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Coexpression cluster:C533: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.144412,0.369826,0.431729,1.25994,0.11364,0.240734,0.300393,0.428015,0.740994,0.0503338,0.218065,0.335828,0.137255,0.291158,0.362746,0.796807,0.489874,0.0827014,0.983369,0.267126,0.431825,0.150959,0.234854,0.722974,0.170101,0.354732,0.512008,0.233219,0.115495,0.242389,1.10654,0.522822,0.506728,0.13985,0.0937035,0.89502,0.0919402,0.241614,0.272549,0.37945,0.0929322,0.190375,1.04855,0.728968,0.267892,0.482397,0.301272,0.603923,0.292932,0.115573,0.366671,0.310813,0.56057,0.592653,2.91856,0.293507,1.2386,0.267557,0.740906,0.266768,0.559896,0.303183,0.0509632,1.17513,0.317765,1.10998,0.818746,1.17567,0.513487,1.01727,1.0232,0.442034,0.0615023,0.73304,0.0326098,0.118275,0.771988,0.450429,0.510572,0.497229,0.647118,0.464358,0.851126,1.63467,0.684728,0.0207599,0.00893619,0.0933568,0.38876,1.27332,0.90828,0.659533,0.537982,0.525061,0.114084,0.558858,0.624534,0.576706,0.392699,0.95583,0.0801198,0.532876,3.51044,1.2348,0.425079,0.214722,0.479058,0.288402,0.507144,0.104263,0.146911,0.569087,0.136085,0.225069,0.862131,0.091073,0.00825856,0.201199,0.433061,1.8892,0.725237,0.386689,0.23864,0.326716,0.968805,0.451097,0.295287,0.542501,0.765493,0.561324,0.660176,0.204142,0.779127,0.323981,0.920697,0.0869056,0.574529,2.67835,0.879842,1.7239,1.32497,0.844052,0.296675,0.573485,0.426604,0.260955,0.412168,1.56567,0.188015,0.0681329,0.0532623,0.00407349,0.660531,0.047435,0.302791,1.04704,0.374997,0.343221,0.507668,0.150717,0.842888,0.643319,0.509866,0.152845,1.12193,0.849678,0.0623453,0.299321,0.154311
|tfbs_overrepresentation_jaspar=MA0003.1;0.00504314,MA0004.1;0.221943,MA0006.1;0.112549,MA0007.1;0.208008,MA0009.1;0.621697,MA0014.1;0.00547893,MA0017.1;0.840365,MA0019.1;0.340029,MA0024.1;0.525161,MA0025.1;0.747404,MA0027.1;2.20546,MA0028.1;0.122394,MA0029.1;1.34042,MA0030.1;0.532314,MA0031.1;0.474026,MA0038.1;0.302644,MA0040.1;0.548121,MA0041.1;0.664972,MA0042.1;1.14502,MA0043.1;0.621991,MA0046.1;0.611559,MA0048.1;0.0140676,MA0050.1;0.609862,MA0051.1;0.299199,MA0052.1;0.551663,MA0055.1;0.157354,MA0056.1;0,MA0057.1;0.0616251,MA0058.1;0.153757,MA0059.1;0.15289,MA0060.1;0.422819,MA0061.1;0.356644,MA0063.1;0,MA0066.1;0.302992,MA0067.1;0.924196,MA0068.1;0.0264141,MA0069.1;2.51353,MA0070.1;0.597583,MA0071.1;0.27142,MA0072.1;0.593415,MA0073.1;0.0135515,MA0074.1;0.298586,MA0076.1;0.164578,MA0077.1;0.586275,MA0078.1;0.382364,MA0081.1;0.465308,MA0083.1;0.628701,MA0084.1;1.10674,MA0087.1;0.591148,MA0088.1;0.00460154,MA0089.1;0,MA0090.1;2.25599,MA0091.1;0.636604,MA0092.1;0.570207,MA0093.1;0.114388,MA0095.1;0,MA0098.1;0,MA0100.1;0.314026,MA0101.1;0.372085,MA0103.1;0.34743,MA0105.1;0.14145,MA0106.1;0.33677,MA0107.1;0.259598,MA0108.2;1.18798,MA0109.1;0,MA0111.1;0.184188,MA0113.1;0.350573,MA0114.1;0.25223,MA0115.1;0.850405,MA0116.1;0.560217,MA0117.1;0.656858,MA0119.1;1.39041,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;0.462123,MA0142.1;1.13296,MA0143.1;0.925263,MA0144.1;2.99887,MA0145.1;0.204689,MA0146.1;0.0122826,MA0147.1;0.0784275,MA0148.1;0.240905,MA0149.1;0.261654,MA0062.2;0.148712,MA0035.2;0.740647,MA0039.2;0.0172323,MA0138.2;0.38342,MA0002.2;0.0459391,MA0137.2;2.53112,MA0104.2;0.0505812,MA0047.2;0.326636,MA0112.2;0.0286692,MA0065.2;0.211898,MA0150.1;0.170499,MA0151.1;0,MA0152.1;0.274535,MA0153.1;0.714423,MA0154.1;1.4034,MA0155.1;0.316202,MA0156.1;0.12788,MA0157.1;0.421609,MA0158.1;0,MA0159.1;0.270712,MA0160.1;0.252705,MA0161.1;0,MA0162.1;0.000394937,MA0163.1;0.166772,MA0164.1;1.69021,MA0080.2;0.366978,MA0018.2;0.337929,MA0099.2;0.754549,MA0079.2;2.40535e-07,MA0102.2;1.14323,MA0258.1;0.476351,MA0259.1;0.28219,MA0442.1;0
}}
}}

Revision as of 19:14, 22 January 2013


Full id: C533_chorionic_amniotic_pancreatic_placenta_choriocarcinoma_Placental_mesothelioma



Phase1 CAGE Peaks

Hg19::chr11:57176838..57176845,-p@chr11:57176838..57176845
-
Hg19::chr11:76366237..76366246,+p@chr11:76366237..76366246
+
Hg19::chr14:59100774..59100790,+p8@DACT1
Hg19::chr14:77950830..77950869,-p3@ISM2
Hg19::chr14:77951201..77951226,-p4@ISM2
Hg19::chr19:52294756..52294758,-p@chr19:52294756..52294758
-
Hg19::chr1:207009817..207009859,+p2@IL19
Hg19::chr22:33000436..33000460,-p@chr22:33000436..33000460
-
Hg19::chr3:46069144..46069152,-p5@XCR1
Hg19::chr5:157345802..157345806,-p@chr5:157345802..157345806
-
Hg19::chr5:76724188..76724195,+p@chr5:76724188..76724195
+
Hg19::chr7:150554388..150554409,+p@chr7:150554388..150554409
+
Hg19::chrX:110507037..110507057,-p4@CAPN6
Hg19::chrX:110507067..110507079,-p6@CAPN6
Hg19::chrX:110507098..110507117,-p3@CAPN6
Hg19::chrX:110507128..110507134,-p8@CAPN6
Hg19::chrX:110507174..110507205,-p7@CAPN6


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
chorionic membrane mesenchymal stem cell2.28e-853
extraembryonic cell2.17e-2419
amnion mesenchymal stem cell6.04e-075
Uber Anatomy
Ontology termp-valuen
acellular anatomical structure2.28e-853
egg chorion2.28e-853
chorion5.80e-657
extraembryonic membrane1.12e-5014
membranous layer1.12e-5014
extraembryonic structure8.12e-3024
organ component layer4.13e-1166
placenta2.11e-084
allantois2.11e-084


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
MA0006.10.112549
MA0007.10.208008
MA0009.10.621697
MA0014.10.00547893
MA0017.10.840365
MA0019.10.340029
MA0024.10.525161
MA0025.10.747404
MA0027.12.20546
MA0028.10.122394
MA0029.11.34042
MA0030.10.532314
MA0031.10.474026
MA0038.10.302644
MA0040.10.548121
MA0041.10.664972
MA0042.11.14502
MA0043.10.621991
MA0046.10.611559
MA0048.10.0140676
MA0050.10.609862
MA0051.10.299199
MA0052.10.551663
MA0055.10.157354
MA0056.10
MA0057.10.0616251
MA0058.10.153757
MA0059.10.15289
MA0060.10.422819
MA0061.10.356644
MA0063.10
MA0066.10.302992
MA0067.10.924196
MA0068.10.0264141
MA0069.12.51353
MA0070.10.597583
MA0071.10.27142
MA0072.10.593415
MA0073.10.0135515
MA0074.10.298586
MA0076.10.164578
MA0077.10.586275
MA0078.10.382364
MA0081.10.465308
MA0083.10.628701
MA0084.11.10674
MA0087.10.591148
MA0088.10.00460154
MA0089.10
MA0090.12.25599
MA0091.10.636604
MA0092.10.570207
MA0093.10.114388
MA0095.10
MA0098.10
MA0100.10.314026
MA0101.10.372085
MA0103.10.34743
MA0105.10.14145
MA0106.10.33677
MA0107.10.259598
MA0108.21.18798
MA0109.10
MA0111.10.184188
MA0113.10.350573
MA0114.10.25223
MA0115.10.850405
MA0116.10.560217
MA0117.10.656858
MA0119.11.39041
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
MA0141.10.462123
MA0142.11.13296
MA0143.10.925263
MA0144.12.99887
MA0145.10.204689
MA0146.10.0122826
MA0147.10.0784275
MA0148.10.240905
MA0149.10.261654
MA0062.20.148712
MA0035.20.740647
MA0039.20.0172323
MA0138.20.38342
MA0002.20.0459391
MA0137.22.53112
MA0104.20.0505812
MA0047.20.326636
MA0112.20.0286692
MA0065.20.211898
MA0150.10.170499
MA0151.10
MA0152.10.274535
MA0153.10.714423
MA0154.11.4034
MA0155.10.316202
MA0156.10.12788
MA0157.10.421609
MA0158.10
MA0159.10.270712
MA0160.10.252705
MA0161.10
MA0162.10.000394937
MA0163.10.166772
MA0164.11.69021
MA0080.20.366978
MA0018.20.337929
MA0099.20.754549
MA0079.22.40535e-07
MA0102.21.14323
MA0258.10.476351
MA0259.10.28219
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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