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Coexpression cluster:C656: Difference between revisions

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{{Coexpression_clusters
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6,0.388062,0.62293,0.561703,0.403967,0.529794,0.927044,1.28869,0.612294,1.12869,0.251183,1.07567,0.294551,0.839414,0.224555,0.205774,0.0498505,0.546008,0.609242,0.233499,0.258113,0.560705,0.403653,2.15178,0.789807,0.14349,0.742322,0.170958,0.480498,1.38705,1.01818,0.763867,0.637885,0.114875,0.171417,0.781249,0.905787,0.67819,0.484706,0.0378976,0.12852,0.632556,0.672898,0.590971,0.519171,0.289709,0.576179,0.371864,0.238217,0.15924,0.211112,0.670274,0.198172,0.301413,0.971251,0.863968,0.327238,0.274314,2.25208,0.373,0.831412,0.478284,0.849318,0.413695,1.0796,0.546713,0.379419,0.642598,0.872646,0.124214,0.76453,0.277675,0.886589,0.410725,1.03079,0.369137,0.270369,0.311068,0.989273,1.83943,1.43902,0.95284,1.75904,0.674844,0.52079,0.904915,0.505455,1.68078,0.259186,0.112739,0.26835,0.159485,0.764896,0.286124,1.00661,1.15881,0.465765,0.160686,0.670668,0.21563,0.951654,0.747146,0.608503,0.623024,0.535644,0.402951,0.69704,0.998288,0.570123|tfbs_overrepresentation_jaspar=MA0003.1;0.186635,MA0004.1;0.297884,MA0006.1;0.169524,MA0007.1;0.771118,MA0009.1;0.724811,MA0014.1;0.0622624,MA0017.1;1.72263,MA0019.1;0.428118,MA0024.1;0.6245,MA0025.1;0.854131,MA0027.1;2.32165,MA0028.1;0.181601,MA0029.1;0.642879,MA0030.1;0.63197,MA0031.1;0.570886,MA0038.1;0.387473,MA0040.1;0.648455,MA0041.1;0.84273,MA0042.1;0.781261,MA0043.1;0.725115,MA0046.1;0.714324,MA0048.1;0.0323146,MA0050.1;1.4276,MA0051.1;0.997995,MA0052.1;0.652145,MA0055.1;0.3329,MA0056.1;0,MA0057.1;0.542827,MA0058.1;0.625569,MA0059.1;0.218203,MA0060.1;0.0892161,MA0061.1;3.84843,MA0063.1;0,MA0066.1;0.387854,MA0067.1;1.03434,MA0068.1;2.74747,MA0069.1;0.710614,MA0070.1;0.69985,MA0071.1;0.35315,MA0072.1;0.695528,MA0073.1;0.394983,MA0074.1;0.383033,MA0076.1;0.231962,MA0077.1;0.688123,MA0078.1;1.19307,MA0081.1;0.218332,MA0083.1;0.732051,MA0084.1;1.21913,MA0087.1;0.693179,MA0088.1;0.854057,MA0089.1;0,MA0090.1;0.243681,MA0091.1;0.30011,MA0092.1;1.35806,MA0093.1;0.511707,MA0095.1;0,MA0098.1;0,MA0100.1;0.399896,MA0101.1;1.58055,MA0103.1;0.162663,MA0105.1;4.33548,MA0106.1;1.0872,MA0107.1;3.18822,MA0108.2;0.568002,MA0109.1;0,MA0111.1;0.708492,MA0113.1;0.439505,MA0114.1;1.23864,MA0115.1;0.959312,MA0116.1;0.123927,MA0117.1;0.76111,MA0119.1;0.593096,MA0122.1;0.786181,MA0124.1;0.918678,MA0125.1;0.83671,MA0130.1;0,MA0131.1;0.490408,MA0132.1;0,MA0133.1;0,MA0135.1;0.754112,MA0136.1;0.393782,MA0139.1;0.235473,MA0140.1;0.350813,MA0141.1;0.619886,MA0142.1;1.33676,MA0143.1;1.11985,MA0144.1;0.108694,MA0145.1;0.0753792,MA0146.1;0.312689,MA0147.1;0.126316,MA0148.1;0.855011,MA0149.1;0.90664,MA0062.2;0.0702147,MA0035.2;0.350194,MA0039.2;0.0823621,MA0138.2;0.474787,MA0002.2;0.0821804,MA0137.2;0.186529,MA0104.2;0.088751,MA0047.2;0.413608,MA0112.2;0.0689988,MA0065.2;1.73813,MA0150.1;0.671641,MA0151.1;0,MA0152.1;0.356591,MA0153.1;1.91857,MA0154.1;1.13157,MA0155.1;0.333744,MA0156.1;0.18827,MA0157.1;0.515488,MA0158.1;0,MA0159.1;0.126752,MA0160.1;0.332385,MA0161.1;0,MA0162.1;0.535498,MA0163.1;0.139091,MA0164.1;0.450848,MA0080.2;0.511865,MA0018.2;0.425847,MA0099.2;0.938958,MA0079.2;0.15174,MA0102.2;1.25596,MA0258.1;0.335505,MA0259.1;0.132107,MA0442.1;0}}
|full_id=C656_CD14_immature_Dendritic_Basophils_CD34_CD133_CD19
|id=C656
}}

Latest revision as of 11:27, 17 September 2013


Full id: C656_CD14_immature_Dendritic_Basophils_CD34_CD133_CD19



Phase1 CAGE Peaks

Hg19::chr11:64039133..64039136,+p@chr11:64039133..64039136
+
Hg19::chr12:111844666..111844678,-p@chr12:111844666..111844678
-
Hg19::chr18:13217774..13217781,-p@chr18:13217774..13217781
-
Hg19::chr2:202021629..202021643,+p@chr2:202021629..202021643
+
Hg19::chr3:170074447..170074452,+p@chr3:170074447..170074452
+
Hg19::chr3:195633911..195633922,+p@chr3:195633911..195633922
+
Hg19::chr3:4793475..4793490,+p@chr3:4793475..4793490
+
Hg19::chr4:15657351..15657354,+p@chr4:15657351..15657354
+
Hg19::chr5:98269499..98269504,+p@chr5:98269499..98269504
+
Hg19::chr6:291825..291875,+p6@DUSP22
Hg19::chr7:108165902..108165905,+p@chr7:108165902..108165905
+
Hg19::chr9:134604636..134604648,-p@chr9:134604636..134604648
-
Hg19::chr9:80786687..80786703,-p@chr9:80786687..80786703
-


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 monocyte7.35e-7942
CD14-positive, CD16-negative classical monocyte7.35e-7942
leukocyte4.95e-74136
defensive cell7.52e-6848
phagocyte7.52e-6848
myeloid leukocyte2.05e-6672
granulocyte monocyte progenitor cell4.12e-6567
macrophage dendritic cell progenitor1.84e-6161
hematopoietic stem cell7.74e-60168
angioblastic mesenchymal cell7.74e-60168
myeloid lineage restricted progenitor cell9.93e-5966
hematopoietic lineage restricted progenitor cell2.71e-56120
hematopoietic cell3.76e-56177
monopoietic cell4.21e-5659
monocyte4.21e-5659
monoblast4.21e-5659
promonocyte4.21e-5659
nongranular leukocyte4.76e-54115
hematopoietic oligopotent progenitor cell6.05e-49161
hematopoietic multipotent progenitor cell6.05e-49161
myeloid cell3.14e-48108
common myeloid progenitor3.14e-48108
stuff accumulating cell2.43e-3387
intermediate monocyte8.41e-289
CD14-positive, CD16-positive monocyte8.41e-289
mesenchymal cell1.47e-21354
connective tissue cell6.95e-21361
motile cell1.66e-18386
stem cell1.55e-16441
multi fate stem cell1.36e-15427
somatic stem cell3.42e-15433
plasmacytoid dendritic cell2.52e-113
basophil9.76e-113
dendritic cell1.22e-1010
single nucleate cell1.86e-103
mononuclear cell1.86e-103
natural killer cell2.12e-103
pro-NK cell2.12e-103
non-classical monocyte2.59e-093
CD14-low, CD16-positive monocyte2.59e-093
CD1a-positive Langerhans cell3.89e-082
immature CD1a-positive Langerhans cell3.89e-082
somatic cell1.55e-07588
Uber Anatomy
Ontology termp-valuen
bone marrow1.91e-5976
bone element2.22e-5482
hematopoietic system9.81e-5298
blood island9.81e-5298
skeletal element1.15e-4890
immune system8.98e-4793
hemolymphoid system5.78e-46108
skeletal system8.50e-43100
musculoskeletal system1.47e-21167
connective tissue5.79e-20371
lateral plate mesoderm1.97e-19203
mesoderm1.80e-09315
mesoderm-derived structure1.80e-09315
presumptive mesoderm1.80e-09315


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)
MA0003.10.186635
MA0004.10.297884
MA0006.10.169524
MA0007.10.771118
MA0009.10.724811
MA0014.10.0622624
MA0017.11.72263
MA0019.10.428118
MA0024.10.6245
MA0025.10.854131
MA0027.12.32165
MA0028.10.181601
MA0029.10.642879
MA0030.10.63197
MA0031.10.570886
MA0038.10.387473
MA0040.10.648455
MA0041.10.84273
MA0042.10.781261
MA0043.10.725115
MA0046.10.714324
MA0048.10.0323146
MA0050.11.4276
MA0051.10.997995
MA0052.10.652145
MA0055.10.3329
MA0056.10
MA0057.10.542827
MA0058.10.625569
MA0059.10.218203
MA0060.10.0892161
MA0061.13.84843
MA0063.10
MA0066.10.387854
MA0067.11.03434
MA0068.12.74747
MA0069.10.710614
MA0070.10.69985
MA0071.10.35315
MA0072.10.695528
MA0073.10.394983
MA0074.10.383033
MA0076.10.231962
MA0077.10.688123
MA0078.11.19307
MA0081.10.218332
MA0083.10.732051
MA0084.11.21913
MA0087.10.693179
MA0088.10.854057
MA0089.10
MA0090.10.243681
MA0091.10.30011
MA0092.11.35806
MA0093.10.511707
MA0095.10
MA0098.10
MA0100.10.399896
MA0101.11.58055
MA0103.10.162663
MA0105.14.33548
MA0106.11.0872
MA0107.13.18822
MA0108.20.568002
MA0109.10
MA0111.10.708492
MA0113.10.439505
MA0114.11.23864
MA0115.10.959312
MA0116.10.123927
MA0117.10.76111
MA0119.10.593096
MA0122.10.786181
MA0124.10.918678
MA0125.10.83671
MA0130.10
MA0131.10.490408
MA0132.10
MA0133.10
MA0135.10.754112
MA0136.10.393782
MA0139.10.235473
MA0140.10.350813
MA0141.10.619886
MA0142.11.33676
MA0143.11.11985
MA0144.10.108694
MA0145.10.0753792
MA0146.10.312689
MA0147.10.126316
MA0148.10.855011
MA0149.10.90664
MA0062.20.0702147
MA0035.20.350194
MA0039.20.0823621
MA0138.20.474787
MA0002.20.0821804
MA0137.20.186529
MA0104.20.088751
MA0047.20.413608
MA0112.20.0689988
MA0065.21.73813
MA0150.10.671641
MA0151.10
MA0152.10.356591
MA0153.11.91857
MA0154.11.13157
MA0155.10.333744
MA0156.10.18827
MA0157.10.515488
MA0158.10
MA0159.10.126752
MA0160.10.332385
MA0161.10
MA0162.10.535498
MA0163.10.139091
MA0164.10.450848
MA0080.20.511865
MA0018.20.425847
MA0099.20.938958
MA0079.20.15174
MA0102.21.25596
MA0258.10.335505
MA0259.10.132107
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
BCL11A#5333536.546797331601630.009600332311689340.0361341035858629
BCL3#60237.972408339324230.005575358717057480.025227888265273
EBF1#187964.110677006108770.0017009226757290.0106239258017141
SPI1#668863.786610850087410.002614000338510870.0144522806433953



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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