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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0.0842546465117019

Latest revision as of 11:37, 17 September 2013


Full id: C1105_CD14_CD19_acute_CD14CD16_CD4_Mast_granulocyte



Phase1 CAGE Peaks

Hg19::chr10:114134954..114135003,+p5@ACSL5
Hg19::chr10:114135952..114136022,+p1@ACSL5
Hg19::chr15:81293457..81293493,+p3@MESDC1
Hg19::chr19:14247942..14248026,+p1@LOC100507373
Hg19::chr19:54876447..54876469,-p3@LAIR1
Hg19::chr19:54876483..54876501,-p2@LAIR1
Hg19::chr1:209941862..209941887,+p6@TRAF3IP3


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:0004467long-chain-fatty-acid-CoA ligase activity0.0269268105022804
GO:0015645fatty-acid ligase activity0.0269268105022804
GO:0016877ligase activity, forming carbon-sulfur bonds0.0361194873165629
GO:0031903microbody membrane0.0361194873165629
GO:0005778peroxisomal membrane0.0361194873165629
GO:0044439peroxisomal part0.0361194873165629
GO:0044438microbody part0.0361194873165629
GO:0005741mitochondrial outer membrane0.0383650411735975
GO:0016021integral to membrane0.0383650411735975
GO:0031224intrinsic to membrane0.0383650411735975
GO:0031968organelle outer membrane0.0383650411735975
GO:0019867outer membrane0.0383650411735975
GO:0042579microbody0.0383650411735975
GO:0005777peroxisome0.0383650411735975
GO:0044425membrane part0.0478199413750389



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>disease_data<br>

Cell Type
Ontology termp-valuen
hematopoietic stem cell2.31e-86168
angioblastic mesenchymal cell2.31e-86168
hematopoietic cell4.92e-82177
hematopoietic oligopotent progenitor cell1.30e-81161
hematopoietic multipotent progenitor cell1.30e-81161
leukocyte8.41e-78136
hematopoietic lineage restricted progenitor cell2.19e-71120
nongranular leukocyte2.00e-70115
myeloid cell3.37e-50108
common myeloid progenitor3.37e-50108
myeloid leukocyte6.00e-4572
granulocyte monocyte progenitor cell3.26e-4367
myeloid lineage restricted progenitor cell1.47e-4266
macrophage dendritic cell progenitor6.67e-4061
monopoietic cell9.50e-4059
monocyte9.50e-4059
monoblast9.50e-4059
promonocyte9.50e-4059
defensive cell3.62e-3748
phagocyte3.62e-3748
classical monocyte1.40e-3442
CD14-positive, CD16-negative classical monocyte1.40e-3442
nucleate cell8.54e-2755
lymphocyte2.19e-2653
common lymphoid progenitor2.19e-2653
lymphoid lineage restricted progenitor cell5.34e-2652
mesenchymal cell2.56e-14354
T cell3.72e-1425
pro-T cell3.72e-1425
stuff accumulating cell2.67e-1387
connective tissue cell4.31e-13361
mature alpha-beta T cell7.93e-1318
alpha-beta T cell7.93e-1318
immature T cell7.93e-1318
mature T cell7.93e-1318
immature alpha-beta T cell7.93e-1318
lymphocyte of B lineage2.34e-1124
pro-B cell2.34e-1124
CD8-positive, alpha-beta T cell4.60e-0911
motile cell5.05e-09386
B cell7.78e-0914
intermediate monocyte9.27e-089
CD14-positive, CD16-positive monocyte9.27e-089
Uber Anatomy
Ontology termp-valuen
hematopoietic system3.81e-4998
blood island3.81e-4998
hemolymphoid system3.61e-45108
bone marrow2.45e-3776
immune system1.71e-3693
bone element2.50e-3282
skeletal element8.76e-2790
skeletal system7.61e-22100
adult organism1.14e-19114
connective tissue2.11e-12371
lateral plate mesoderm3.21e-12203
blood3.34e-0915
haemolymphatic fluid3.34e-0915
organism substance3.34e-0915
Disease
Ontology termp-valuen
hematologic cancer8.26e-1151
immune system cancer8.26e-1151
leukemia1.85e-1039
myeloid leukemia5.49e-0831


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)
MA0003.11.69543
MA0004.10.502801
MA0006.10.341337
MA0007.10.483857
MA0009.10.973289
MA0014.10.367415
MA0017.10.380797
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.35747
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.10.382278
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.10.158296
MA0056.10
MA0057.10.115382
MA0058.10.406232
MA0059.10.404929
MA0060.10.638423
MA0061.10.198335
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.488375
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.10.065183
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.11.04478
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.0723293
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.10.467172
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.12.55597
MA0101.10.347695
MA0103.10.332048
MA0105.10.340955
MA0106.10.648997
MA0107.10.274127
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.11.59862
MA0114.10.269076
MA0115.11.21667
MA0116.10.277571
MA0117.11.01134
MA0119.11.00897
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.11.65047
MA0140.10.564957
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.10.254954
MA0145.10.276317
MA0146.10.547931
MA0147.10.281049
MA0148.10.528066
MA0149.10.555119
MA0062.21.07166
MA0035.20.564239
MA0039.20.128723
MA0138.20.704862
MA0002.20.611548
MA0137.20.36398
MA0104.20.223944
MA0047.20.636643
MA0112.21.95102
MA0065.20.282161
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.102476
MA0155.10.250175
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.10.770207
MA0160.10.543522
MA0161.10
MA0162.10.106355
MA0163.10.0167306
MA0164.11.62495
MA0080.20.911393
MA0018.20.650405
MA0099.20.572
MA0079.20.263996
MA0102.21.51913
MA0258.11.27333
MA0259.10.289405
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
POLR2A#543072.147453176558070.004747636447610280.0223209868979909
TFAP2A#702037.079414731304980.006452554472180970.0280265475782952



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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