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Coexpression cluster:C475: Difference between revisions

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{{Coexpression_clusters
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0.0667305,1.09331,0.0564451,0.117466,0.238949,0.904491,1.0357,0.0834931,0.151936,0.394509,0.253928,0.97806,1.57095,0.0865963,0.315441,0.262847,0.403678,1.31921,0.671855,0.246686,0.0887806,0.222594,0.167169,0.221865,1.25147,0.255713,0.319823,1.05455,0.742048,0.380605,0.754286,1.10771,0.456006,0.950487,0.143869,0.953411,3.40323,0.670004,0.020227,0.956609,0.067953,0.395294,0.45319,0.130356,1.15966,0.408665,0.269087,0.141606,0.622646,0.320674,0.507279,0.0595657,0.336397,1.20481,0.84263,0.598,0.4797,1.111,1.01418,0.199002,0.25404,0.517267,0.340143,0.473931,1.20998,0.474756,0.512318,0.436368,0.371019,0.174162,0.422802,0.241933,0.417285,0.952905,0.113655,0.509866,1.14641,0.183573,0.797061,0.23451,3.92871,0.161925,0.378653,0.73226,0.662347,0.334429,0.57027,0.277756,2.08708,1.81065,0.248345,0.484077,0.701879,0.442144,0.598629,0.956028,0.715286,0.275188,0.854902,0.148502,0.479764,0.191402,0.814541,1.65405,1.25623,0.779227,0.249639,0.514137,2.60266,0.216494,0.35869,1.49614,0.895588,1.09525,0.197863,1.59835,0.598976,0.127482,0.255347,0.980005,0.32333,0.56727,0.134125,0.116987,0.77808,0.582159,0.452507,0.378488,0.385896,0.268483,0.0427574,0.702336,0.478654|tfbs_overrepresentation_jaspar=MA0003.1;0.185667,MA0004.1;1.02175,MA0006.1;1.49379,MA0007.1;0.168078,MA0009.1;0.561062,MA0014.1;0.211507,MA0017.1;0.342408,MA0019.1;2.20095,MA0024.1;0.467291,MA0025.1;0.684106,MA0027.1;2.13512,MA0028.1;0.0924235,MA0029.1;0.484339,MA0030.1;0.474212,MA0031.1;0.41796,MA0038.1;0.25521,MA0040.1;0.489524,MA0041.1;0.193578,MA0042.1;0.171628,MA0043.1;0.561349,MA0046.1;0.551181,MA0048.1;0.650948,MA0050.1;0.172223,MA0051.1;0.251994,MA0052.1;0.492957,MA0055.1;0.0396812,MA0056.1;0,MA0057.1;0.395732,MA0058.1;3.92311,MA0059.1;2.45139,MA0060.1;0.0338613,MA0061.1;0.26253,MA0063.1;0,MA0066.1;2.0234,MA0067.1;0.858361,MA0068.1;0.0158377,MA0069.1;0.547689,MA0070.1;0.537571,MA0071.1;0.22617,MA0072.1;0.533514,MA0073.1;0.0303421,MA0074.1;0.251422,MA0076.1;0.405173,MA0077.1;0.526569,MA0078.1;0.33032,MA0081.1;0.37884,MA0083.1;0.567893,MA0084.1;1.03923,MA0087.1;0.531309,MA0088.1;0.207879,MA0089.1;0,MA0090.1;0.844653,MA0091.1;0.182521,MA0092.1;0.157193,MA0093.1;1.50898,MA0095.1;0,MA0098.1;0,MA0100.1;0.265855,MA0101.1;0.294344,MA0103.1;0.27232,MA0105.1;0.19282,MA0106.1;0.28721,MA0107.1;0.195292,MA0108.2;0.415325,MA0109.1;0,MA0111.1;0.449411,MA0113.1;0.300221,MA0114.1;0.421069,MA0115.1;0.785493,MA0116.1;2.1855,MA0117.1;0.595385,MA0119.1;0.109564,MA0122.1;0.619196,MA0124.1;0.746208,MA0125.1;0.667416,MA0130.1;0,MA0131.1;0.345226,MA0132.1;0,MA0133.1;0,MA0135.1;0.588754,MA0136.1;0.721948,MA0139.1;1.07274,MA0140.1;0.637307,MA0141.1;0.117869,MA0142.1;0.39079,MA0143.1;0.300362,MA0144.1;0.0449457,MA0145.1;0.0550611,MA0146.1;0.253174,MA0147.1;1.6733,MA0148.1;0.198049,MA0149.1;0.21714,MA0062.2;0.102633,MA0035.2;0.223695,MA0039.2;0.544801,MA0138.2;0.882113,MA0002.2;0.860866,MA0137.2;0.0959012,MA0104.2;2.27545,MA0047.2;0.277681,MA0112.2;2.97327,MA0065.2;0.252091,MA0150.1;0.828845,MA0151.1;0,MA0152.1;0.229055,MA0153.1;0.65174,MA0154.1;0.186884,MA0155.1;0.345204,MA0156.1;0.32108,MA0157.1;0.367703,MA0158.1;0,MA0159.1;0.204897,MA0160.1;0.20889,MA0161.1;0,MA0162.1;0.680828,MA0163.1;0.0840723,MA0164.1;0.310173,MA0080.2;0.605142,MA0018.2;0.785268,MA0099.2;0.229319,MA0079.2;0.00354552,MA0102.2;1.07547,MA0258.1;2.47748,MA0259.1;0.469431,MA0442.1;0}}
|full_id=C475_CD14_Basophils_CD14CD16_Peripheral_CD133_large_immature
|id=C475
}}

Latest revision as of 11:23, 17 September 2013


Full id: C475_CD14_Basophils_CD14CD16_Peripheral_CD133_large_immature



Phase1 CAGE Peaks

Hg19::chr10:23727673..23727693,-p@chr10:23727673..23727693
-
Hg19::chr11:10921401..10921434,-p@chr11:10921401..10921434
-
Hg19::chr11:10921615..10921626,+p@chr11:10921615..10921626
+
Hg19::chr11:68847955..68847972,-p@chr11:68847955..68847972
-
Hg19::chr12:125110878..125110906,-p@chr12:125110878..125110906
-
Hg19::chr17:73291353..73291364,+p@chr17:73291353..73291364
+
Hg19::chr17:76837499..76837540,-p@chr17:76837499..76837540
-
Hg19::chr17:81039657..81039682,-p@chr17:81039657..81039682
-
Hg19::chr5:56021776..56021780,-p@chr5:56021776..56021780
-
Hg19::chr6:159541174..159541187,+p@chr6:159541174..159541187
+
Hg19::chr6:88428781..88428805,-p@chr6:88428781..88428805
-
Hg19::chr7:2778019..2778050,+p@chr7:2778019..2778050
+
Hg19::chr8:16054579..16054589,-p@chr8:16054579..16054589
-
Hg19::chr9:110250629..110250642,-p7@KLF4
Hg19::chr9:110250651..110250662,-p11@KLF4
Hg19::chr9:110250697..110250738,-p2@KLF4
Hg19::chr9:110250834..110250861,+p@chr9:110250834..110250861
+
Hg19::chr9:110250881..110250903,+p@chr9:110250881..110250903
+
Hg19::chr9:97416545..97416564,-p@chr9:97416545..97416564
-
Hg19::chrX:152991865..152991874,+p@chrX:152991865..152991874
+


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 monocyte5.48e-10842
CD14-positive, CD16-negative classical monocyte5.48e-10842
defensive cell6.03e-9348
phagocyte6.03e-9348
granulocyte monocyte progenitor cell9.46e-8967
macrophage dendritic cell progenitor4.55e-8761
myeloid leukocyte4.80e-8672
myeloid lineage restricted progenitor cell6.94e-8366
monopoietic cell1.24e-8259
monocyte1.24e-8259
monoblast1.24e-8259
promonocyte1.24e-8259
leukocyte1.51e-66136
myeloid cell4.74e-60108
common myeloid progenitor4.74e-60108
hematopoietic lineage restricted progenitor cell2.07e-54120
nongranular leukocyte2.69e-53115
hematopoietic stem cell6.01e-51168
angioblastic mesenchymal cell6.01e-51168
hematopoietic cell1.43e-47177
stuff accumulating cell8.47e-4687
hematopoietic oligopotent progenitor cell4.07e-44161
hematopoietic multipotent progenitor cell4.07e-44161
intermediate monocyte9.28e-269
CD14-positive, CD16-positive monocyte9.28e-269
mesenchymal cell1.10e-17354
connective tissue cell4.90e-17361
motile cell9.43e-15386
dendritic cell7.40e-1310
multi fate stem cell5.70e-12427
stem cell9.13e-12441
somatic stem cell1.38e-11433
immature conventional dendritic cell5.78e-105
common dendritic progenitor5.78e-105
non-classical monocyte1.60e-093
CD14-low, CD16-positive monocyte1.60e-093
basophil3.10e-093
conventional dendritic cell4.68e-098
single nucleate cell8.38e-093
mononuclear cell8.38e-093
plasmacytoid dendritic cell4.39e-083
Uber Anatomy
Ontology termp-valuen
bone marrow9.23e-7776
bone element3.25e-7082
hematopoietic system5.03e-7098
blood island5.03e-7098
immune system2.88e-6893
hemolymphoid system9.97e-65108
skeletal element7.89e-6390
skeletal system3.01e-55100
musculoskeletal system3.97e-29167
lateral plate mesoderm8.60e-28203
connective tissue3.76e-16371
mesoderm3.57e-15315
mesoderm-derived structure3.57e-15315
presumptive mesoderm3.57e-15315


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)
MA0003.10.185667
MA0004.11.02175
MA0006.11.49379
MA0007.10.168078
MA0009.10.561062
MA0014.10.211507
MA0017.10.342408
MA0019.12.20095
MA0024.10.467291
MA0025.10.684106
MA0027.12.13512
MA0028.10.0924235
MA0029.10.484339
MA0030.10.474212
MA0031.10.41796
MA0038.10.25521
MA0040.10.489524
MA0041.10.193578
MA0042.10.171628
MA0043.10.561349
MA0046.10.551181
MA0048.10.650948
MA0050.10.172223
MA0051.10.251994
MA0052.10.492957
MA0055.10.0396812
MA0056.10
MA0057.10.395732
MA0058.13.92311
MA0059.12.45139
MA0060.10.0338613
MA0061.10.26253
MA0063.10
MA0066.12.0234
MA0067.10.858361
MA0068.10.0158377
MA0069.10.547689
MA0070.10.537571
MA0071.10.22617
MA0072.10.533514
MA0073.10.0303421
MA0074.10.251422
MA0076.10.405173
MA0077.10.526569
MA0078.10.33032
MA0081.10.37884
MA0083.10.567893
MA0084.11.03923
MA0087.10.531309
MA0088.10.207879
MA0089.10
MA0090.10.844653
MA0091.10.182521
MA0092.10.157193
MA0093.11.50898
MA0095.10
MA0098.10
MA0100.10.265855
MA0101.10.294344
MA0103.10.27232
MA0105.10.19282
MA0106.10.28721
MA0107.10.195292
MA0108.20.415325
MA0109.10
MA0111.10.449411
MA0113.10.300221
MA0114.10.421069
MA0115.10.785493
MA0116.12.1855
MA0117.10.595385
MA0119.10.109564
MA0122.10.619196
MA0124.10.746208
MA0125.10.667416
MA0130.10
MA0131.10.345226
MA0132.10
MA0133.10
MA0135.10.588754
MA0136.10.721948
MA0139.11.07274
MA0140.10.637307
MA0141.10.117869
MA0142.10.39079
MA0143.10.300362
MA0144.10.0449457
MA0145.10.0550611
MA0146.10.253174
MA0147.11.6733
MA0148.10.198049
MA0149.10.21714
MA0062.20.102633
MA0035.20.223695
MA0039.20.544801
MA0138.20.882113
MA0002.20.860866
MA0137.20.0959012
MA0104.22.27545
MA0047.20.277681
MA0112.22.97327
MA0065.20.252091
MA0150.10.828845
MA0151.10
MA0152.10.229055
MA0153.10.65174
MA0154.10.186884
MA0155.10.345204
MA0156.10.32108
MA0157.10.367703
MA0158.10
MA0159.10.204897
MA0160.10.20889
MA0161.10
MA0162.10.680828
MA0163.10.0840723
MA0164.10.310173
MA0080.20.605142
MA0018.20.785268
MA0099.20.229319
MA0079.20.00354552
MA0102.21.07547
MA0258.12.47748
MA0259.10.469431
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
SMARCA4#6597215.67659033078880.007157742659359380.0297259219659947
SMARCB1#659854.563178945289350.003821359955514560.0188699296640182
SMARCC1#659936.549503897944720.01022451876559340.03807453880624
TFAP2A#702064.955590311913490.0009093672692604040.006619278522044
TFAP2C#702284.323691443944090.0002427975840692140.00264113497371156



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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