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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:58, 17 September 2013


Full id: C2069_CD14_Neutrophils_Peripheral_Eosinophils_Basophils_immature_CD14CD16



Phase1 CAGE Peaks

Hg19::chr10:70815943..70815956,-p@chr10:70815943..70815956
-
Hg19::chr11:47396114..47396124,-p@chr11:47396114..47396124
-
Hg19::chr9:132536258..132536280,+p@chr9:132536258..132536280
+
Hg19::chr9:132536282..132536289,+p@chr9:132536282..132536289
+


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 monocyte8.61e-12642
CD14-positive, CD16-negative classical monocyte8.61e-12642
defensive cell7.56e-10948
phagocyte7.56e-10948
myeloid leukocyte2.11e-10272
macrophage dendritic cell progenitor8.64e-9161
monopoietic cell1.64e-8959
monocyte1.64e-8959
monoblast1.64e-8959
promonocyte1.64e-8959
granulocyte monocyte progenitor cell6.84e-8267
myeloid lineage restricted progenitor cell4.02e-7966
myeloid cell5.07e-68108
common myeloid progenitor5.07e-68108
leukocyte7.78e-68136
nongranular leukocyte6.01e-57115
stuff accumulating cell1.14e-5587
hematopoietic stem cell7.57e-53168
angioblastic mesenchymal cell7.57e-53168
hematopoietic cell1.33e-49177
hematopoietic lineage restricted progenitor cell1.55e-48120
hematopoietic oligopotent progenitor cell2.37e-48161
hematopoietic multipotent progenitor cell2.37e-48161
intermediate monocyte2.07e-319
CD14-positive, CD16-positive monocyte2.07e-319
granulocyte2.79e-228
mesenchymal cell3.94e-19354
connective tissue cell1.55e-18361
motile cell1.94e-16386
blood cell6.62e-1611
multi fate stem cell7.16e-14427
somatic stem cell1.62e-13433
stem cell4.65e-13441
single nucleate cell3.00e-123
mononuclear cell3.00e-123
basophil1.98e-113
non-classical monocyte6.51e-113
CD14-low, CD16-positive monocyte6.51e-113
natural killer cell2.30e-103
pro-NK cell2.30e-103
eosinophil9.59e-092
somatic cell2.33e-07588
Uber Anatomy
Ontology termp-valuen
bone marrow3.84e-7176
hematopoietic system1.59e-6598
blood island1.59e-6598
bone element2.86e-6582
skeletal element1.20e-5890
hemolymphoid system1.54e-58108
immune system1.88e-5693
skeletal system7.68e-52100
musculoskeletal system3.75e-27167
lateral plate mesoderm2.54e-26203
connective tissue1.01e-17371
mesoderm3.07e-13315
mesoderm-derived structure3.07e-13315
presumptive mesoderm3.07e-13315


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)
MA0003.10.720743
MA0004.11.69588
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
MA0017.11.41335
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.12.36201
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.396851
MA0056.10
MA0057.10.69331
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.946082
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.100363
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.536981
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.12.27878
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.656404
MA0106.10.869173
MA0107.11.1497
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.11.98562
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.12.4958
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.481
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.0247757
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.21.09513
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.649108
MA0155.10.180766
MA0156.10.560797
MA0157.12.23474
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.253219
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.20937
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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
BRCA1#672210.09211532161190.0137713969900260.0484592631482926
FOS#235336.74846648167080.005032452776317940.0234520697651095
FOXA2#3170212.31523187633260.009361916285467240.0353335203432319
JUN#372539.384621894252250.001918994502030470.0112803437157404
JUND#372735.245997956403270.01043432751748420.0386614656259458
NR2C2#7182216.30730545262040.005411825344648220.024548541833292
PRDM1#639265.91547788873040.0003415175120768950.0034672642601146
SMARCB1#6598313.68953683586810.0006305783409379340.00517906349081605
SMARCC1#6599221.83167965981570.003051207456162050.0160901315583998
SMARCC2#6601247.07768721344880.0006669282967095870.00544890279121118
STAT1#6772210.35329374859960.01310777476171260.0464827302413671
TFAP2C#702238.106921457395170.002947011739866440.015713634507577



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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