.0261079,0.0105076,0.032974,4.25152,0.526516,3.76222,4.08298,0.253512,0.521477,1.70695,1.37019,0.0454402,0.648329,0.183375,0.702527,0.427029,0.558863,0.976882,3.87377,0.149516,0.698608,0.148912,0.397292,0.177305,0.0636824,0.841377,0.188939,0.286902,0.638114,0.983449,0.355656,0.828977,0.0867459,2.56711,0.0015812,0.557091,0.00675389,2.71358,1.33939,0.812161,0.353062,0.0765849,0.00941029,0.312308,0.188707,0.0669558,0.511911,0.494566,0.131433,0.0034953,0.691411,1.07932,0.723727,0.488513,0.377556,0.233848,0.0445871,0.0246063,0.256997,0.412519,0.250711,0.121425,0.269738,0.372975,0.407897,0.337605,0.278278,0.355988,0.325192,0.165662,0.0792544,0.352559,0.0643507,0.405608,0.0576237,0.117734,0.679489,0.562692,0.00710701,0.100646,2.17505,0.0963336,0.549768,0.245647,3.26547,0.57069,0.782053,0.300752,0.171066,0.993409,0.587649,0.10582,0.489108,0.102719,0.600533,0.193939,0.735665,0.00305065,0.0982282,0.124016,0.696441,1.52541,1.13019,0.662221,2.98048,1.8574,0.279588,0.144474,2.90423,1.36826,2.78299,0.020754,0.270424,0.0094323,0.489437,0.313905,0.176994,0.857896,1.9201,3.01828,8.12528,0.0667606,0.661111,0.47352,0.352434,0.0681178,0.291674,0.18819,4.51294,0.174248,0.424859
|tfbs_overrepresentation_jaspar=MA0003.1;0.0138919,MA0004.1;7.30755,MA0006.1;0.043712,MA0007.1;0.699342,MA0009.1;1.14995,MA0014.1;7.47681,MA0017.1;1.71139,MA0019.1;0.206961,MA0024.1;0.366071,MA0025.1;0.570597,MA0027.1;2.00534,MA0028.1;0.0494049,MA0029.1;0.381857,MA0030.1;0.372472,MA0031.1;0.320773,MA0038.1;0.176878,MA0040.1;0.38667,MA0041.1;0.125771,MA0042.1;0.108251,MA0043.1;0.453881,MA0046.1;0.444311,MA0048.1;0.00182717,MA0050.1;0.108721,MA0051.1;0.174152,MA0052.1;0.389861,MA0055.1;0.343507,MA0056.1;0,MA0057.1;0.0369704,MA0058.1;1.85666,MA0059.1;1.8492,MA0060.1;0.0133608,MA0061.1;0.00915103,MA0063.1;0,MA0066.1;4.71374,MA0067.1;2.93153,MA0068.1;2.623,MA0069.1;0.441028,MA0070.1;0.431528,MA0071.1;0.464021,MA0072.1;0.427724,MA0073.1;0.00179168,MA0074.1;0.173668,MA0076.1;0.0757217,MA0077.1;0.421218,MA0078.1;0.242013,MA0081.1;0.0682163,MA0083.1;0.460049,MA0084.1;0.916043,MA0087.1;0.425657,MA0088.1;4.63691,MA0089.1;0,MA0090.1;0.082384,MA0091.1;0.116893,MA0092.1;0.659672,MA0093.1;11.0842,MA0095.1;0,MA0098.1;0,MA0100.1;0.185942,MA0101.1;0.0459133,MA0103.1;1.92099,MA0105.1;0.0736484,MA0106.1;0.204305,MA0107.1;0.023874,MA0108.2;0.318371,MA0109.1;0,MA0111.1;1.54045,MA0113.1;0.617,MA0114.1;2.43855,MA0115.1;5.25075,MA0116.1;0.0247359,MA0117.1;0.486035,MA0119.1;0.0614144,MA0122.1;3.23049,MA0124.1;0.630319,MA0125.1;0.554615,MA0130.1;0,MA0131.1;0.255226,MA0132.1;0,MA0133.1;0,MA0135.1;0.479757,MA0136.1;0.181467,MA0139.1;1.63514,MA0140.1;0.150858,MA0141.1;2.41447,MA0142.1;0.296096,MA0143.1;0.215723,MA0144.1;0.0193859,MA0145.1;0.813115,MA0146.1;5.40381e-05,MA0147.1;0.263899,MA0148.1;0.129389,MA0149.1;0.145006,MA0062.2;0.00844267,MA0035.2;0.150428,MA0039.2;0.0214864,MA0138.2;0.242899,MA0002.2;1.11033,MA0137.2;0.051801,MA0104.2;0.559425,MA0047.2;0.196083,MA0112.2;13.2771,MA0065.2;2.77177,MA0150.1;0.0796342,MA0151.1;0,MA0152.1;0.154883,MA0153.1;0.539635,MA0154.1;2.84258,MA0155.1;0.135045,MA0156.1;0.0526574,MA0157.1;0.275302,MA0158.1;0,MA0159.1;2.04402,MA0160.1;4.19251,MA0161.1;0,MA0162.1;0.000474891,MA0163.1;0.0543687,MA0164.1;0.224291,MA0080.2;0.387204,MA0018.2;0.205249,MA0099.2;0.155103,MA0079.2;0.00058132,MA0102.2;0.951693,MA0258.1;2.21065,MA0259.1;0.279278,MA0442.1;0
}}
}}

Revision as of 19:08, 22 January 2013


Full id: C394_submaxillary_small_colon_throat_appendix_tonsil_trachea



Phase1 CAGE Peaks

Hg19::chr14:106053917..106053929,-p@chr14:106053917..106053929
-
Hg19::chr14:106053932..106053964,-p@chr14:106053932..106053964
-
Hg19::chr14:106054084..106054129,-p@chr14:106054084..106054129
-
Hg19::chr14:106054501..106054541,-p@chr14:106054501..106054541
-
Hg19::chr14:106054591..106054622,-p@chr14:106054591..106054622
-
Hg19::chr14:106174127..106174171,+p@chr14:106174127..106174171
+
Hg19::chr14:106174141..106174197,-p@chr14:106174141..106174197
-
Hg19::chr14:106174211..106174218,-p@chr14:106174211..106174218
-
Hg19::chr14:106174229..106174238,-p@chr14:106174229..106174238
-
Hg19::chr14:106174321..106174354,-p@chr14:106174321..106174354
-
Hg19::chr14:106174389..106174443,+p@chr14:106174389..106174443
+
Hg19::chr14:106174426..106174472,-p1@Z14961
Hg19::chr14:106174454..106174459,+p@chr14:106174454..106174459
+
Hg19::chr14:106174473..106174476,-p3@Z14961
Hg19::chr14:106174479..106174485,-p2@Z14961
Hg19::chr14:106174726..106174747,-p4@BC113815
Hg19::chr14:106174746..106174757,+p@chr14:106174746..106174757
+
Hg19::chr14:106174766..106174818,-p2@BC113815
Hg19::chr14:106174826..106174853,+p@chr14:106174826..106174853
+
Hg19::chr14:106174854..106174882,-p3@BC113815
Hg19::chr14:106174884..106174895,-p5@BC113815
Hg19::chr14:106174928..106174952,-p1@BC113815
Hg19::chr14:106174942..106174961,+p@chr14:106174942..106174961
+
Hg19::chr14:106174960..106174999,-p1@IGHA1
Hg19::chr14:106963409..106963427,-p1@IGHV1-45
Hg19::chr4:71522035..71522046,-p@chr4:71522035..71522046
-
Hg19::chr4:71542660..71542684,-p@chr4:71542660..71542684
-


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
B cell2.55e-2614
lymphocyte of B lineage1.68e-1424
pro-B cell1.68e-1424
Uber Anatomy
Ontology termp-valuen
adult organism3.61e-40114
major salivary gland1.47e-092
saliva-secreting gland6.89e-076
gland of oral region6.89e-076
gland of foregut6.89e-076
oral gland6.89e-076
oral cavity6.89e-076


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)
MA0003.10.0138919
MA0004.17.30755
MA0006.10.043712
MA0007.10.699342
MA0009.11.14995
MA0014.17.47681
MA0017.11.71139
MA0019.10.206961
MA0024.10.366071
MA0025.10.570597
MA0027.12.00534
MA0028.10.0494049
MA0029.10.381857
MA0030.10.372472
MA0031.10.320773
MA0038.10.176878
MA0040.10.38667
MA0041.10.125771
MA0042.10.108251
MA0043.10.453881
MA0046.10.444311
MA0048.10.00182717
MA0050.10.108721
MA0051.10.174152
MA0052.10.389861
MA0055.10.343507
MA0056.10
MA0057.10.0369704
MA0058.11.85666
MA0059.11.8492
MA0060.10.0133608
MA0061.10.00915103
MA0063.10
MA0066.14.71374
MA0067.12.93153
MA0068.12.623
MA0069.10.441028
MA0070.10.431528
MA0071.10.464021
MA0072.10.427724
MA0073.10.00179168
MA0074.10.173668
MA0076.10.0757217
MA0077.10.421218
MA0078.10.242013
MA0081.10.0682163
MA0083.10.460049
MA0084.10.916043
MA0087.10.425657
MA0088.14.63691
MA0089.10
MA0090.10.082384
MA0091.10.116893
MA0092.10.659672
MA0093.111.0842
MA0095.10
MA0098.10
MA0100.10.185942
MA0101.10.0459133
MA0103.11.92099
MA0105.10.0736484
MA0106.10.204305
MA0107.10.023874
MA0108.20.318371
MA0109.10
MA0111.11.54045
MA0113.10.617
MA0114.12.43855
MA0115.15.25075
MA0116.10.0247359
MA0117.10.486035
MA0119.10.0614144
MA0122.13.23049
MA0124.10.630319
MA0125.10.554615
MA0130.10
MA0131.10.255226
MA0132.10
MA0133.10
MA0135.10.479757
MA0136.10.181467
MA0139.11.63514
MA0140.10.150858
MA0141.12.41447
MA0142.10.296096
MA0143.10.215723
MA0144.10.0193859
MA0145.10.813115
MA0146.15.40381e-05
MA0147.10.263899
MA0148.10.129389
MA0149.10.145006
MA0062.20.00844267
MA0035.20.150428
MA0039.20.0214864
MA0138.20.242899
MA0002.21.11033
MA0137.20.051801
MA0104.20.559425
MA0047.20.196083
MA0112.213.2771
MA0065.22.77177
MA0150.10.0796342
MA0151.10
MA0152.10.154883
MA0153.10.539635
MA0154.12.84258
MA0155.10.135045
MA0156.10.0526574
MA0157.10.275302
MA0158.10
MA0159.12.04402
MA0160.14.19251
MA0161.10
MA0162.10.000474891
MA0163.10.0543687
MA0164.10.224291
MA0080.20.387204
MA0018.20.205249
MA0099.20.155103
MA0079.20.00058132
MA0102.20.951693
MA0258.12.21065
MA0259.10.279278
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
POLR2A#5430191.51117075387420.01076843159943720.0397386745278831
USF1#7391122.827333012092430.0003838846203746230.00376844871391157



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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