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Coexpression cluster:C273: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 11:11, 17 September 2013


Full id: C273_Neutrophils_CD14_Eosinophils_Monocytederived_CD4_Natural_Mast



Phase1 CAGE Peaks

Hg19::chr10:121154442..121154449,-p@chr10:121154442..121154449
-
Hg19::chr11:47377641..47377656,-p@chr11:47377641..47377656
-
Hg19::chr11:47377786..47377798,-p@chr11:47377786..47377798
-
Hg19::chr11:47378636..47378650,-p@chr11:47378636..47378650
-
Hg19::chr11:47379735..47379747,-p@chr11:47379735..47379747
-
Hg19::chr11:47379860..47379874,-p@chr11:47379860..47379874
-
Hg19::chr14:35871286..35871297,-p@chr14:35871286..35871297
-
Hg19::chr15:58447767..58447778,+p@chr15:58447767..58447778
+
Hg19::chr15:86212972..86212989,+p20@AKAP13
Hg19::chr16:31926161..31926175,+p@chr16:31926161..31926175
+
Hg19::chr17:21194520..21194548,+p7@MAP2K3
Hg19::chr19:47993823..47993862,-p@chr19:47993823..47993862
-
Hg19::chr1:183556727..183556731,-p@chr1:183556727..183556731
-
Hg19::chr1:27947499..27947502,-p@chr1:27947499..27947502
-
Hg19::chr1:27951156..27951162,-p@chr1:27951156..27951162
-
Hg19::chr1:27951294..27951312,-p@chr1:27951294..27951312
-
Hg19::chr1:27951368..27951397,-p@chr1:27951368..27951397
-
Hg19::chr1:27951398..27951454,-p@chr1:27951398..27951454
-
Hg19::chr1:27955714..27955719,-p@chr1:27955714..27955719
-
Hg19::chr1:33424609..33424645,-p@chr1:33424609..33424645
-
Hg19::chr1:89589346..89589358,-p@chr1:89589346..89589358
-
Hg19::chr20:48500628..48500646,+p@chr20:48500628..48500646
+
Hg19::chr22:35738610..35738623,+p@chr22:35738610..35738623
+
Hg19::chr22:35738627..35738686,+p@chr22:35738627..35738686
+
Hg19::chr22:35738688..35738740,+p@chr22:35738688..35738740
+
Hg19::chr22:35738813..35738828,+p@chr22:35738813..35738828
+
Hg19::chr22:35738894..35738925,+p@chr22:35738894..35738925
+
Hg19::chr22:35738945..35738954,+p@chr22:35738945..35738954
+
Hg19::chr22:35738968..35738980,+p@chr22:35738968..35738980
+
Hg19::chr22:35739061..35739082,+p@chr22:35739061..35739082
+
Hg19::chr22:35739086..35739098,+p@chr22:35739086..35739098
+
Hg19::chr22:35739277..35739390,+p@chr22:35739277..35739390
+
Hg19::chr22:35739411..35739459,+p@chr22:35739411..35739459
+
Hg19::chr22:35739472..35739491,+p@chr22:35739472..35739491
+
Hg19::chr22:35739601..35739650,+p@chr22:35739601..35739650
+
Hg19::chr22:35739658..35739678,+p@chr22:35739658..35739678
+
Hg19::chr22:35739706..35739737,+p4@TOM1
Hg19::chr22:35739742..35739814,+p2@TOM1
Hg19::chr22:35739816..35739887,+p3@TOM1
Hg19::chr2:114700995..114701006,+p@chr2:114700995..114701006
+
Hg19::chr2:145240683..145240706,-p@chr2:145240683..145240706
-
Hg19::chr2:145246478..145246502,-p@chr2:145246478..145246502
-
Hg19::chr2:28619598..28619640,+p@chr2:28619598..28619640
+
Hg19::chr5:169716803..169716815,-p@chr5:169716803..169716815
-
Hg19::chr6:13316777..13316781,-p@chr6:13316777..13316781
-
Hg19::chr7:130586359..130586363,-p@chr7:130586359..130586363
-
Hg19::chr8:59473361..59473383,+p@chr8:59473361..59473383
+


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

GO IDGO nameFDR corrected p-value
GO:0004691cAMP-dependent protein kinase activity0.0302731887304975
GO:0004708MAP kinase kinase activity0.0302731887304975
GO:0004712protein serine/threonine/tyrosine kinase activity0.0302731887304975
GO:0004690cyclic nucleotide-dependent protein kinase activity0.0302731887304975
GO:0004674protein serine/threonine kinase activity0.0302731887304975



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
myeloid leukocyte5.81e-5372
defensive cell2.51e-5248
phagocyte2.51e-5248
classical monocyte4.13e-5242
CD14-positive, CD16-negative classical monocyte4.13e-5242
leukocyte5.29e-46136
granulocyte monocyte progenitor cell2.11e-4467
myeloid lineage restricted progenitor cell1.79e-4366
monopoietic cell1.88e-4159
monocyte1.88e-4159
monoblast1.88e-4159
promonocyte1.88e-4159
macrophage dendritic cell progenitor2.18e-4161
myeloid cell7.55e-38108
common myeloid progenitor7.55e-38108
hematopoietic stem cell4.99e-37168
angioblastic mesenchymal cell4.99e-37168
hematopoietic lineage restricted progenitor cell1.20e-36120
nongranular leukocyte4.57e-36115
hematopoietic oligopotent progenitor cell5.14e-36161
hematopoietic multipotent progenitor cell5.14e-36161
hematopoietic cell1.20e-33177
stuff accumulating cell5.62e-2187
intermediate monocyte5.14e-119
CD14-positive, CD16-positive monocyte5.14e-119
granulocyte1.56e-088
mesenchymal cell2.05e-08354
connective tissue cell8.55e-08361
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.18e-4198
blood island1.18e-4198
bone marrow2.17e-3876
hemolymphoid system8.81e-37108
bone element1.00e-3682
immune system1.35e-3393
skeletal element1.13e-3190
skeletal system1.09e-27100
lateral plate mesoderm2.15e-14203
adult organism6.01e-12114
musculoskeletal system5.60e-10167
connective tissue2.57e-07371
neural tube4.38e-0756
neural rod4.38e-0756
future spinal cord4.38e-0756
neural keel4.38e-0756


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)
MA0003.15.35202e-15
MA0004.10.143101
MA0006.10.0388776
MA0007.10.0311376
MA0009.111.6855
MA0014.14.67245e-06
MA0017.10.0577259
MA0019.10.0887288
MA0024.10.204363
MA0025.10.376628
MA0027.11.7662
MA0028.10.00904529
MA0029.11.16434
MA0030.10.209437
MA0031.10.169247
MA0038.10.0698955
MA0040.10.22078
MA0041.10.365392
MA0042.10.896306
MA0043.10.757231
MA0046.10.267991
MA0048.10.134218
MA0050.10.569819
MA0051.10.0682529
MA0052.10.223346
MA0055.10.00152145
MA0056.10
MA0057.10.0344353
MA0058.10.0155786
MA0059.10.0153731
MA0060.10.000988009
MA0061.10.000515303
MA0063.10
MA0066.10.0700626
MA0067.10.529198
MA0068.10.177372
MA0069.10.265257
MA0070.10.257372
MA0071.10.782793
MA0072.10.707234
MA0073.1486.846
MA0074.10.240126
MA0076.10.0182587
MA0077.10.694833
MA0078.10.360912
MA0081.10.185811
MA0083.10.281174
MA0084.10.695499
MA0087.10.252522
MA0088.10.00218846
MA0089.10
MA0090.10.437286
MA0091.10.0366706
MA0092.10.114054
MA0093.10.00767494
MA0095.10
MA0098.10
MA0100.10.075437
MA0101.10.00800713
MA0103.10.385713
MA0105.10.000901005
MA0106.10.0870163
MA0107.10.00266283
MA0108.20.501004
MA0109.10
MA0111.10.0236602
MA0113.10.0943593
MA0114.10.0152793
MA0115.10.464275
MA0116.10.0562776
MA0117.10.303182
MA0119.10.0129611
MA0122.10.322548
MA0124.10.429905
MA0125.10.362554
MA0130.10
MA0131.10.121301
MA0132.10
MA0133.10
MA0135.10.297838
MA0136.10.253606
MA0139.10.000371125
MA0140.10.775021
MA0141.10.183298
MA0142.10.150759
MA0143.10.09444
MA0144.10.0121944
MA0145.12.92324e-06
MA0146.16.61834e-06
MA0147.10.0182639
MA0148.10.0430398
MA0149.10.0514353
MA0062.20.00354484
MA0035.20.200553
MA0039.23.92428e-05
MA0138.20.112735
MA0002.20.00558463
MA0137.20.0491622
MA0104.20.00694771
MA0047.20.0817751
MA0112.20.000177281
MA0065.20.0012066
MA0150.10.0198164
MA0151.10
MA0152.10.456823
MA0153.10.349438
MA0154.10.000815748
MA0155.10.213651
MA0156.10.484466
MA0157.10.421465
MA0158.10
MA0159.10.136485
MA0160.10.404496
MA0161.10
MA0162.111.966
MA0163.12.58272e-05
MA0164.10.100116
MA0080.20.0402168
MA0018.20.0876241
MA0099.20.0571009
MA0079.20
MA0102.20.729507
MA0258.10.00154929
MA0259.10.0649546
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

No analysis results for this cluster

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

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