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Coexpression cluster:C505: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=1.25961,1.46071,0.373702,1.14604,0.643195,0.606129,2.08609,0.154541,1.40167,0.282303,0.189673,0.301621,0.485349,0.258863,0.0927703,0.343795,0.450873,0.0660543,0.0286164,0.362204,0.11705,3.81361,0.205464,0.30387,2.71962,1.54467,0.218477,0.203923,0.315774,0.189331,0.174693,0.483059,0.0517705,0.108443,0.0757346,0.23618,0.257826,0.6081,0.226317,6.12561,0.0750527,0.163791,0.128236,0.0919607,2.20996,0.833707,0.74012,2.3124,0.112517,1.08463,4.30207,4.8602,0.125437,3.42157,0.691633,0.261104,0.662384,0.236404,0.613944,4.453,0.519357,0.270343,1.40474,1.91633,0.284296,0.397545,0.774525,1.12911,1.19366,0.971498,0.470686,0.0416193,0.00841861,0.689771,0.101827,0.0203916,0.642482,0.412445,0.471083,0.141103,0.294658,0.426001,0.284019,0.0405501,0.642096,0.14449,0.0920104,0.593236,0.352635,1.2264,0.863265,0.617268,0.497892,0.201541,0.0939013,0.476068,0.831692,1.32572,0.356444,3.40224,0.850238,0.492893,0.530844,1.15092,1.00701,2.34447,0.440324,0.256236,0.14483,3.36832,0.123668,0.528368,0.737452,0.196252,0.817503,0.255662,0.881923,0.173882,0.395564,0.451443,0.682065,0.350633,0.209033,0.292875,0.923346,1.06222,0.262802,0.502315,0.721838,0.0609207,0.617901,0.176632,0.73532,0.290252,0.875585,0.563858,1.55976,0.204325,0.83506,1.67608,1.2779,0.799588,0.264127,0.532681,1.01026,0.23014,0.375295,1.51807,0.161595,0.43693,0.623601,0.566686,0.618251,0.602047,0.269969,1.0011,0.339339,0.0861459,0.145027,0.127152,1.87354,0.601304,0.470393,0.805591,0.402913,0.283401,0.0484397,2.90043,0.31617
|tfbs_overrepresentation_for_novel_motifs=1.25961,1.46071,0.373702,1.14604,0.643195,0.606129,2.08609,0.154541,1.40167,0.282303,0.189673,0.301621,0.485349,0.258863,0.0927703,0.343795,0.450873,0.0660543,0.0286164,0.362204,0.11705,3.81361,0.205464,0.30387,2.71962,1.54467,0.218477,0.203923,0.315774,0.189331,0.174693,0.483059,0.0517705,0.108443,0.0757346,0.23618,0.257826,0.6081,0.226317,6.12561,0.0750527,0.163791,0.128236,0.0919607,2.20996,0.833707,0.74012,2.3124,0.112517,1.08463,4.30207,4.8602,0.125437,3.42157,0.691633,0.261104,0.662384,0.236404,0.613944,4.453,0.519357,0.270343,1.40474,1.91633,0.284296,0.397545,0.774525,1.12911,1.19366,0.971498,0.470686,0.0416193,0.00841861,0.689771,0.101827,0.0203916,0.642482,0.412445,0.471083,0.141103,0.294658,0.426001,0.284019,0.0405501,0.642096,0.14449,0.0920104,0.593236,0.352635,1.2264,0.863265,0.617268,0.497892,0.201541,0.0939013,0.476068,0.831692,1.32572,0.356444,3.40224,0.850238,0.492893,0.530844,1.15092,1.00701,2.34447,0.440324,0.256236,0.14483,3.36832,0.123668,0.528368,0.737452,0.196252,0.817503,0.255662,0.881923,0.173882,0.395564,0.451443,0.682065,0.350633,0.209033,0.292875,0.923346,1.06222,0.262802,0.502315,0.721838,0.0609207,0.617901,0.176632,0.73532,0.290252,0.875585,0.563858,1.55976,0.204325,0.83506,1.67608,1.2779,0.799588,0.264127,0.532681,1.01026,0.23014,0.375295,1.51807,0.161595,0.43693,0.623601,0.566686,0.618251,0.602047,0.269969,1.0011,0.339339,0.0861459,0.145027,0.127152,1.87354,0.601304,0.470393,0.805591,0.402913,0.283401,0.0484397,2.90043,0.31617
|tfbs_overrepresentation_jaspar=MA0003.1;2.8722e-05,MA0004.1;0.193314,MA0006.1;0.0925234,MA0007.1;0.180248,MA0009.1;0.580032,MA0014.1;0.096993,MA0017.1;0.114723,MA0019.1;0.305657,MA0024.1;0.485346,MA0025.1;0.70396,MA0027.1;2.15732,MA0028.1;0.101383,MA0029.1;0.50258,MA0030.1;0.492344,MA0031.1;0.435419,MA0038.1;0.743126,MA0040.1;0.507819,MA0041.1;0.206566,MA0042.1;0.183918,MA0043.1;0.580321,MA0046.1;1.39813,MA0048.1;0.465769,MA0050.1;0.184533,MA0051.1;0.266537,MA0052.1;0.511289,MA0055.1;2.90103,MA0056.1;0,MA0057.1;1.31669,MA0058.1;0.12994,MA0059.1;0.129144,MA0060.1;0.0387582,MA0061.1;0.290613,MA0063.1;0,MA0066.1;0.270161,MA0067.1;0.879057,MA0068.1;0.213016,MA0069.1;0.566544,MA0070.1;0.556335,MA0071.1;0.240074,MA0072.1;0.552241,MA0073.1;0.660244,MA0074.1;0.265952,MA0076.1;0.139892,MA0077.1;0.545231,MA0078.1;0.346453,MA0081.1;0.129245,MA0083.1;2.44546,MA0084.1;1.06048,MA0087.1;0.550016,MA0088.1;0.398465,MA0089.1;0,MA0090.1;0.149167,MA0091.1;0.195166,MA0092.1;0.974084,MA0093.1;0.0941737,MA0095.1;0,MA0098.1;0,MA0100.1;0.280715,MA0101.1;0.0959778,MA0103.1;0.0875643,MA0105.1;0.220534,MA0106.1;1.48277,MA0107.1;0.0591705,MA0108.2;0.432749,MA0109.1;0,MA0111.1;0.15804,MA0113.1;0.315797,MA0114.1;1.20883,MA0115.1;0.805883,MA0116.1;2.91094,MA0117.1;0.614633,MA0119.1;0.119385,MA0122.1;2.6121,MA0124.1;0.766407,MA0125.1;0.687166,MA0130.1;0,MA0131.1;0.361613,MA0132.1;0,MA0133.1;0,MA0135.1;0.60795,MA0136.1;0.27535,MA0139.1;0.792683,MA0140.1;0.238066,MA0141.1;0.128074,MA0142.1;0.407878,MA0143.1;0.315941,MA0144.1;0.422223,MA0145.1;0.940442,MA0146.1;0.759001,MA0147.1;0.485912,MA0148.1;0.211171,MA0149.1;0.230803,MA0062.2;0.027823,MA0035.2;0.237534,MA0039.2;0.00287338,MA0138.2;2.48276,MA0002.2;0.324376,MA0137.2;0.697429,MA0104.2;0.0384802,MA0047.2;0.292798,MA0112.2;0.00303039,MA0065.2;0.468021,MA0150.1;0.145358,MA0151.1;0,MA0152.1;0.243034,MA0153.1;1.61049,MA0154.1;0.100086,MA0155.1;0.236629,MA0156.1;0.106343,MA0157.1;0.384449,MA0158.1;0,MA0159.1;0.840681,MA0160.1;0.222325,MA0161.1;0,MA0162.1;1.2531,MA0163.1;0.0100696,MA0164.1;0.32594,MA0080.2;0.0942207,MA0018.2;0.30364,MA0099.2;0.243305,MA0079.2;0.0183721,MA0102.2;1.09681,MA0258.1;0.399676,MA0259.1;0.0662172,MA0442.1;0
}}
}}

Revision as of 19:13, 22 January 2013


Full id: C505_mature_CD14_sacrococcigeal_Mast_chorionic_glassy_oral



Phase1 CAGE Peaks

Hg19::chr5:137801160..137801176,+p1@EGR1
Hg19::chr5:137802449..137802462,+p@chr5:137802449..137802462
+
Hg19::chr5:137802469..137802557,+p@chr5:137802469..137802557
+
Hg19::chr5:137802584..137802608,+p@chr5:137802584..137802608
+
Hg19::chr5:137802614..137802705,+p@chr5:137802614..137802705
+
Hg19::chr5:137802741..137802781,+p@chr5:137802741..137802781
+
Hg19::chr5:137802806..137802857,+p@chr5:137802806..137802857
+
Hg19::chr5:137802917..137802941,+p@chr5:137802917..137802941
+
Hg19::chr5:137802943..137802955,+p@chr5:137802943..137802955
+
Hg19::chr5:137802959..137803004,+p@chr5:137802959..137803004
+
Hg19::chr5:137803005..137803079,+p@chr5:137803005..137803079
+
Hg19::chr5:137803081..137803110,+p@chr5:137803081..137803110
+
Hg19::chr5:137803118..137803156,+p@chr5:137803118..137803156
+
Hg19::chr5:137803163..137803193,+p@chr5:137803163..137803193
+
Hg19::chr5:137803308..137803321,+p@chr5:137803308..137803321
+
Hg19::chr5:137803432..137803463,+p@chr5:137803432..137803463
+
Hg19::chr5:137803467..137803483,+p@chr5:137803467..137803483
+
Hg19::chr5:137803485..137803515,+p@chr5:137803485..137803515
+
Hg19::chr5:137804130..137804156,+p5@EGR1


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><br><br><br>


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)
MA0003.12.8722e-05
MA0004.10.193314
MA0006.10.0925234
MA0007.10.180248
MA0009.10.580032
MA0014.10.096993
MA0017.10.114723
MA0019.10.305657
MA0024.10.485346
MA0025.10.70396
MA0027.12.15732
MA0028.10.101383
MA0029.10.50258
MA0030.10.492344
MA0031.10.435419
MA0038.10.743126
MA0040.10.507819
MA0041.10.206566
MA0042.10.183918
MA0043.10.580321
MA0046.11.39813
MA0048.10.465769
MA0050.10.184533
MA0051.10.266537
MA0052.10.511289
MA0055.12.90103
MA0056.10
MA0057.11.31669
MA0058.10.12994
MA0059.10.129144
MA0060.10.0387582
MA0061.10.290613
MA0063.10
MA0066.10.270161
MA0067.10.879057
MA0068.10.213016
MA0069.10.566544
MA0070.10.556335
MA0071.10.240074
MA0072.10.552241
MA0073.10.660244
MA0074.10.265952
MA0076.10.139892
MA0077.10.545231
MA0078.10.346453
MA0081.10.129245
MA0083.12.44546
MA0084.11.06048
MA0087.10.550016
MA0088.10.398465
MA0089.10
MA0090.10.149167
MA0091.10.195166
MA0092.10.974084
MA0093.10.0941737
MA0095.10
MA0098.10
MA0100.10.280715
MA0101.10.0959778
MA0103.10.0875643
MA0105.10.220534
MA0106.11.48277
MA0107.10.0591705
MA0108.20.432749
MA0109.10
MA0111.10.15804
MA0113.10.315797
MA0114.11.20883
MA0115.10.805883
MA0116.12.91094
MA0117.10.614633
MA0119.10.119385
MA0122.12.6121
MA0124.10.766407
MA0125.10.687166
MA0130.10
MA0131.10.361613
MA0132.10
MA0133.10
MA0135.10.60795
MA0136.10.27535
MA0139.10.792683
MA0140.10.238066
MA0141.10.128074
MA0142.10.407878
MA0143.10.315941
MA0144.10.422223
MA0145.10.940442
MA0146.10.759001
MA0147.10.485912
MA0148.10.211171
MA0149.10.230803
MA0062.20.027823
MA0035.20.237534
MA0039.20.00287338
MA0138.22.48276
MA0002.20.324376
MA0137.20.697429
MA0104.20.0384802
MA0047.20.292798
MA0112.20.00303039
MA0065.20.468021
MA0150.10.145358
MA0151.10
MA0152.10.243034
MA0153.11.61049
MA0154.10.100086
MA0155.10.236629
MA0156.10.106343
MA0157.10.384449
MA0158.10
MA0159.10.840681
MA0160.10.222325
MA0161.10
MA0162.11.2531
MA0163.10.0100696
MA0164.10.32594
MA0080.20.0942207
MA0018.20.30364
MA0099.20.243305
MA0079.20.0183721
MA0102.21.09681
MA0258.10.399676
MA0259.10.0662172
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
HEY1#23462194.040111043105713.00127317794054e-123.98284586316305e-10
HMGN3#9324135.595848442292511.79498246336419e-081.29465589427688e-06
JUND#3727196.994663941871038.8515729556251e-171.78810334219058e-14
POLR2A#5430192.147453176558074.9316078952508e-072.31276244711315e-05
TAF7#68791911.43306940492397.77521211134875e-212.04542916296512e-18
USF2#73921610.94079779795331.16459706215979e-152.17973750134241e-13



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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