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Coexpression cluster:C450: Difference between revisions

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{{Coexpression_clusters
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16715,0.717665,0.0156564,0.624423,0.524832,0.980021,0.401017,0.403034,0.403831,0.0575111,0.303125,0.129045,0.169484,0.516065,0.368471,0.75697,0.154326,0.168077,0.250879,0.464564,0.141557,0.432083,0.143261,0.191773,0.78124,0.0764988,0.199614,0.999899,1.06784,0.0212383,0.445121,0.131762,0.428928,0.243124,0.0543932,0.705024,0.64558,0.148323,0.385689,0.251047,0.286755,0.236257,0.324106,0.49846,0.635443,0.629339,0.928082,0.197918,0.268962,0.197226,0.467239,0.22944,0.496542,0.377975,0.242486,0.349807,0.716956,1.06805,0.423263,0.911622,0.124048,0.281099,0.0256534,0.633615,0.0690346,0.0124209,1.41923,0.364079,0.420511,0.111572,0.68355,0.377089,0.242227,0.275429,0.586887,0.0048652,0.246917,0.12387,0.827525,1.1648,0.804514,0.562601,0.446434,0.348406,0.0706505,0.376385,0.399529,0.483243,0.835676,0.21846,1.51946,0.441596,0.47839,0.404088,0.340503,0.904802,0.39086,0.216299,0.3681,0.490839,0.31873,0.475985,0.615165,0.161084,0.759328,0.19772,0.00796778,0.140827,0.91903,0.154062,0.626054,0.305079,0.514048,0.698687,0.863933,0.364702,0.222409,0.450719,0.66511,0.166515,0.563221,1.39703,0.678365,0.692985,0.81669,0.420713,1.36399,0.168444,0.776656,1.61314,1.21607,0.741657,0.635967,0.480173,0.341918,0.192136,0.875921,1.45545,0.406714,0.616486,0.0212532,0.00728883,0.563563,0.250074,0.648756,0.940968,0.294363,0.0641085,0.115044,0.0993076,0.740521,1.34939,0.419845,0.101015,0.354946,0.678077,0.134701,0.225998,0.000348233|tfbs_overrepresentation_jaspar=MA0003.1;0.00111244,MA0004.1;2.13245,MA0006.1;0.895237,MA0007.1;0.449227,MA0009.1;0.526253,MA0014.1;0.000793314,MA0017.1;1.03696,MA0019.1;0.726406,MA0024.1;0.434294,MA0025.1;0.647545,MA0027.1;2.09389,MA0028.1;0.0770177,MA0029.1;0.450974,MA0030.1;0.441064,MA0031.1;0.386141,MA0038.1;1.21054,MA0040.1;0.456051,MA0041.1;0.98026,MA0042.1;0.894828,MA0043.1;0.526535,MA0046.1;0.516541,MA0048.1;0.0283321,MA0050.1;0.897174,MA0051.1;0.22589,MA0052.1;0.459414,MA0055.1;0.0584391,MA0056.1;0,MA0057.1;0.0257204,MA0058.1;2.26256,MA0059.1;0.331581,MA0060.1;0.496174,MA0061.1;0.214431,MA0063.1;0,MA0066.1;0.22927,MA0067.1;0.820123,MA0068.1;0.514926,MA0069.1;0.51311,MA0070.1;0.503171,MA0071.1;0.583044,MA0072.1;0.499187,MA0073.1;0.0764727,MA0074.1;0.225345,MA0076.1;0.110503,MA0077.1;0.49237,MA0078.1;0.30111,MA0081.1;0.679272,MA0083.1;0.532971,MA0084.1;0.999884,MA0087.1;1.24309,MA0088.1;0.154793,MA0089.1;0,MA0090.1;0.759616,MA0091.1;0.160096,MA0092.1;0.136418,MA0093.1;2.47105,MA0095.1;0,MA0098.1;0,MA0100.1;0.239133,MA0101.1;0.25283,MA0103.1;0.232452,MA0105.1;0.447321,MA0106.1;0.259598,MA0107.1;0.369945,MA0108.2;0.383574,MA0109.1;0,MA0111.1;0.126618,MA0113.1;0.272101,MA0114.1;0.643657,MA0115.1;0.747865,MA0116.1;0.377517,MA0117.1;0.560027,MA0119.1;0.0925355,MA0122.1;0.583485,MA0124.1;0.70896,MA0125.1;0.631059,MA0130.1;0,MA0131.1;0.315517,MA0132.1;0,MA0133.1;0,MA0135.1;0.553498,MA0136.1;1.23017,MA0139.1;0.0745458,MA0140.1;0.199454,MA0141.1;0.329072,MA0142.1;0.359701,MA0143.1;0.272236,MA0144.1;0.0352516,MA0145.1;0.0109701,MA0146.1;0.00599554,MA0147.1;0.684477,MA0148.1;0.99741,MA0149.1;2.38986,MA0062.2;0.396181,MA0035.2;0.198962,MA0039.2;0.0101604,MA0138.2;0.816468,MA0002.2;1.0893,MA0137.2;0.0801516,MA0104.2;1.15361,MA0047.2;1.29176,MA0112.2;1.16768,MA0065.2;0.192051,MA0150.1;1.22035,MA0151.1;0,MA0152.1;0.589582,MA0153.1;0.615584,MA0154.1;0.435492,MA0155.1;0.0746593,MA0156.1;0.58361,MA0157.1;0.337287,MA0158.1;0,MA0159.1;0.386598,MA0160.1;0.543697,MA0161.1;0,MA0162.1;0.00890769,MA0163.1;0.0106129,MA0164.1;0.770204,MA0080.2;2.47169,MA0018.2;0.260646,MA0099.2;0.59018,MA0079.2;3.16399e-06,MA0102.2;1.03595,MA0258.1;0.892318,MA0259.1;0.403807,MA0442.1;0}}
|full_id=C450_Eosinophils_Basophils_CD14_Neutrophils_CD14CD16_Peripheral_immature
|id=C450
}}

Latest revision as of 11:23, 17 September 2013


Full id: C450_Eosinophils_Basophils_CD14_Neutrophils_CD14CD16_Peripheral_immature



Phase1 CAGE Peaks

Hg19::chr12:124876522..124876535,-p@chr12:124876522..124876535
-
Hg19::chr12:6248326..6248349,+p@chr12:6248326..6248349
+
Hg19::chr12:68726405..68726424,+p1@AK125933
Hg19::chr12:90256830..90256843,+p@chr12:90256830..90256843
+
Hg19::chr14:75735777..75735796,+p@chr14:75735777..75735796
+
Hg19::chr15:102182198..102182220,-p@chr15:102182198..102182220
-
Hg19::chr15:70013853..70013886,-p@chr15:70013853..70013886
-
Hg19::chr17:10055364..10055380,-p@chr17:10055364..10055380
-
Hg19::chr17:518487..518500,-p@chr17:518487..518500
-
Hg19::chr18:74774284..74774295,-p@chr18:74774284..74774295
-
Hg19::chr18:74774299..74774343,-p@chr18:74774299..74774343
-
Hg19::chr18:74775300..74775343,-p@chr18:74775300..74775343
-
Hg19::chr18:74777707..74777722,-p@chr18:74777707..74777722
-
Hg19::chr18:74826697..74826728,+p@chr18:74826697..74826728
+
Hg19::chr18:74826780..74826808,+p@chr18:74826780..74826808
+
Hg19::chr18:74843295..74843307,-p@chr18:74843295..74843307
-
Hg19::chr18:74843519..74843533,+p@chr18:74843519..74843533
+
Hg19::chr1:234977970..234977991,+p@chr1:234977970..234977991
+
Hg19::chr2:157188594..157188608,+p@chr2:157188594..157188608
+
Hg19::chr3:158520366..158520377,-p@chr3:158520366..158520377
-
Hg19::chr8:37595079..37595155,-p1@ENST00000330539
p1@uc003xkb.1
Hg19::chrX:154256125..154256129,-p@chrX:154256125..154256129
-


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 monocyte4.12e-10542
CD14-positive, CD16-negative classical monocyte4.12e-10542
myeloid leukocyte3.62e-9772
defensive cell1.91e-9048
phagocyte1.91e-9048
granulocyte monocyte progenitor cell9.16e-8067
leukocyte2.19e-78136
macrophage dendritic cell progenitor9.94e-7861
myeloid lineage restricted progenitor cell4.29e-7466
monopoietic cell2.40e-7359
monocyte2.40e-7359
monoblast2.40e-7359
promonocyte2.40e-7359
myeloid cell2.23e-65108
common myeloid progenitor2.23e-65108
hematopoietic stem cell1.68e-62168
angioblastic mesenchymal cell1.68e-62168
hematopoietic cell1.63e-58177
hematopoietic lineage restricted progenitor cell2.69e-57120
nongranular leukocyte4.97e-56115
hematopoietic oligopotent progenitor cell3.03e-55161
hematopoietic multipotent progenitor cell3.03e-55161
stuff accumulating cell1.78e-4487
intermediate monocyte4.73e-259
CD14-positive, CD16-positive monocyte4.73e-259
granulocyte1.54e-228
mesenchymal cell3.81e-21354
connective tissue cell2.04e-20361
motile cell7.39e-18386
blood cell6.20e-1611
multi fate stem cell9.89e-15427
stem cell1.72e-14441
somatic stem cell2.67e-14433
basophil1.28e-093
neutrophil2.70e-093
non-classical monocyte2.78e-093
CD14-low, CD16-positive monocyte2.78e-093
single nucleate cell1.28e-083
mononuclear cell1.28e-083
natural killer cell7.06e-083
pro-NK cell7.06e-083
eosinophil5.03e-072
Uber Anatomy
Ontology termp-valuen
hematopoietic system4.85e-7498
blood island4.85e-7498
bone marrow6.24e-7276
hemolymphoid system6.92e-66108
bone element9.39e-6682
immune system1.98e-6193
skeletal element8.70e-5990
skeletal system1.24e-51100
lateral plate mesoderm2.39e-28203
musculoskeletal system9.21e-26167
connective tissue2.00e-19371
mesoderm5.67e-14315
mesoderm-derived structure5.67e-14315
presumptive mesoderm5.67e-14315


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)
MA0003.10.00111244
MA0004.12.13245
MA0006.10.895237
MA0007.10.449227
MA0009.10.526253
MA0014.10.000793314
MA0017.11.03696
MA0019.10.726406
MA0024.10.434294
MA0025.10.647545
MA0027.12.09389
MA0028.10.0770177
MA0029.10.450974
MA0030.10.441064
MA0031.10.386141
MA0038.11.21054
MA0040.10.456051
MA0041.10.98026
MA0042.10.894828
MA0043.10.526535
MA0046.10.516541
MA0048.10.0283321
MA0050.10.897174
MA0051.10.22589
MA0052.10.459414
MA0055.10.0584391
MA0056.10
MA0057.10.0257204
MA0058.12.26256
MA0059.10.331581
MA0060.10.496174
MA0061.10.214431
MA0063.10
MA0066.10.22927
MA0067.10.820123
MA0068.10.514926
MA0069.10.51311
MA0070.10.503171
MA0071.10.583044
MA0072.10.499187
MA0073.10.0764727
MA0074.10.225345
MA0076.10.110503
MA0077.10.49237
MA0078.10.30111
MA0081.10.679272
MA0083.10.532971
MA0084.10.999884
MA0087.11.24309
MA0088.10.154793
MA0089.10
MA0090.10.759616
MA0091.10.160096
MA0092.10.136418
MA0093.12.47105
MA0095.10
MA0098.10
MA0100.10.239133
MA0101.10.25283
MA0103.10.232452
MA0105.10.447321
MA0106.10.259598
MA0107.10.369945
MA0108.20.383574
MA0109.10
MA0111.10.126618
MA0113.10.272101
MA0114.10.643657
MA0115.10.747865
MA0116.10.377517
MA0117.10.560027
MA0119.10.0925355
MA0122.10.583485
MA0124.10.70896
MA0125.10.631059
MA0130.10
MA0131.10.315517
MA0132.10
MA0133.10
MA0135.10.553498
MA0136.11.23017
MA0139.10.0745458
MA0140.10.199454
MA0141.10.329072
MA0142.10.359701
MA0143.10.272236
MA0144.10.0352516
MA0145.10.0109701
MA0146.10.00599554
MA0147.10.684477
MA0148.10.99741
MA0149.12.38986
MA0062.20.396181
MA0035.20.198962
MA0039.20.0101604
MA0138.20.816468
MA0002.21.0893
MA0137.20.0801516
MA0104.21.15361
MA0047.21.29176
MA0112.21.16768
MA0065.20.192051
MA0150.11.22035
MA0151.10
MA0152.10.589582
MA0153.10.615584
MA0154.10.435492
MA0155.10.0746593
MA0156.10.58361
MA0157.10.337287
MA0158.10
MA0159.10.386598
MA0160.10.543697
MA0161.10
MA0162.10.00890769
MA0163.10.0106129
MA0164.10.770204
MA0080.22.47169
MA0018.20.260646
MA0099.20.59018
MA0079.23.16399e-06
MA0102.21.03595
MA0258.10.892318
MA0259.10.403807
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#1053866.643036852446450.0002017924440377120.00239706563499256
BCL11A#5333556.447603432637970.0008654585595952050.00645856566670694
IRF4#366254.980571065169120.002710389575557860.0148882541882758
MAX#414982.346383821457140.01378982480437180.0485126659057427
MEF2A#420565.111790248084740.0008177710503483180.00623000880642848
NFKB1#479092.245116855352020.01109493267881160.040806580998817
PAX5#507992.728458626390930.002952719530386470.0157424613320758
SPI1#6688145.220933141787191.94204115573741e-081.38921120728808e-06



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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