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Coexpression cluster:C343: Difference between revisions

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{{Coexpression_clusters
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otifs=0.0391464,0.00254248,0.0369474,0.0925076,0.495643,1.06002,0.13057,0.0995429,0.0329752,0.0581611,0.268855,2.10871,0.413404,0.392606,1.15023,0.12818,0.274123,1.23697,0.153151,0.321495,0.960081,0.0444592,0.296637,0.481875,0.192249,0.169033,0.337933,0.293913,0.0265947,0.444762,0.242813,0.301321,0.0494746,0.256542,0.0827481,0.115837,0.0177865,0.0922784,0.171279,0.00455194,0.978537,0.224075,0.412896,1.55788,0.00348222,0.0465565,0.131171,0.0734603,0.503289,0.11199,0.177819,0.137739,0.430141,0.360536,0.486376,0.125892,0.516012,0.351905,0.0815711,0.350556,0.332512,0.132479,0.0973965,0.254197,0.142578,0.230153,0.562972,0.901485,0.293563,0.749341,0.0574197,1.21502,0.00357758,0.48467,0.0164828,0.00206097,0.0362778,0.24229,0.291149,0.415044,0.710094,0.253435,0.862965,0.21869,0.441299,0.00072851,0.315204,0.0299496,1.69457,0.996295,0.646289,0.418934,1.52397,1.86035,0.109936,0.163009,0.0664439,0.346841,0.197346,0.732058,0.342828,0.30972,0.342487,0.759064,0.222295,0.0761449,0.265312,1.2665,0.0516066,0.0966072,0.360197,0.340332,0.141117,0.0822381,0.603172,0.392926,0.00482095,0.241412,0.228549,0.055086,0.477624,0.192794,0.30296,0.148875,1.6769,0.242821,0.127096,0.317804,0.514129,0.164312,0.419503,0.246165,0.526577,0.146943,0.657947,0.0683077,0.0664814,0.294623,1.50245,1.43971,1.0467,0.586378,1.88863,0.344087,0.223488,0.694671,2.52963,1.2832,0.220325,0.0516244,0.0324351,4.98319e-05,0.419817,0.193031,1.32838,0.777752,1.03495,0.0981586,0.749387,0.162724,0.585299,1.0438,0.790405,0.0431301,0.661441,0.861039,0.00883143,0.406823,3.09231e-05|tfbs_overrepresentation_jaspar=MA0003.1;5.98086e-07,MA0004.1;0.579206,MA0006.1;0.107826,MA0007.1;0.0722718,MA0009.1;0.385713,MA0014.1;8.76096e-06,MA0017.1;0.332079,MA0019.1;0.158371,MA0024.1;0.303271,MA0025.1;0.497679,MA0027.1;1.91867,MA0028.1;0.0294248,MA0029.1;1.53836,MA0030.1;0.832636,MA0031.1;0.261233,MA0038.1;0.13211,MA0040.1;0.862479,MA0041.1;1.03949,MA0042.1;1.39887,MA0043.1;0.38597,MA0046.1;0.376892,MA0048.1;0.000540668,MA0050.1;0.074905,MA0051.1;0.129756,MA0052.1;0.325534,MA0055.1;0.0131594,MA0056.1;0,MA0057.1;0.000455305,MA0058.1;0.379924,MA0059.1;0.165985,MA0060.1;0.0331347,MA0061.1;0.29157,MA0063.1;0,MA0066.1;0.132349,MA0067.1;0.661236,MA0068.1;0.0117561,MA0069.1;0.373781,MA0070.1;1.70304,MA0071.1;1.74482,MA0072.1;0.361192,MA0073.1;3.09059e-06,MA0074.1;0.129338,MA0076.1;0.0488952,MA0077.1;0.355047,MA0078.1;0.189533,MA0081.1;0.166149,MA0083.1;0.391829,MA0084.1;0.834984,MA0087.1;0.359239,MA0088.1;0.000620757,MA0089.1;0,MA0090.1;0.440418,MA0091.1;0.0815509,MA0092.1;0.863695,MA0093.1;0.26762,MA0095.1;0,MA0098.1;0,MA0100.1;0.432601,MA0101.1;0.273268,MA0103.1;0.100295,MA0105.1;0.135316,MA0106.1;0.156032,MA0107.1;0.31847,MA0108.2;2.04146,MA0109.1;0,MA0111.1;0.21427,MA0113.1;0.961857,MA0114.1;0.0115288,MA0115.1;0.592273,MA0116.1;0.0128273,MA0117.1;0.416571,MA0119.1;0.976089,MA0122.1;0.438159,MA0124.1;0.555413,MA0125.1;1.21157,MA0130.1;0,MA0131.1;0.201414,MA0132.1;0,MA0133.1;0,MA0135.1;0.410584,MA0136.1;0.422748,MA0139.1;0.00305399,MA0140.1;0.719477,MA0141.1;1.96242,MA0142.1;0.238557,MA0143.1;0.166108,MA0144.1;0.471774,MA0145.1;0.00452149,MA0146.1;2.23771e-05,MA0147.1;0.0636933,MA0148.1;1.56876,MA0149.1;0.104897,MA0062.2;0.00348966,MA0035.2;0.717813,MA0039.2;4.84868e-08,MA0138.2;0.190328,MA0002.2;0.784715,MA0137.2;1.26417,MA0104.2;0.0964482,MA0047.2;2.05733,MA0112.2;0.0121201,MA0065.2;0.00104963,MA0150.1;0.428432,MA0151.1;0,MA0152.1;0.735018,MA0153.1;0.467885,MA0154.1;0.00995799,MA0155.1;0.0263338,MA0156.1;0.305765,MA0157.1;0.219589,MA0158.1;0,MA0159.1;0.565109,MA0160.1;0.670196,MA0161.1;0,MA0162.1;7.90637e-06,MA0163.1;6.39674e-05,MA0164.1;2.24917,MA0080.2;0.267767,MA0018.2;0.47492,MA0099.2;0.364364,MA0079.2;5.83418e-15,MA0102.2;0.870137,MA0258.1;0.00837251,MA0259.1;0.014781,MA0442.1;0}}
|full_id=C343_CD4_mycosis_kidney_signet_hairy_b_Mast
|id=C343
}}

Latest revision as of 11:20, 17 September 2013


Full id: C343_CD4_mycosis_kidney_signet_hairy_b_Mast



Phase1 CAGE Peaks

Hg19::chr12:12654214..12654217,-p@chr12:12654214..12654217
-
Hg19::chr12:12654228..12654244,-p@chr12:12654228..12654244
-
Hg19::chr12:12654246..12654268,-p@chr12:12654246..12654268
-
Hg19::chr12:12654286..12654294,-p@chr12:12654286..12654294
-
Hg19::chr12:9807687..9807696,+p@chr12:9807687..9807696
+
Hg19::chr13:42967639..42967658,+p@chr13:42967639..42967658
+
Hg19::chr14:34682595..34682600,-p@chr14:34682595..34682600
-
Hg19::chr14:34682624..34682671,-p@chr14:34682624..34682671
-
Hg19::chr16:3119260..3119271,+p@chr16:3119260..3119271
+
Hg19::chr16:78812540..78812565,+p@chr16:78812540..78812565
+
Hg19::chr16:78996801..78996806,+p@chr16:78996801..78996806
+
Hg19::chr17:53392505..53392514,+p@chr17:53392505..53392514
+
Hg19::chr17:62144141..62144166,-p@chr17:62144141..62144166
-
Hg19::chr17:62144174..62144202,-p@chr17:62144174..62144202
-
Hg19::chr18:9088659..9088670,-p@chr18:9088659..9088670
-
Hg19::chr18:9091167..9091184,-p@chr18:9091167..9091184
-
Hg19::chr18:9095000..9095021,+p@chr18:9095000..9095021
+
Hg19::chr1:117087364..117087378,+p@chr1:117087364..117087378
+
Hg19::chr1:209925409..209925446,+p@chr1:209925409..209925446
+
Hg19::chr1:64117070..64117080,+p12@PGM1
Hg19::chr22:30552802..30552806,+p@chr22:30552802..30552806
+
Hg19::chr2:39444239..39444249,+p@chr2:39444239..39444249
+
Hg19::chr2:39444261..39444268,+p@chr2:39444261..39444268
+
Hg19::chr3:4846563..4846612,+p@chr3:4846563..4846612
+
Hg19::chr3:4948148..4948153,-p4@LOC100507582
Hg19::chr3:4948161..4948169,-p2@LOC100507582
Hg19::chr3:4948180..4948195,-p1@LOC100507582
Hg19::chr3:53778674..53778721,+p@chr3:53778674..53778721
+
Hg19::chr3:53880588..53880603,+p1@IL17RB
Hg19::chr5:131993856..131993873,+p1@IL13
Hg19::chr5:66500832..66500867,+p@chr5:66500832..66500867
+
Hg19::chr7:148907246..148907250,+p@chr7:148907246..148907250
+
Hg19::chr8:97296304..97296346,+p@chr8:97296304..97296346
+


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:0005144interleukin-13 receptor binding0.0127152316779048
GO:0004614phosphoglucomutase activity0.0127152316779048
GO:0006952defense response0.0209988476158347
GO:0016868intramolecular transferase activity, phosphotransferases0.04233920409943
GO:0004907interleukin receptor activity0.04233920409943
GO:0019965interleukin binding0.04233920409943
GO:0005126hematopoietin/interferon-class (D200-domain) cytokine receptor binding0.0486485150110909
GO:0016866intramolecular transferase activity0.0486485150110909
GO:0004896hematopoietin/interferon-class (D200-domain) cytokine receptor activity0.0486485150110909



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)
MA0003.15.98086e-07
MA0004.10.579206
MA0006.10.107826
MA0007.10.0722718
MA0009.10.385713
MA0014.18.76096e-06
MA0017.10.332079
MA0019.10.158371
MA0024.10.303271
MA0025.10.497679
MA0027.11.91867
MA0028.10.0294248
MA0029.11.53836
MA0030.10.832636
MA0031.10.261233
MA0038.10.13211
MA0040.10.862479
MA0041.11.03949
MA0042.11.39887
MA0043.10.38597
MA0046.10.376892
MA0048.10.000540668
MA0050.10.074905
MA0051.10.129756
MA0052.10.325534
MA0055.10.0131594
MA0056.10
MA0057.10.000455305
MA0058.10.379924
MA0059.10.165985
MA0060.10.0331347
MA0061.10.29157
MA0063.10
MA0066.10.132349
MA0067.10.661236
MA0068.10.0117561
MA0069.10.373781
MA0070.11.70304
MA0071.11.74482
MA0072.10.361192
MA0073.13.09059e-06
MA0074.10.129338
MA0076.10.0488952
MA0077.10.355047
MA0078.10.189533
MA0081.10.166149
MA0083.10.391829
MA0084.10.834984
MA0087.10.359239
MA0088.10.000620757
MA0089.10
MA0090.10.440418
MA0091.10.0815509
MA0092.10.863695
MA0093.10.26762
MA0095.10
MA0098.10
MA0100.10.432601
MA0101.10.273268
MA0103.10.100295
MA0105.10.135316
MA0106.10.156032
MA0107.10.31847
MA0108.22.04146
MA0109.10
MA0111.10.21427
MA0113.10.961857
MA0114.10.0115288
MA0115.10.592273
MA0116.10.0128273
MA0117.10.416571
MA0119.10.976089
MA0122.10.438159
MA0124.10.555413
MA0125.11.21157
MA0130.10
MA0131.10.201414
MA0132.10
MA0133.10
MA0135.10.410584
MA0136.10.422748
MA0139.10.00305399
MA0140.10.719477
MA0141.11.96242
MA0142.10.238557
MA0143.10.166108
MA0144.10.471774
MA0145.10.00452149
MA0146.12.23771e-05
MA0147.10.0636933
MA0148.11.56876
MA0149.10.104897
MA0062.20.00348966
MA0035.20.717813
MA0039.24.84868e-08
MA0138.20.190328
MA0002.20.784715
MA0137.21.26417
MA0104.20.0964482
MA0047.22.05733
MA0112.20.0121201
MA0065.20.00104963
MA0150.10.428432
MA0151.10
MA0152.10.735018
MA0153.10.467885
MA0154.10.00995799
MA0155.10.0263338
MA0156.10.305765
MA0157.10.219589
MA0158.10
MA0159.10.565109
MA0160.10.670196
MA0161.10
MA0162.17.90637e-06
MA0163.16.39674e-05
MA0164.12.24917
MA0080.20.267767
MA0018.20.47492
MA0099.20.364364
MA0079.25.83418e-15
MA0102.20.870137
MA0258.10.00837251
MA0259.10.014781
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
BATF#1053853.690576029136910.01058778017317130.0391010315949729



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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