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Coexpression cluster:C712: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.22923,0.854134,0.223258,0.345441,0.190185,0.344001,1.05908,0.104517,0.336485,1.88761,0.317729,0.451026,0.0765797,0.401301,0.189126,0.207465,0.617549,0.148925,0.59696,0.120925,0.223306,0.0148753,0.337221,1.04387,0.260754,0.471832,1.80469,0.335332,0.192587,1.20435,0.298956,0.65246,0.790946,0.0778977,0.953152,2.99133,0.161511,0.345014,0.14439,1.05941,0.48973,0.285097,0.0815132,0.187953,0.912793,0.693545,0.412635,0.308385,0.0157812,0.562381,0.484909,0.423285,0.626062,0.725869,0.873575,0.403938,0.195993,0.374657,0.0564659,0.976149,0.691524,0.414771,0.337335,0.591384,0.43102,1.37484,2.20402,1.32257,0.642589,1.16217,0.273995,0.350755,15.2951,0.871629,0.546891,0.237079,0.059808,0.575479,0.639503,0.255642,1.02516,0.590372,0.4307,0.10636,0.821696,0.524562,0.285494,1.17597,0.508983,1.42111,1.05129,0.795567,0.66846,0.130784,18.5205,1.98752,0.59259,0.709167,0.51326,0.175799,0.446192,0.663075,0.703825,0.621018,0.54826,0.313822,0.606045,0.398205,12.65,7.62104,1.90146,0.701175,0.21882,0.325885,1.00416,0.16034,0.61694,0.297931,0.556847,0.821661,0.863578,0.506732,0.341589,0.44095,1.11293,2.41067,0.405934,1.61431,0.905059,0.140769,0.796235,0.301402,0.919079,0.437919,1.06395,0.421703,0.293853,0.335825,1.02226,1.87395,3.24244,0.985665,0.407489,1.68202,0.549903,0.367151,0.534339,1.71519,0.282284,0.403378,0.902715,11.858,0.796604,0.0978005,0.414334,1.19239,0.494,0.179455,0.722397,0.237047,0.984474,0.778717,0.638755,0.673477,0.564971,0.429983,0.120139,0.410452,0.0701484
|tfbs_overrepresentation_for_novel_motifs=0.22923,0.854134,0.223258,0.345441,0.190185,0.344001,1.05908,0.104517,0.336485,1.88761,0.317729,0.451026,0.0765797,0.401301,0.189126,0.207465,0.617549,0.148925,0.59696,0.120925,0.223306,0.0148753,0.337221,1.04387,0.260754,0.471832,1.80469,0.335332,0.192587,1.20435,0.298956,0.65246,0.790946,0.0778977,0.953152,2.99133,0.161511,0.345014,0.14439,1.05941,0.48973,0.285097,0.0815132,0.187953,0.912793,0.693545,0.412635,0.308385,0.0157812,0.562381,0.484909,0.423285,0.626062,0.725869,0.873575,0.403938,0.195993,0.374657,0.0564659,0.976149,0.691524,0.414771,0.337335,0.591384,0.43102,1.37484,2.20402,1.32257,0.642589,1.16217,0.273995,0.350755,15.2951,0.871629,0.546891,0.237079,0.059808,0.575479,0.639503,0.255642,1.02516,0.590372,0.4307,0.10636,0.821696,0.524562,0.285494,1.17597,0.508983,1.42111,1.05129,0.795567,0.66846,0.130784,18.5205,1.98752,0.59259,0.709167,0.51326,0.175799,0.446192,0.663075,0.703825,0.621018,0.54826,0.313822,0.606045,0.398205,12.65,7.62104,1.90146,0.701175,0.21882,0.325885,1.00416,0.16034,0.61694,0.297931,0.556847,0.821661,0.863578,0.506732,0.341589,0.44095,1.11293,2.41067,0.405934,1.61431,0.905059,0.140769,0.796235,0.301402,0.919079,0.437919,1.06395,0.421703,0.293853,0.335825,1.02226,1.87395,3.24244,0.985665,0.407489,1.68202,0.549903,0.367151,0.534339,1.71519,0.282284,0.403378,0.902715,11.858,0.796604,0.0978005,0.414334,1.19239,0.494,0.179455,0.722397,0.237047,0.984474,0.778717,0.638755,0.673477,0.564971,0.429983,0.120139,0.410452,0.0701484
|tfbs_overrepresentation_jaspar=MA0003.1;2.22856,MA0004.1;0.32225,MA0006.1;0.552945,MA0007.1;0.305951,MA0009.1;0.756202,MA0014.1;0.292292,MA0017.1;0.220105,MA0019.1;0.45566,MA0024.1;0.654931,MA0025.1;0.886436,MA0027.1;2.35633,MA0028.1;0.201461,MA0029.1;0.673506,MA0030.1;0.662482,MA0031.1;0.600685,MA0038.1;0.414169,MA0040.1;0.67914,MA0041.1;0.338572,MA0042.1;0.310552,MA0043.1;0.756508,MA0046.1;0.745626,MA0048.1;1.90675,MA0050.1;0.311321,MA0051.1;0.410316,MA0052.1;0.682867,MA0055.1;2.43781,MA0056.1;0,MA0057.1;9.68219,MA0058.1;0.676094,MA0059.1;0.239727,MA0060.1;0.103131,MA0061.1;1.01669,MA0063.1;0,MA0066.1;0.414559,MA0067.1;1.06751,MA0068.1;1.28029,MA0069.1;0.741884,MA0070.1;0.731026,MA0071.1;0.379038,MA0072.1;0.726666,MA0073.1;15.3057,MA0074.1;0.40963,MA0076.1;0.254045,MA0077.1;0.719193,MA0078.1;1.25378,MA0081.1;0.239862,MA0083.1;0.763502,MA0084.1;1.25286,MA0087.1;0.724294,MA0088.1;0.20556,MA0089.1;0,MA0090.1;0.266215,MA0091.1;0.324543,MA0092.1;0.793019,MA0093.1;0.191154,MA0095.1;0,MA0098.1;0,MA0100.1;0.426863,MA0101.1;0.19375,MA0103.1;0.535462,MA0105.1;4.00007,MA0106.1;0.452066,MA0107.1;0.137948,MA0108.2;0.597764,MA0109.1;0,MA0111.1;0.277713,MA0113.1;0.467266,MA0114.1;0.134281,MA0115.1;0.992167,MA0116.1;0.140463,MA0117.1;0.792789,MA0119.1;0.226505,MA0122.1;0.818044,MA0124.1;0.951337,MA0125.1;0.868909,MA0130.1;0,MA0131.1;3.2772,MA0132.1;0,MA0133.1;0,MA0135.1;0.785738,MA0136.1;1.07857,MA0139.1;0.0781324,MA0140.1;0.376643,MA0141.1;0.238287,MA0142.1;0.570448,MA0143.1;0.467429,MA0144.1;0.124153,MA0145.1;1.05522,MA0146.1;0.0677137,MA0147.1;0.143012,MA0148.1;0.344198,MA0149.1;0.367947,MA0062.2;0.589182,MA0035.2;0.376007,MA0039.2;0.117947,MA0138.2;0.503176,MA0002.2;0.0954816,MA0137.2;0.20663,MA0104.2;0.102626,MA0047.2;0.440861,MA0112.2;1.00671,MA0065.2;6.17287,MA0150.1;0.261236,MA0151.1;0,MA0152.1;0.382565,MA0153.1;0.852412,MA0154.1;0.126936,MA0155.1;2.72279,MA0156.1;1.13151,MA0157.1;0.544523,MA0158.1;0,MA0159.1;0.441451,MA0160.1;0.357736,MA0161.1;0,MA0162.1;7.17161,MA0163.1;16.9603,MA0164.1;0.478818,MA0080.2;1.677,MA0018.2;0.453345,MA0099.2;0.382887,MA0079.2;51.6326,MA0102.2;1.28978,MA0258.1;0.375,MA0259.1;0.149181,MA0442.1;0
}}
}}

Revision as of 19:23, 22 January 2013


Full id: C712_thymus_biphenotypic_CD4_non_granulocyte_merkel_acute



Phase1 CAGE Peaks

Hg19::chr3:18480105..18480108,-p48@SATB1
Hg19::chr3:18480151..18480162,-p18@SATB1
Hg19::chr3:18480173..18480189,-p6@SATB1
Hg19::chr3:18486202..18486209,-p5@TBC1D5
Hg19::chr3:18486296..18486319,-p3@TBC1D5
Hg19::chr3:18486324..18486338,-p4@TBC1D5
Hg19::chr3:18486354..18486377,-p2@SATB1
Hg19::chr3:18486459..18486481,+p2@ENST00000414198
Hg19::chr3:18486486..18486500,+p1@ENST00000414198
Hg19::chr3:18487033..18487044,-p23@SATB1
Hg19::chr3:18487057..18487105,-p4@SATB1
Hg19::chr8:66754259..66754276,-p2@PDE7A


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:00041153',5'-cyclic-AMP phosphodiesterase activity0.0284167707669588
GO:0016571histone methylation0.0284167707669588
GO:0005720nuclear heterochromatin0.0284167707669588
GO:0000792heterochromatin0.0284167707669588
GO:0008213protein amino acid alkylation0.0284167707669588
GO:0006479protein amino acid methylation0.0284167707669588
GO:0000790nuclear chromatin0.0284167707669588
GO:00041143',5'-cyclic-nucleotide phosphodiesterase activity0.0360071200977271
GO:0043414biopolymer methylation0.0360071200977271
GO:0004112cyclic-nucleotide phosphodiesterase activity0.0360071200977271
GO:0016570histone modification0.0360071200977271
GO:0016569covalent chromatin modification0.0360071200977271
GO:0044454nuclear chromosome part0.0444142842183568
GO:0032259methylation0.0444142842183568



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>disease_data<br>

Cell Type
Ontology termp-valuen
hematopoietic stem cell8.80e-36168
angioblastic mesenchymal cell8.80e-36168
hematopoietic cell2.16e-34177
hematopoietic oligopotent progenitor cell6.27e-31161
hematopoietic multipotent progenitor cell6.27e-31161
leukocyte5.82e-28136
nongranular leukocyte1.66e-26115
lymphoid lineage restricted progenitor cell4.62e-2552
lymphocyte2.86e-2453
common lymphoid progenitor2.86e-2453
hematopoietic lineage restricted progenitor cell3.02e-23120
nucleate cell8.87e-2355
T cell4.51e-2125
pro-T cell4.51e-2125
mature alpha-beta T cell1.77e-1818
alpha-beta T cell1.77e-1818
immature T cell1.77e-1818
mature T cell1.77e-1818
immature alpha-beta T cell1.77e-1818
CD8-positive, alpha-beta T cell4.57e-1211
myeloid cell2.04e-10108
common myeloid progenitor2.04e-10108
B cell1.42e-0914
CD4-positive, alpha-beta T cell2.41e-076
Uber Anatomy
Ontology termp-valuen
hematopoietic system6.04e-1398
blood island6.04e-1398
blood2.29e-1215
haemolymphatic fluid2.29e-1215
organism substance2.29e-1215
hemolymphoid system9.84e-12108
neocortex4.60e-0920
adult organism6.34e-09114
regional part of cerebral cortex8.11e-0922
cerebral cortex3.55e-0725
pallium3.55e-0725
Disease
Ontology termp-valuen
hematologic cancer2.29e-1151
immune system cancer2.29e-1151
leukemia1.62e-1039
myeloid leukemia3.30e-0931


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)
MA0003.12.22856
MA0004.10.32225
MA0006.10.552945
MA0007.10.305951
MA0009.10.756202
MA0014.10.292292
MA0017.10.220105
MA0019.10.45566
MA0024.10.654931
MA0025.10.886436
MA0027.12.35633
MA0028.10.201461
MA0029.10.673506
MA0030.10.662482
MA0031.10.600685
MA0038.10.414169
MA0040.10.67914
MA0041.10.338572
MA0042.10.310552
MA0043.10.756508
MA0046.10.745626
MA0048.11.90675
MA0050.10.311321
MA0051.10.410316
MA0052.10.682867
MA0055.12.43781
MA0056.10
MA0057.19.68219
MA0058.10.676094
MA0059.10.239727
MA0060.10.103131
MA0061.11.01669
MA0063.10
MA0066.10.414559
MA0067.11.06751
MA0068.11.28029
MA0069.10.741884
MA0070.10.731026
MA0071.10.379038
MA0072.10.726666
MA0073.115.3057
MA0074.10.40963
MA0076.10.254045
MA0077.10.719193
MA0078.11.25378
MA0081.10.239862
MA0083.10.763502
MA0084.11.25286
MA0087.10.724294
MA0088.10.20556
MA0089.10
MA0090.10.266215
MA0091.10.324543
MA0092.10.793019
MA0093.10.191154
MA0095.10
MA0098.10
MA0100.10.426863
MA0101.10.19375
MA0103.10.535462
MA0105.14.00007
MA0106.10.452066
MA0107.10.137948
MA0108.20.597764
MA0109.10
MA0111.10.277713
MA0113.10.467266
MA0114.10.134281
MA0115.10.992167
MA0116.10.140463
MA0117.10.792789
MA0119.10.226505
MA0122.10.818044
MA0124.10.951337
MA0125.10.868909
MA0130.10
MA0131.13.2772
MA0132.10
MA0133.10
MA0135.10.785738
MA0136.11.07857
MA0139.10.0781324
MA0140.10.376643
MA0141.10.238287
MA0142.10.570448
MA0143.10.467429
MA0144.10.124153
MA0145.11.05522
MA0146.10.0677137
MA0147.10.143012
MA0148.10.344198
MA0149.10.367947
MA0062.20.589182
MA0035.20.376007
MA0039.20.117947
MA0138.20.503176
MA0002.20.0954816
MA0137.20.20663
MA0104.20.102626
MA0047.20.440861
MA0112.21.00671
MA0065.26.17287
MA0150.10.261236
MA0151.10
MA0152.10.382565
MA0153.10.852412
MA0154.10.126936
MA0155.12.72279
MA0156.11.13151
MA0157.10.544523
MA0158.10
MA0159.10.441451
MA0160.10.357736
MA0161.10
MA0162.17.17161
MA0163.116.9603
MA0164.10.478818
MA0080.21.677
MA0018.20.453345
MA0099.20.382887
MA0079.251.6326
MA0102.21.28978
MA0258.10.375
MA0259.10.149181
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
CTCF#1066473.12681621762710.002570345138407310.0142199531682446



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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