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Coexpression cluster:C1320: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.44418,0.333388,0.436508,0.58616,0.393082,0.584466,0.662701,0.742622,0.736703,0.555913,0.553339,0.707204,0.223349,0.650887,0.391663,0.415981,0.889639,0.336106,0.236034,0.127969,0.436569,0.6169,1.41165,0.387783,1.21515,1.73319,0.585619,0.574247,0.396295,0.186644,0.530785,0.92701,0.302275,0.225641,0.35719,0.0334022,0.35388,0.585658,0.329602,0.248856,0.936389,0.513952,0.0979105,0.390088,0.154075,0.468392,0.66382,0.542147,0.630853,1.02586,0.745008,1.61993,0.149032,1.00488,1.15929,0.653901,0.400834,0.62023,0.186533,1.50144,0.968558,1.59978,0.737866,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.275507,0.146905,1.15727,0.218784,2.48597,0.192925,0.84426,2.10892,0.477584,0.240887,0.86037,0.684313,0.272514,1.10535,0.181326,0.126687,0.181871,0.771626,1.71797,1.34233,1.07807,0.94406,0.83374,1.02023,0.32338,0.661488,0.987239,1.82799,0.962826,0.330999,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,0.647343,1.21459,0.376529,0.44815,0.978783,0.430775,0.563054,1.29401,0.352243,0.0577227,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,0.324369,1.07876,0.53374,1.20639,0.692462,1.35529,0.175219,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,0.306342,1.35665,0.0926553,1.07915,0.258882,0.665754,1.48627,0.755083,0.986797,0.484017,0.454152,1.27379,1.06043,0.912368,0.457485,0.83286,0.683502,0.79772,0.661335,0.152397
|tfbs_overrepresentation_jaspar=MA0003.1;0.176622,MA0004.1;0.558729,MA0006.1;0.391183,MA0007.1;0.539222,MA0009.1;1.03681,MA0014.1;0.491287,MA0017.1;0.432438,MA0019.1;0.7124,MA0024.1;2.14259,MA0025.1;1.17262,MA0027.1;2.65688,MA0028.1;1.05129,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;0.906394,MA0050.1;0.545671,MA0051.1;0.661179,MA0052.1;0.959373,MA0055.1;1.22849,MA0056.1;0,MA0057.1;0.882847,MA0058.1;0.458909,MA0059.1;0.457555,MA0060.1;0.267412,MA0061.1;0.671725,MA0063.1;0,MA0066.1;0.66601,MA0067.1;1.35893,MA0068.1;1.72313,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;2.07987,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;0.32124,MA0089.1;0,MA0090.1;0.490736,MA0091.1;1.37996,MA0092.1;0.522012,MA0093.1;0.394379,MA0095.1;0,MA0098.1;0,MA0100.1;0.679972,MA0101.1;0.397846,MA0103.1;0.381434,MA0105.1;0.419295,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;1.19942,MA0140.1;0.622527,MA0141.1;0.455728,MA0142.1;0.838805,MA0143.1;0.725558,MA0144.1;0.299851,MA0145.1;0.347815,MA0146.1;0.441872,MA0147.1;0.327615,MA0148.1;0.584698,MA0149.1;0.612449,MA0062.2;1.22729,MA0035.2;0.621793,MA0039.2;1.13151,MA0138.2;0.765223,MA0002.2;0.255126,MA0137.2;0.414885,MA0104.2;0.735746,MA0047.2;0.695777,MA0112.2;0.332548,MA0065.2;0.718489,MA0150.1;0.484557,MA0151.1;0,MA0152.1;0.629368,MA0153.1;1.13732,MA0154.1;0.413181,MA0155.1;0.318517,MA0156.1;0.417278,MA0157.1;0.810597,MA0158.1;0,MA0159.1;0.328286,MA0160.1;1.46233,MA0161.1;0,MA0162.1;0.978497,MA0163.1;0.508943,MA0164.1;0.738243,MA0080.2;0.394469,MA0018.2;0.709805,MA0099.2;0.629739,MA0079.2;1.19591,MA0102.2;1.58513,MA0258.1;0.289793,MA0259.1;0.336472,MA0442.1;0
}}
}}

Revision as of 19:51, 22 January 2013


Full id: C1320_Neutrophils_Eosinophils_CD14_Natural_Peripheral_Basophils_CD8



Phase1 CAGE Peaks

Hg19::chr10:70849864..70849882,-p@chr10:70849864..70849882
-
Hg19::chr12:19593186..19593212,-p@chr12:19593186..19593212
-
Hg19::chr15:79165517..79165535,-p@chr15:79165517..79165535
-
Hg19::chr17:36981699..36981722,+p2@MIR4727
Hg19::chr19:13957456..13957468,-p@chr19:13957456..13957468
-
Hg19::chrX:70331529..70331558,+p@chrX:70331529..70331558
+


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
leukocyte1.93e-66136
hematopoietic stem cell5.46e-57168
angioblastic mesenchymal cell5.46e-57168
hematopoietic cell6.76e-55177
hematopoietic oligopotent progenitor cell5.84e-52161
hematopoietic multipotent progenitor cell5.84e-52161
hematopoietic lineage restricted progenitor cell1.91e-51120
nongranular leukocyte2.67e-50115
classical monocyte1.53e-4542
CD14-positive, CD16-negative classical monocyte1.53e-4542
myeloid leukocyte3.65e-4072
defensive cell1.05e-3748
phagocyte1.05e-3748
granulocyte monocyte progenitor cell3.37e-3267
myeloid cell2.19e-31108
common myeloid progenitor2.19e-31108
macrophage dendritic cell progenitor4.70e-3061
myeloid lineage restricted progenitor cell8.40e-3066
monopoietic cell2.17e-2859
monocyte2.17e-2859
monoblast2.17e-2859
promonocyte2.17e-2859
lymphoid lineage restricted progenitor cell1.12e-1852
lymphocyte4.29e-1853
common lymphoid progenitor4.29e-1853
nucleate cell5.33e-1755
stuff accumulating cell1.34e-1487
mesenchymal cell7.22e-14354
connective tissue cell5.53e-13361
motile cell1.68e-11386
granulocyte3.70e-118
T cell4.23e-1125
pro-T cell4.23e-1125
intermediate monocyte5.01e-119
CD14-positive, CD16-positive monocyte5.01e-119
mature alpha-beta T cell1.23e-1018
alpha-beta T cell1.23e-1018
immature T cell1.23e-1018
mature T cell1.23e-1018
immature alpha-beta T cell1.23e-1018
blood cell2.33e-0911
stem cell3.59e-09441
multi fate stem cell1.91e-08427
CD4-positive, alpha-beta T cell5.28e-086
somatic stem cell6.31e-08433
Uber Anatomy
Ontology termp-valuen
hematopoietic system3.13e-3998
blood island3.13e-3998
hemolymphoid system1.56e-34108
bone marrow1.27e-2776
immune system1.49e-2693
bone element2.68e-2482
skeletal element1.35e-2090
skeletal system8.96e-18100
connective tissue3.28e-12371
lateral plate mesoderm3.61e-11203
blood4.22e-0915
haemolymphatic fluid4.22e-0915
organism substance4.22e-0915


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)
MA0003.10.176622
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.10.491287
MA0017.10.432438
MA0019.10.7124
MA0024.12.14259
MA0025.11.17262
MA0027.12.65688
MA0028.11.05129
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
MA0048.10.906394
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.11.22849
MA0056.10
MA0057.10.882847
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.10.671725
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.11.72313
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.959858
MA0074.10.660398
MA0076.12.07987
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.32124
MA0089.10
MA0090.10.490736
MA0091.11.37996
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.10.419295
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
MA0139.11.19942
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.347815
MA0146.10.441872
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.21.22729
MA0035.20.621793
MA0039.21.13151
MA0138.20.765223
MA0002.20.255126
MA0137.20.414885
MA0104.20.735746
MA0047.20.695777
MA0112.20.332548
MA0065.20.718489
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.413181
MA0155.10.318517
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.11.46233
MA0161.10
MA0162.10.978497
MA0163.10.508943
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.21.19591
MA0102.21.58513
MA0258.10.289793
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
BRF2#552901179.0959302325580.005570700836719840.0252089962600712
MEF2C#4208213.77045149754130.008235596942270060.0324633896604545
NFKB1#479043.658708949462560.01207927289015230.0438204585562061
POLR2A#543062.147453176558070.01019570676818780.0379889196989927
TBP#690853.088975572580320.006645448275786930.028279845671702
XRCC4#75181716.3837209302320.001395107170798050.00907867143192582
YY1#752854.092642291544880.001743365462849530.0107229296569224



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C1320&oldid=2569831"