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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:26, 17 September 2013


Full id: C569_CD14_immature_CD19_Basophils_migratory_Dendritic_Peripheral



Phase1 CAGE Peaks

Hg19::chr16:87498643..87498677,+p@chr16:87498643..87498677
+
Hg19::chr5:149792614..149792625,+p@chr5:149792614..149792625
+
Hg19::chr6:30227370..30227387,+p2@HLA-L
Hg19::chr6:32441310..32441322,-p2@HLA-DRB9
Hg19::chr6:32441341..32441365,-p1@HLA-DRB9
Hg19::chr6:32572499..32572517,+p@chr6:32572499..32572517
+
Hg19::chr6:32577605..32577616,-p@chr6:32577605..32577616
-
Hg19::chr6:32577619..32577667,-p@chr6:32577619..32577667
-
Hg19::chr6:32577678..32577698,-p@chr6:32577678..32577698
-
Hg19::chr6:32577917..32577935,+p@chr6:32577917..32577935
+
Hg19::chr6:32997441..32997457,+p@chr6:32997441..32997457
+
Hg19::chr6:32997459..32997492,+p@chr6:32997459..32997492
+
Hg19::chr6:32997495..32997511,+p@chr6:32997495..32997511
+
Hg19::chr6:33043568..33043579,-p@chr6:33043568..33043579
-
Hg19::chr7:140017476..140017487,-p@chr7:140017476..140017487
-
Hg19::chr7:39664276..39664287,-p@chr7:39664276..39664287
-


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
leukocyte1.27e-98136
nongranular leukocyte6.14e-88115
hematopoietic lineage restricted progenitor cell1.38e-83120
classical monocyte4.22e-8142
CD14-positive, CD16-negative classical monocyte4.22e-8142
hematopoietic stem cell6.12e-78168
angioblastic mesenchymal cell6.12e-78168
hematopoietic cell9.84e-75177
defensive cell1.61e-7248
phagocyte1.61e-7248
hematopoietic oligopotent progenitor cell3.26e-69161
hematopoietic multipotent progenitor cell3.26e-69161
macrophage dendritic cell progenitor2.56e-6261
monopoietic cell2.75e-5859
monocyte2.75e-5859
monoblast2.75e-5859
promonocyte2.75e-5859
granulocyte monocyte progenitor cell4.94e-5867
myeloid leukocyte1.37e-5572
myeloid lineage restricted progenitor cell3.83e-5366
myeloid cell2.49e-41108
common myeloid progenitor2.49e-41108
stuff accumulating cell5.96e-3487
mesenchymal cell1.94e-26354
connective tissue cell1.69e-25361
lymphoid lineage restricted progenitor cell1.45e-2452
lymphocyte6.10e-2453
common lymphoid progenitor6.10e-2453
nucleate cell9.23e-2355
motile cell3.44e-22386
lymphocyte of B lineage1.34e-2124
pro-B cell1.34e-2124
B cell5.76e-2114
intermediate monocyte1.44e-189
CD14-positive, CD16-positive monocyte1.44e-189
stem cell2.18e-18441
multi fate stem cell3.74e-18427
somatic stem cell1.35e-17433
dendritic cell5.09e-1110
Langerhans cell1.28e-105
conventional dendritic cell4.67e-088
somatic cell1.28e-07588
basophil1.51e-073
single nucleate cell4.83e-073
mononuclear cell4.83e-073
plasmacytoid dendritic cell8.41e-073
Uber Anatomy
Ontology termp-valuen
bone marrow5.62e-5276
hematopoietic system1.66e-5098
blood island1.66e-5098
immune system2.33e-4793
bone element3.82e-4782
hemolymphoid system3.46e-46108
skeletal element1.06e-4190
skeletal system4.00e-36100
connective tissue3.23e-24371
lateral plate mesoderm2.69e-17203
musculoskeletal system3.58e-16167


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)
MA0003.10.00302458
MA0004.10.238283
MA0006.10.124371
MA0007.10.223897
MA0009.11.55479
MA0014.10.0018064
MA0017.10.45828
MA0019.10.359322
MA0024.10.547222
MA0025.10.771296
MA0027.12.23171
MA0028.10.134741
MA0029.12.37434
MA0030.10.554453
MA0031.10.495474
MA0038.10.321141
MA0040.10.570428
MA0041.10.252793
MA0042.10.227947
MA0043.11.55541
MA0046.10.634468
MA0048.10.0172925
MA0050.10.647665
MA0051.10.317617
MA0052.10.574006
MA0055.10.19033
MA0056.10
MA0057.10.189848
MA0058.10.167587
MA0059.10.166682
MA0060.14.20665
MA0061.13.20126
MA0063.10
MA0066.10.860141
MA0067.10.948938
MA0068.10.55611
MA0069.10.630852
MA0070.10.620368
MA0071.10.289163
MA0072.10.616162
MA0073.10.000310801
MA0074.11.53464
MA0076.10.178863
MA0077.10.608956
MA0078.10.402443
MA0081.10.499456
MA0083.10.651755
MA0084.11.13204
MA0087.10.613875
MA0088.10.0328284
MA0089.10
MA0090.11.0561
MA0091.10.240316
MA0092.10.211423
MA0093.10.397767
MA0095.10
MA0098.10
MA0100.10.332778
MA0101.13.27443
MA0103.10.118522
MA0105.11.55776
MA0106.10.93695
MA0107.13.35342
MA0108.20.492699
MA0109.10
MA0111.10.578093
MA0113.10.370073
MA0114.10.584594
MA0115.10.874839
MA0116.10.0861811
MA0117.10.680135
MA0119.10.155538
MA0122.10.70466
MA0124.10.834787
MA0125.10.75419
MA0130.10
MA0131.10.418384
MA0132.10
MA0133.10
MA0135.10.673296
MA0136.10.327047
MA0139.10.0410754
MA0140.10.286995
MA0141.10.165463
MA0142.10.4668
MA0143.10.370225
MA0144.14.60185
MA0145.10.00760196
MA0146.10.0175001
MA0147.10.0881384
MA0148.10.257816
MA0149.11.39788
MA0062.20.0439512
MA0035.20.286421
MA0039.20.0116984
MA0138.20.403517
MA0002.20.196222
MA0137.27.85021
MA0104.20.0580852
MA0047.20.345656
MA0112.20.103673
MA0065.20.118053
MA0150.11.64205
MA0151.10
MA0152.10.292357
MA0153.10.738108
MA0154.10.321153
MA0155.10.204406
MA0156.10.140505
MA0157.10.442323
MA0158.10
MA0159.10.0884959
MA0160.10.26995
MA0161.10
MA0162.10.0005964
MA0163.10.00206968
MA0164.10.380804
MA0080.20.397909
MA0018.20.357181
MA0099.21.44708
MA0079.20.000905193
MA0102.21.16862
MA0258.10.242841
MA0259.10.0929051
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#10538710.65653828413281.61542932578931e-066.13281800640166e-05
BCL11A#5333547.092363775901760.001996726919506420.0116104984547815
BCL3#60236.477581775700930.0102327923622150.0380971981148357
EBF1#187984.45323342328450.0001406612198143210.00183402211438051
FOS#2353137.310838688476711.58896378173251e-101.67288093145526e-08
FOSL1#806149.928394929093250.0005732096671019780.0048399583169588
GATA1#262365.085115553925160.0006728445994713830.00542970306940131
IRF4#366245.478628171686030.005068546010533350.0235992098789217
JUN#372564.692310947126130.001030862620745210.00729270888356089
JUNB#372659.56582270619410.0001199540053341380.00162615217589461
MEF2A#420544.685807727411010.008783099930456450.033363576548954
NFKB1#4790124.116047568145381.1672690224261e-064.76204724348277e-05
NFYA#480066.909592762436450.0001272357021845650.00169278592362469
NFYB#480155.237435391730140.001892131820411660.0111469063172368
PAX5#507972.91793491989030.005570360390464740.0252096402833881
POLR2A#5430162.147453176558074.88536678567824e-060.000151087598972298
POU2F2#5452126.829593043306893.64282080840165e-092.99568946778472e-07
RFX5#5993139.788927547096023.88993456139909e-125.14254272984759e-10
SP1#6667103.561488361338067.84823393273076e-050.00120290828250729
SPI1#668894.614931973544033.01826774164688e-050.000620765783122998
STAT1#677256.470808592874750.0007317668712721070.00582774136562357
STAT3#677463.944799373932840.002544236462237630.0140874515894198
TAF1#6872142.925165500027132.86208202997623e-069.84237685639406e-05
TAL1#688659.333942711700060.0001345934653965960.00176460041834736
TBP#6908143.243424351209347.26082897616864e-073.23374719591504e-05
TRIM28#1015544.647631261315630.009036390425926160.0342584427070314
USF2#739254.060061682834250.005732377623791920.0258354026949987
YY1#752892.762533546792790.001686710741936190.0105408319277809



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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