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Coexpression cluster:C1322: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.44418,0.946942,0.436508,0.58616,0.393082,0.584466,0.662701,0.742622,0.267027,0.075749,0.553339,0.707204,0.223349,0.650887,0.391663,0.415981,0.889639,0.892779,0.664996,0.402028,0.436569,0.29639,0.576478,0.387783,0.483957,0.730467,0.202389,0.574247,0.396295,1.04549,0.530785,0.92701,0.302275,0.640661,0.35719,0.134746,0.35388,0.585658,0.329602,0.248856,0.355745,0.513952,0.323162,0.390088,0.354447,0.468392,0.66382,0.542147,0.304272,0.396429,0.745008,0.675919,0.149032,1.00488,1.15929,0.653901,0.400834,0.62023,0.186533,0.619193,0.968558,0.666252,0.267534,0.861462,0.684675,0.826413,1.24834,1.61834,2.11566,1.45553,0.500342,0.275507,0.146905,1.15727,0.218784,0.206105,0.562953,0.84426,0.913168,0.477584,0.240887,0.86037,0.684313,0.272514,1.10535,0.181326,0.126687,0.536262,0.771626,1.71797,1.34233,1.07807,0.94406,0.30974,0.393853,0.32338,0.661488,0.987239,0.776336,0.166235,0.881389,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,0.647343,0.483695,0.376529,0.44815,0.978783,0.430775,0.563054,1.29401,0.352243,0.210279,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,1.57878,0.949126,1.1919,0.866571,1.07876,0.53374,1.20639,0.692462,1.35529,0.175219,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,0.306342,0.424432,0.0926553,1.07915,0.717973,0.665754,1.48627,0.755083,0.378604,0.484017,0.454152,1.27379,1.06043,0.912368,0.457485,0.83286,0.683502,0.29379,0.661335,1.48859
|tfbs_overrepresentation_jaspar=MA0003.1;0.321379,MA0004.1;0.558729,MA0006.1;0.391183,MA0007.1;0.539222,MA0009.1;1.03681,MA0014.1;0.0254709,MA0017.1;0.432438,MA0019.1;0.7124,MA0024.1;0.929647,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;2.19519,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;0.147053,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;0.578694,MA0069.1;1.02175,MA0070.1;1.01032,MA0071.1;0.625297,MA0072.1;1.00572,MA0073.1;0.00563817,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;0.32124,MA0089.1;0,MA0090.1;0.490736,MA0091.1;0.561458,MA0092.1;0.522012,MA0093.1;0.394379,MA0095.1;0,MA0098.1;0,MA0100.1;0.679972,MA0101.1;1.02896,MA0103.1;0.381434,MA0105.1;0.419295,MA0106.1;1.68738,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;0.323925,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;1.61362,MA0139.1;0.226048,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;1.44958,MA0147.1;0.327615,MA0148.1;0.584698,MA0149.1;0.612449,MA0062.2;0.658749,MA0035.2;1.50688,MA0039.2;0.00570825,MA0138.2;0.765223,MA0002.2;1.3092,MA0137.2;0.414885,MA0104.2;0.26661,MA0047.2;0.695777,MA0112.2;0.332548,MA0065.2;0.354331,MA0150.1;1.21643,MA0151.1;0,MA0152.1;0.629368,MA0153.1;1.13732,MA0154.1;1.3291,MA0155.1;0.65596,MA0156.1;1.88357,MA0157.1;0.810597,MA0158.1;0,MA0159.1;0.875329,MA0160.1;0.600559,MA0161.1;0,MA0162.1;0.150673,MA0163.1;0.113377,MA0164.1;0.738243,MA0080.2;1.80563,MA0018.2;0.709805,MA0099.2;0.629739,MA0079.2;7.22997e-05,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: C1322_Eosinophils_Basophils_CD14_Mast_Neutrophils_CD34_Peripheral



Phase1 CAGE Peaks

Hg19::chr10:81046569..81046581,+p@chr10:81046569..81046581
+
Hg19::chr14:55770665..55770674,-p@chr14:55770665..55770674
-
Hg19::chr1:19923760..19923771,+p@chr1:19923760..19923771
+
Hg19::chr3:5058332..5058341,-p@chr3:5058332..5058341
-
Hg19::chr4:185214760..185214771,-p@chr4:185214760..185214771
-
Hg19::chr5:142183048..142183059,-p@chr5:142183048..142183059
-


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
classical monocyte2.52e-10142
CD14-positive, CD16-negative classical monocyte2.52e-10142
myeloid leukocyte3.83e-8872
defensive cell1.83e-8748
phagocyte1.83e-8748
macrophage dendritic cell progenitor1.11e-7761
granulocyte monocyte progenitor cell2.58e-7767
monopoietic cell5.20e-7259
monocyte5.20e-7259
monoblast5.20e-7259
promonocyte5.20e-7259
myeloid lineage restricted progenitor cell1.51e-7066
leukocyte3.24e-66136
myeloid cell4.09e-61108
common myeloid progenitor4.09e-61108
hematopoietic stem cell1.53e-53168
angioblastic mesenchymal cell1.53e-53168
nongranular leukocyte8.65e-51115
hematopoietic lineage restricted progenitor cell1.64e-50120
hematopoietic cell3.18e-50177
hematopoietic oligopotent progenitor cell1.80e-47161
hematopoietic multipotent progenitor cell1.80e-47161
stuff accumulating cell5.59e-4487
intermediate monocyte2.33e-229
CD14-positive, CD16-positive monocyte2.33e-229
mesenchymal cell4.26e-19354
connective tissue cell1.73e-18361
motile cell2.39e-16386
granulocyte4.60e-168
stem cell1.20e-14441
multi fate stem cell9.94e-14427
somatic stem cell2.29e-13433
basophil5.74e-123
blood cell1.81e-1111
natural killer cell9.75e-113
pro-NK cell9.75e-113
single nucleate cell1.08e-103
mononuclear cell1.08e-103
CD1a-positive Langerhans cell6.42e-082
immature CD1a-positive Langerhans cell6.42e-082
Uber Anatomy
Ontology termp-valuen
bone marrow1.77e-7076
bone element1.28e-6482
hematopoietic system4.68e-6498
blood island4.68e-6498
skeletal element5.19e-5890
hemolymphoid system3.70e-57108
immune system8.02e-5693
skeletal system3.20e-51100
musculoskeletal system1.33e-26167
lateral plate mesoderm2.30e-25203
connective tissue1.16e-17371
mesoderm1.73e-12315
mesoderm-derived structure1.73e-12315
presumptive mesoderm1.73e-12315


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)
MA0003.10.321379
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.10.0254709
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.11.05129
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.12.19519
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
MA0057.10.147053
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.10.671725
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.578694
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.00563817
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.32124
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.11.02896
MA0103.10.381434
MA0105.10.419295
MA0106.11.68738
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.10.323925
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
MA0136.11.61362
MA0139.10.226048
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.347815
MA0146.11.44958
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.658749
MA0035.21.50688
MA0039.20.00570825
MA0138.20.765223
MA0002.21.3092
MA0137.20.414885
MA0104.20.26661
MA0047.20.695777
MA0112.20.332548
MA0065.20.354331
MA0150.11.21643
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.11.3291
MA0155.10.65596
MA0156.11.88357
MA0157.10.810597
MA0158.10
MA0159.10.875329
MA0160.10.600559
MA0161.10
MA0162.10.150673
MA0163.10.113377
MA0164.10.738243
MA0080.21.80563
MA0018.20.709805
MA0099.20.629739
MA0079.27.22997e-05
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
SPI1#668845.469549005681820.00269730053614140.0148397708841633
ZBTB33#10009210.55490834332710.01374250737140590.0483787955425981



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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