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Coexpression cluster:C524: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.443805,0.369826,0.431729,0.241986,0.736765,0.240734,0.300393,0.192644,0.42191,0.0503338,0.622824,0.335828,0.321549,0.291158,0.733068,0.3998,0.489874,0.281675,0.0386732,0.267126,0.139663,0.944153,0.234854,0.110606,0.170101,0.354732,0.275679,0.233219,0.115495,0.242389,1.10654,0.522822,0.0662338,0.326663,0.311809,0.0287933,0.0919402,0.677998,0.0794192,0.37945,0.0929322,0.556817,0.518689,0.111922,1.02895,0.482397,0.301272,0.21008,0.702528,0.369939,0.366671,0.836154,0.167715,0.592653,0.734926,0.293507,0.376618,0.737918,0.740906,0.266768,0.559896,0.303183,0.423107,0.465305,0.317765,0.4351,0.818746,1.17567,0.513487,1.01727,0.534356,1.1788,0.0128276,0.73304,0.132135,0.836315,0.25554,0.450429,0.510572,0.165891,0.0404655,0.464358,0.851126,0.43491,0.684728,0.0553549,0.045598,0.232513,0.38876,1.27332,0.90828,0.659533,0.537982,0.897208,0.114084,0.558858,0.346672,0.576706,0.392699,0.200942,0.577898,0.532876,0.571612,0.493139,0.425079,0.214722,0.479058,0.288402,0.169928,0.340143,0.146911,0.569087,0.136085,0.225069,0.862131,0.631548,0.268578,0.201199,0.433061,0.532361,0.725237,0.386689,0.671072,0.326716,0.968805,0.451097,0.295287,0.542501,0.765493,0.265268,0.660176,1.74884,0.779127,0.323981,0.920697,0.218934,0.19775,0.233646,0.879842,1.7239,1.32497,0.844052,0.804252,0.573485,0.426604,0.722747,0.412168,1.56567,0.188015,0.0681329,0.766653,0.00407349,0.660531,0.40276,0.818076,1.04704,1.73848,0.105422,0.507668,0.150717,0.842888,0.643319,0.509866,0.152845,0.440625,0.316832,0.486038,0.299321,0.0105099
|tfbs_overrepresentation_jaspar=MA0003.1;0.00504314,MA0004.1;0.221943,MA0006.1;0.362024,MA0007.1;0.599001,MA0009.1;0.621697,MA0014.1;0.154351,MA0017.1;0.137108,MA0019.1;0.340029,MA0024.1;0.525161,MA0025.1;0.747404,MA0027.1;2.20546,MA0028.1;0.122394,MA0029.1;0.542771,MA0030.1;0.532314,MA0031.1;0.474026,MA0038.1;0.302644,MA0040.1;0.548121,MA0041.1;0.236024,MA0042.1;1.14502,MA0043.1;0.621991,MA0046.1;0.611559,MA0048.1;0.0663643,MA0050.1;0.609862,MA0051.1;0.299199,MA0052.1;0.551663,MA0055.1;0.0307766,MA0056.1;0,MA0057.1;0.0616251,MA0058.1;0.153757,MA0059.1;0.15289,MA0060.1;0.0509127,MA0061.1;0.0397345,MA0063.1;0,MA0066.1;0.302992,MA0067.1;0.924196,MA0068.1;0.111262,MA0069.1;0.607975,MA0070.1;0.597583,MA0071.1;0.746772,MA0072.1;0.593415,MA0073.1;0.102168,MA0074.1;1.46857,MA0076.1;0.493997,MA0077.1;2.44337,MA0078.1;0.382364,MA0081.1;0.152999,MA0083.1;0.628701,MA0084.1;1.10674,MA0087.1;0.591148,MA0088.1;0.514158,MA0089.1;0,MA0090.1;2.25599,MA0091.1;0.223914,MA0092.1;0.195947,MA0093.1;0.114388,MA0095.1;0,MA0098.1;0,MA0100.1;0.314026,MA0101.1;0.116395,MA0103.1;0.706501,MA0105.1;0.0516824,MA0106.1;0.33677,MA0107.1;0.0748038,MA0108.2;0.471286,MA0109.1;0,MA0111.1;0.541878,MA0113.1;0.350573,MA0114.1;0.537797,MA0115.1;0.850405,MA0116.1;0.949722,MA0117.1;0.656858,MA0119.1;0.862312,MA0122.1;0.681203,MA0124.1;0.810546,MA0125.1;0.730403,MA0130.1;0,MA0131.1;0.398042,MA0132.1;0,MA0133.1;0,MA0135.1;0.650071,MA0136.1;0.30842,MA0139.1;0.0351037,MA0140.1;0.269307,MA0141.1;0.151722,MA0142.1;0.445733,MA0143.1;0.350722,MA0144.1;0.231909,MA0145.1;0.204689,MA0146.1;0.307985,MA0147.1;0.0784275,MA0148.1;0.676348,MA0149.1;0.261654,MA0062.2;0.0377014,MA0035.2;0.268747,MA0039.2;0.106686,MA0138.2;0.38342,MA0002.2;0.0459391,MA0137.2;0.126444,MA0104.2;0.0505812,MA0047.2;0.87164,MA0112.2;0.08608,MA0065.2;0.098884,MA0150.1;0.98029,MA0151.1;0,MA0152.1;0.753898,MA0153.1;0.714423,MA0154.1;0.280624,MA0155.1;0.316202,MA0156.1;0.4018,MA0157.1;0.421609,MA0158.1;0,MA0159.1;0.96592,MA0160.1;0.703717,MA0161.1;0,MA0162.1;0.0130334,MA0163.1;0.00623,MA0164.1;0.948242,MA0080.2;0.366978,MA0018.2;0.337929,MA0099.2;2.12264,MA0079.2;0.0126595,MA0102.2;2.57682,MA0258.1;0.218609,MA0259.1;0.0828875,MA0442.1;0
}}
}}

Revision as of 19:14, 22 January 2013


Full id: C524_serous_endometrioid_endometrial_mesothelioma_gall_clear_papillotubular



Phase1 CAGE Peaks

Hg19::chr10:30151938..30151956,-p@chr10:30151938..30151956
-
Hg19::chr10:73848549..73848564,-p13@SPOCK2
Hg19::chr10:73848636..73848651,-p12@SPOCK2
Hg19::chr11:13984141..13984144,+p6@SPON1
Hg19::chr17:39093082..39093091,-p4@KRT23
Hg19::chr1:64100468..64100494,+p@chr1:64100468..64100494
+
Hg19::chr1:64100517..64100532,+p@chr1:64100517..64100532
+
Hg19::chr22:30653574..30653606,-p@chr22:30653574..30653606
-
Hg19::chr22:30653778..30653783,-p@chr22:30653778..30653783
-
Hg19::chr2:102600220..102600233,+p@chr2:102600220..102600233
+
Hg19::chr2:220080970..220081009,-p16@ABCB6
Hg19::chr3:177158035..177158056,+p@chr3:177158035..177158056
+
Hg19::chr3:191991378..191991384,-p@chr3:191991378..191991384
-
Hg19::chr3:93707380..93707414,+p@chr3:93707380..93707414
+
Hg19::chr7:47675013..47675019,-p@chr7:47675013..47675019
-
Hg19::chr8:117466423..117466434,+p@chr8:117466423..117466434
+
Hg19::chr8:120220206..120220214,+p23@MAL2


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><br>disease_data<br>

Cell Type
Ontology termp-valuen
epithelial cell of uterus7.67e-186
stromal cell of endometrium7.67e-186
Disease
Ontology termp-valuen
female reproductive endometrioid cancer7.67e-186


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)
MA0003.10.00504314
MA0004.10.221943
MA0006.10.362024
MA0007.10.599001
MA0009.10.621697
MA0014.10.154351
MA0017.10.137108
MA0019.10.340029
MA0024.10.525161
MA0025.10.747404
MA0027.12.20546
MA0028.10.122394
MA0029.10.542771
MA0030.10.532314
MA0031.10.474026
MA0038.10.302644
MA0040.10.548121
MA0041.10.236024
MA0042.11.14502
MA0043.10.621991
MA0046.10.611559
MA0048.10.0663643
MA0050.10.609862
MA0051.10.299199
MA0052.10.551663
MA0055.10.0307766
MA0056.10
MA0057.10.0616251
MA0058.10.153757
MA0059.10.15289
MA0060.10.0509127
MA0061.10.0397345
MA0063.10
MA0066.10.302992
MA0067.10.924196
MA0068.10.111262
MA0069.10.607975
MA0070.10.597583
MA0071.10.746772
MA0072.10.593415
MA0073.10.102168
MA0074.11.46857
MA0076.10.493997
MA0077.12.44337
MA0078.10.382364
MA0081.10.152999
MA0083.10.628701
MA0084.11.10674
MA0087.10.591148
MA0088.10.514158
MA0089.10
MA0090.12.25599
MA0091.10.223914
MA0092.10.195947
MA0093.10.114388
MA0095.10
MA0098.10
MA0100.10.314026
MA0101.10.116395
MA0103.10.706501
MA0105.10.0516824
MA0106.10.33677
MA0107.10.0748038
MA0108.20.471286
MA0109.10
MA0111.10.541878
MA0113.10.350573
MA0114.10.537797
MA0115.10.850405
MA0116.10.949722
MA0117.10.656858
MA0119.10.862312
MA0122.10.681203
MA0124.10.810546
MA0125.10.730403
MA0130.10
MA0131.10.398042
MA0132.10
MA0133.10
MA0135.10.650071
MA0136.10.30842
MA0139.10.0351037
MA0140.10.269307
MA0141.10.151722
MA0142.10.445733
MA0143.10.350722
MA0144.10.231909
MA0145.10.204689
MA0146.10.307985
MA0147.10.0784275
MA0148.10.676348
MA0149.10.261654
MA0062.20.0377014
MA0035.20.268747
MA0039.20.106686
MA0138.20.38342
MA0002.20.0459391
MA0137.20.126444
MA0104.20.0505812
MA0047.20.87164
MA0112.20.08608
MA0065.20.098884
MA0150.10.98029
MA0151.10
MA0152.10.753898
MA0153.10.714423
MA0154.10.280624
MA0155.10.316202
MA0156.10.4018
MA0157.10.421609
MA0158.10
MA0159.10.96592
MA0160.10.703717
MA0161.10
MA0162.10.0130334
MA0163.10.00623
MA0164.10.948242
MA0080.20.366978
MA0018.20.337929
MA0099.22.12264
MA0079.20.0126595
MA0102.22.57682
MA0258.10.218609
MA0259.10.0828875
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
NR3C1#290854.403830391521480.004161988042321540.0198309169739504



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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