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Coexpression cluster:C1473: Difference between revisions

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{{Coexpression_clusters
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0.232711,0.327419,0.402268,0.479755,0.163801,0.245045,0.373321,0.433875,0.395243,0.130132,0.373481,0.462042,0.213394,0.270174,0.406219,0.298,0.0963341,0.30902,0.0755079,0.12783,0.101672,0.0890286,0.465261,0.362561,0.578088,0.285875,0.225945,0.18761,0.20516,0.115576,0.385234,0.291842,0.392097,0.352327,0.232997,0.451856,0.521039,0.328594,0.294205,0.448388,0.278746,0.387086,0.232479,0.334662,0.336321,0.139427,0.450171,0.454978,0.366035,0.381922,0.372037,0.263608,0.3488,0.113083,0.218495,0.0928446,0.431643,0.316114,0.360691,0.0371914,0.35537,0.423126,0.0463025,0.244977,0.119936,0.395958,0.314638,0.322324,0.184473,0.363414,0.524458,0.482957,0.388728,0.157712,0.3633,0.202084,0.104337,0.104656,0.279419,0.149946,0.0797883,0.104584,0.537494,0.454949,0.378002,0.340219,0.412672,0.343186,0.155969,0.186603,0.124175,0.228962,0.12366,0.198264,0.128253,0.14669,0.240899,0.206424,0.0862744,0.129421,0.171188,0.0721407,0.251724,0.36701,0.156256,0.491191,0.573638,0.263371,0.457065,0.446399,0.360168,0.403229,0.507716,0.442751,0.323763,0.486842,0.458912,0.246162,0.295506,0.369944,0.358783,0.491474,0.417013,0.544575,0.21822,0.388558,0.397562,0.21727,0.351946,0.345508,0.484083,0.486223,0.437432,0.302171,0.398223,0.178399,0.547908,0.400541,0.372405,0.182559,0.164471,0.533328,0.313891,0.292462,0.46896,0.137165,0.467981,0.191837,0.395568,0.320916,0.289812,0.384881,0.441686,0.369492,0.592234|tfbs_overrepresentation_for_novel_motifs=1.97464,1.35536,0.436508,0.58616,0.393082,0.584466,0.662701,0.269608,0.267027,1.41135,0.553339,0.707204,0.635275,0.650887,0.391663,0.415981,0.889639,0.336106,0.236034,0.402028,0.436569,0.0880431,0.576478,0.387783,0.483957,0.730467,0.202389,0.574247,1.02557,0.547818,0.530785,0.92701,0.816912,1.19786,0.35719,0.909936,2.51365,0.585658,0.329602,0.69481,0.355745,0.513952,0.664116,0.390088,0.992846,1.18176,0.66382,0.542147,0.304272,0.396429,0.745008,0.675919,0.455399,1.00488,1.15929,0.653901,0.400834,0.62023,0.186533,0.619193,0.968558,0.666252,0.737866,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.275507,2.04216,1.15727,1.17153,0.594475,0.192925,0.84426,0.913168,1.20149,0.240887,0.86037,0.684313,0.749276,1.10535,0.406668,0.398737,0.536262,0.771626,1.71797,1.34233,1.07807,0.94406,0.30974,0.393853,0.32338,0.234532,0.987239,0.776336,0.166235,0.330999,0.938327,0.981588,0.893363,0.814675,1.35291,0.877269,0.647343,1.21459,0.982236,0.44815,0.978783,0.430775,0.563054,1.29401,0.352243,1.21803,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,0.324369,1.07876,1.32127,1.20639,0.692462,1.35529,0.999497,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,0.306342,0.424432,4.24288,1.07915,0.717973,0.665754,1.48627,0.755083,0.378604,0.484017,1.15112,1.27379,1.06043,0.912368,0.457485,0.83286,0.683502,0.29379,0.661335,0.0564726|tfbs_overrepresentation_jaspar=MA0003.1;0.756372,MA0004.1;0.558729,MA0006.1;0.391183,MA0007.1;0.539222,MA0009.1;1.03681,MA0014.1;0.108006,MA0017.1;0.432438,MA0019.1;0.7124,MA0024.1;0.929647,MA0025.1;1.17262,MA0027.1;2.65688,MA0028.1;0.408079,MA0029.1;0.949428,MA0030.1;0.937696,MA0031.1;0.871496,MA0038.1;0.665566,MA0040.1;0.955415,MA0041.1;0.578072,MA0042.1;0.544748,MA0043.1;1.03713,MA0046.1;1.02569,MA0048.1;0.152639,MA0050.1;0.545671,MA0051.1;0.661179,MA0052.1;0.959373,MA0055.1;0.465994,MA0056.1;0,MA0057.1;0.882847,MA0058.1;0.458909,MA0059.1;0.457555,MA0060.1;0.267412,MA0061.1;0.23892,MA0063.1;0,MA0066.1;1.59928,MA0067.1;1.35893,MA0068.1;0.199491,MA0069.1;1.02175,MA0070.1;1.01032,MA0071.1;0.625297,MA0072.1;1.00572,MA0073.1;0.959858,MA0074.1;0.660398,MA0076.1;0.475586,MA0077.1;0.997832,MA0078.1;0.763954,MA0081.1;0.457725,MA0083.1;1.04447,MA0084.1;1.5477,MA0087.1;1.00322,MA0088.1;0.660742,MA0089.1;0,MA0090.1;0.490736,MA0091.1;0.561458,MA0092.1;1.29635,MA0093.1;0.394379,MA0095.1;0,MA0098.1;0,MA0100.1;0.679972,MA0101.1;0.397846,MA0103.1;0.381434,MA0105.1;0.134725,MA0106.1;0.70837,MA0107.1;0.320267,MA0108.2;0.868347,MA0109.1;0,MA0111.1;0.504913,MA0113.1;0.725375,MA0114.1;0.314898,MA0115.1;1.28169,MA0116.1;0.865577,MA0117.1;1.07516,MA0119.1;0.440684,MA0122.1;1.10154,MA0124.1;1.23968,MA0125.1;1.15445,MA0130.1;0,MA0131.1;0.782708,MA0132.1;0,MA0133.1;0,MA0135.1;1.06778,MA0136.1;0.672893,MA0139.1;0.641617,MA0140.1;0.622527,MA0141.1;0.455728,MA0142.1;0.838805,MA0143.1;0.725558,MA0144.1;0.299851,MA0145.1;0.707171,MA0146.1;0.093337,MA0147.1;0.327615,MA0148.1;0.584698,MA0149.1;0.612449,MA0062.2;0.658749,MA0035.2;0.621793,MA0039.2;1.47843,MA0138.2;0.765223,MA0002.2;0.709311,MA0137.2;0.414885,MA0104.2;1.35181,MA0047.2;0.695777,MA0112.2;0.680553,MA0065.2;0.354331,MA0150.1;0.484557,MA0151.1;0,MA0152.1;0.629368,MA0153.1;1.13732,MA0154.1;0.413181,MA0155.1;1.09123,MA0156.1;0.417278,MA0157.1;0.810597,MA0158.1;0,MA0159.1;0.328286,MA0160.1;0.600559,MA0161.1;0,MA0162.1;3.59546,MA0163.1;3.1714,MA0164.1;0.738243,MA0080.2;0.394469,MA0018.2;0.709805,MA0099.2;0.629739,MA0079.2;5.1832,MA0102.2;1.58513,MA0258.1;0.788656,MA0259.1;0.336472,MA0442.1;0}}
|full_id=C1473_CD4_cerebellum_thymus_neuroblastoma_CD8_Peripheral_caudate
|gostat_on_coexpression_clusters=GO:0007270!nerve-nerve synaptic transmission!0.0432581913920992!814$GO:0004683!calmodulin-dependent protein kinase activity!0.0432581913920992!814
|id=C1473
}}

Latest revision as of 11:45, 17 September 2013


Full id: C1473_CD4_cerebellum_thymus_neuroblastoma_CD8_Peripheral_caudate



Phase1 CAGE Peaks

Hg19::chr1:24829320..24829332,+p6@RCAN3
Hg19::chr1:24829340..24829375,+p4@RCAN3
Hg19::chr5:110560072..110560106,+p1@CAMK4
Hg19::chr5:110560211..110560222,+p6@CAMK4
Hg19::chr5:110574533..110574537,+p@chr5:110574533..110574537
+
Hg19::chr5:110576837..110576844,+p@chr5:110576837..110576844
+


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:0007270nerve-nerve synaptic transmission0.0432581913920992
GO:0004683calmodulin-dependent protein kinase activity0.0432581913920992



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
lymphocyte1.13e-1753
common lymphoid progenitor1.13e-1753
lymphoid lineage restricted progenitor cell2.75e-1752
T cell2.53e-1625
pro-T cell2.53e-1625
nucleate cell1.55e-1555
mature alpha-beta T cell1.24e-1318
alpha-beta T cell1.24e-1318
immature T cell1.24e-1318
mature T cell1.24e-1318
immature alpha-beta T cell1.24e-1318
CD8-positive, alpha-beta T cell6.73e-0911
leukocyte2.19e-07136
nongranular leukocyte4.56e-07115
Uber Anatomy
Ontology termp-valuen
adult organism5.07e-22114
nervous system6.88e-2289
central nervous system1.65e-2181
neural tube3.58e-2056
neural rod3.58e-2056
future spinal cord3.58e-2056
neural keel3.58e-2056
regional part of nervous system7.07e-1953
regional part of brain7.07e-1953
brain1.91e-1768
future brain1.91e-1768
neural plate4.43e-1682
presumptive neural plate4.43e-1682
regional part of forebrain2.26e-1441
forebrain2.26e-1441
anterior neural tube2.26e-1441
future forebrain2.26e-1441
ecto-epithelium2.51e-14104
neurectoderm9.97e-1486
ectoderm-derived structure2.58e-12171
ectoderm2.58e-12171
presumptive ectoderm2.58e-12171
organ system subdivision4.17e-12223
pre-chordal neural plate6.97e-1261
brain grey matter1.37e-1134
gray matter1.37e-1134
telencephalon1.52e-1134
cerebral hemisphere6.73e-1132
regional part of telencephalon1.03e-1032
structure with developmental contribution from neural crest2.86e-09132
blood7.97e-0915
haemolymphatic fluid7.97e-0915
organism substance7.97e-0915
regional part of cerebral cortex4.24e-0822
neocortex4.29e-0820
cerebral cortex5.23e-0825
pallium5.23e-0825
posterior neural tube4.18e-0715
chordal neural plate4.18e-0715


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)
MA0003.10.756372
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.10.108006
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.10.152639
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.465994
MA0056.10
MA0057.10.882847
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.11.59928
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.959858
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.660742
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.11.29635
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.10.134725
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.10.865577
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.10.641617
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.707171
MA0146.10.093337
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.658749
MA0035.20.621793
MA0039.21.47843
MA0138.20.765223
MA0002.20.709311
MA0137.20.414885
MA0104.21.35181
MA0047.20.695777
MA0112.20.680553
MA0065.20.354331
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.413181
MA0155.11.09123
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.13.59546
MA0163.13.1714
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.25.1832
MA0102.21.58513
MA0258.10.788656
MA0259.10.336472
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
ZBTB7A#5134144.901272871917260.004079628118843750.019490063634048



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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