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

Latest revision as of 11:28, 17 September 2013


Full id: C691_Monocytederived_CD14_Macrophage_CD19_Dendritic_immature_Whole



Phase1 CAGE Peaks

Hg19::chr11:67771024..67771043,-p2@UNC93B1
Hg19::chr11:67771513..67771604,-p1@UNC93B1
Hg19::chr14:21249200..21249248,+p1@RNASE6
Hg19::chr14:21249254..21249267,+p3@RNASE6
Hg19::chr14:21249300..21249314,+p2@RNASE6
Hg19::chr14:21249998..21250018,+p5@RNASE6
Hg19::chr5:66492562..66492635,-p1@CD180
Hg19::chr6:32908739..32908746,-p3@HLA-DMB
Hg19::chr6:32908765..32908786,-p2@HLA-DMB
Hg19::chr6:32908792..32908830,-p1@HLA-DMB
Hg19::chr6:6588941..6588960,+p1@LY86
Hg19::chr6:6588974..6589011,+p2@LY86


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

p.valueFDRnGenesnPathwayName
5.55202746254732e-050.01757216691896233511Signaling in Immune system (Reactome):REACT_6900
3.63134547651233e-050.0175721669189623255{TRAF6,55} (Static Module):NA



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:0006952defense response0.00398983501859937
GO:0006955immune response0.0145573104414221
GO:0002376immune system process0.0145573104414221
GO:0006954inflammatory response0.0145573104414221
GO:0009611response to wounding0.0244421873004799
GO:0009605response to external stimulus0.0357037352160071
GO:0004522pancreatic ribonuclease activity0.0357037352160071
GO:0016892endoribonuclease activity, producing 3'-phosphomonoesters0.0357037352160071
GO:0031902late endosome membrane0.0357037352160071
GO:0016894endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters0.0357037352160071
GO:0006401RNA catabolic process0.0466318094114567
GO:0005765lysosomal membrane0.0466318094114567
GO:0005770late endosome0.0466318094114567
GO:0005774vacuolar membrane0.0485780051467031
GO:0044437vacuolar part0.0485780051467031
GO:0004521endoribonuclease activity0.0485780051467031
GO:0006959humoral immune response0.0485780051467031
GO:0005886plasma membrane0.0485780051467031
GO:0006950response to stress0.0485780051467031
GO:0010008endosome membrane0.0485780051467031
GO:0044440endosomal part0.0485780051467031



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
leukocyte2.17e-56136
nongranular leukocyte1.19e-52115
hematopoietic stem cell1.14e-51168
angioblastic mesenchymal cell1.14e-51168
hematopoietic lineage restricted progenitor cell1.04e-48120
hematopoietic oligopotent progenitor cell9.91e-48161
hematopoietic multipotent progenitor cell9.91e-48161
hematopoietic cell1.92e-46177
macrophage dendritic cell progenitor4.70e-4361
monopoietic cell2.59e-4159
monocyte2.59e-4159
monoblast2.59e-4159
promonocyte2.59e-4159
granulocyte monocyte progenitor cell3.23e-4167
myeloid leukocyte4.01e-4072
myeloid lineage restricted progenitor cell3.86e-3766
defensive cell6.01e-3748
phagocyte6.01e-3748
myeloid cell2.31e-34108
common myeloid progenitor2.31e-34108
classical monocyte2.09e-3142
CD14-positive, CD16-negative classical monocyte2.09e-3142
lymphocyte of B lineage2.65e-1624
pro-B cell2.65e-1624
B cell1.22e-1214
stuff accumulating cell8.16e-1287
lymphocyte8.50e-1253
common lymphoid progenitor8.50e-1253
lymphoid lineage restricted progenitor cell2.65e-1152
nucleate cell6.77e-1155
dendritic cell5.16e-0810
intermediate monocyte1.38e-079
CD14-positive, CD16-positive monocyte1.38e-079
macrophage6.28e-076
Uber Anatomy
Ontology termp-valuen
hematopoietic system5.74e-4498
blood island5.74e-4498
adult organism3.89e-43114
hemolymphoid system1.55e-39108
bone marrow1.34e-3576
immune system1.33e-3293
bone element6.13e-3182
skeletal element9.06e-2690
skeletal system4.39e-22100
neural tube3.11e-1356
neural rod3.11e-1356
future spinal cord3.11e-1356
neural keel3.11e-1356
lateral plate mesoderm1.09e-12203
regional part of nervous system8.14e-1253
regional part of brain8.14e-1253
regional part of forebrain9.77e-1141
forebrain9.77e-1141
anterior neural tube9.77e-1141
future forebrain9.77e-1141
telencephalon3.49e-0934
brain grey matter3.54e-0934
gray matter3.54e-0934
regional part of telencephalon2.21e-0832
cerebral hemisphere3.45e-0832
blood1.52e-0715
haemolymphatic fluid1.52e-0715
organism substance1.52e-0715
central nervous system1.61e-0781
brain1.81e-0768
future brain1.81e-0768
neural plate2.59e-0782
presumptive neural plate2.59e-0782
tissue3.01e-07773
musculoskeletal system3.17e-07167
regional part of cerebral cortex3.44e-0722


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)
MA0003.10.0958548
MA0004.10.861826
MA0006.10.552945
MA0007.10.305951
MA0009.11.78642
MA0014.10.0339142
MA0017.10.627635
MA0019.10.45566
MA0024.10.654931
MA0025.10.886436
MA0027.12.35633
MA0028.10.201461
MA0029.10.673506
MA0030.10.662482
MA0031.10.600685
MA0038.11.87299
MA0040.10.67914
MA0041.10.338572
MA0042.10.310552
MA0043.10.756508
MA0046.10.745626
MA0048.10.357781
MA0050.11.51437
MA0051.11.85986
MA0052.10.682867
MA0055.10.107116
MA0056.10
MA0057.10.147728
MA0058.10.676094
MA0059.10.239727
MA0060.10.337131
MA0061.10.605357
MA0063.10
MA0066.11.87432
MA0067.11.06751
MA0068.10.0633085
MA0069.12.94053
MA0070.10.731026
MA0071.10.379038
MA0072.10.726666
MA0073.10.0284577
MA0074.10.40963
MA0076.10.254045
MA0077.10.719193
MA0078.10.502027
MA0081.11.25193
MA0083.10.763502
MA0084.11.25286
MA0087.10.724294
MA0088.10.20556
MA0089.10
MA0090.10.266215
MA0091.10.324543
MA0092.10.291716
MA0093.10.558691
MA0095.10
MA0098.10
MA0100.11.09213
MA0101.10.19375
MA0103.10.535462
MA0105.10.307721
MA0106.10.452066
MA0107.10.137948
MA0108.20.597764
MA0109.10
MA0111.10.277713
MA0113.10.467266
MA0114.10.134281
MA0115.10.992167
MA0116.10.433848
MA0117.10.792789
MA0119.10.226505
MA0122.10.818044
MA0124.10.951337
MA0125.10.868909
MA0130.10
MA0131.10.519055
MA0132.10
MA0133.10
MA0135.10.785738
MA0136.11.07857
MA0139.10.961223
MA0140.10.376643
MA0141.10.238287
MA0142.10.570448
MA0143.10.467429
MA0144.10.124153
MA0145.10.441471
MA0146.10.0677137
MA0147.10.440281
MA0148.10.344198
MA0149.10.367947
MA0062.20.589182
MA0035.20.376007
MA0039.20.0300713
MA0138.20.503176
MA0002.20.316618
MA0137.20.595725
MA0104.20.102626
MA0047.20.440861
MA0112.20.416057
MA0065.20.0221687
MA0150.10.261236
MA0151.10
MA0152.10.382565
MA0153.10.852412
MA0154.10.0310431
MA0155.10.0793743
MA0156.11.77254
MA0157.10.544523
MA0158.10
MA0159.10.143477
MA0160.10.357736
MA0161.10
MA0162.10.0602299
MA0163.10.0369192
MA0164.10.478818
MA0080.21.677
MA0018.20.453345
MA0099.20.382887
MA0079.20.00539704
MA0102.21.28978
MA0258.10.375
MA0259.10.455773
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#1053836.089450448075910.01151367035494970.042112356174287
BCL11A#53335511.82060629316963.49540037901642e-050.00068145626317733
IRF4#366259.131046952810050.0001194522965794710.00162145547211637
MEF2C#4208310.3278386231560.002646808953776950.0146205151702285
NANOG#7992337.311194620253160.006971199585208680.02948109465013
NFKB1#479073.201370330779740.002228657911514870.0128023103031022
PAX5#507963.334782765588910.004629821511058920.0218615575003835
POLR2A#5430111.968498745178230.00153515886455670.0097601787700394
POU2F2#545253.794218357392720.006499616292676570.0278350525276109
SP1#666794.273786033605672.0740195727163e-050.000458333749798811
SPI1#668885.469549005681821.52450635998341e-050.000360466198166871
TBP#690882.471180458064260.004672713706606670.0220551157772989
USF2#739266.49609869253480.0001276632672591170.00169782554046542



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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