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{{Coexpression_clusters
{
|full_id=C1488_CD4_CD19_CD14CD16_CD8_Neutrophils_Basophils_Natural
 

Latest revision as of 11:46, 17 September 2013


Full id: C1488_CD4_CD19_CD14CD16_CD8_Neutrophils_Basophils_Natural



Phase1 CAGE Peaks

Hg19::chr21:43482969..43482994,+p2@UMODL1
Hg19::chr4:83295323..83295348,+p@chr4:83295323..83295348
+
Hg19::chr5:1386528..1386539,-p2@AK127466
Hg19::chr7:144533055..144533069,-p2@TPK1
Hg19::chr8:132916684..132916697,-p@chr8:132916684..132916697
-
Hg19::chr9:115095363..115095398,+p@chr9:115095363..115095398
+


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:0042357thiamin diphosphate metabolic process0.00144820886924134
GO:0004788thiamin diphosphokinase activity0.00144820886924134
GO:0009229thiamin diphosphate biosynthetic process0.00144820886924134
GO:0042724thiamin and derivative biosynthetic process0.00144820886924134
GO:0006772thiamin metabolic process0.00144820886924134
GO:0042723thiamin and derivative metabolic process0.00201134199617551
GO:0016778diphosphotransferase activity0.00482658131089662
GO:0006767water-soluble vitamin metabolic process0.0192921145785954
GO:0006766vitamin metabolic process0.0230358905860548
GO:0009108coenzyme biosynthetic process0.0469337764260271
GO:0051188cofactor biosynthetic process0.0481194432595581



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
leukocyte6.91e-57136
hematopoietic stem cell1.65e-48168
angioblastic mesenchymal cell1.65e-48168
hematopoietic lineage restricted progenitor cell7.52e-47120
nongranular leukocyte1.26e-46115
hematopoietic cell2.45e-45177
hematopoietic oligopotent progenitor cell2.60e-44161
hematopoietic multipotent progenitor cell2.60e-44161
myeloid leukocyte4.26e-2872
granulocyte monocyte progenitor cell1.57e-2467
macrophage dendritic cell progenitor1.17e-2261
lymphoid lineage restricted progenitor cell1.54e-2252
classical monocyte2.44e-2242
CD14-positive, CD16-negative classical monocyte2.44e-2242
myeloid lineage restricted progenitor cell2.49e-2266
lymphocyte5.03e-2253
common lymphoid progenitor5.03e-2253
monopoietic cell8.84e-2259
monocyte8.84e-2259
monoblast8.84e-2259
promonocyte8.84e-2259
myeloid cell1.50e-21108
common myeloid progenitor1.50e-21108
nucleate cell4.68e-2155
defensive cell1.63e-2048
phagocyte1.63e-2048
mature alpha-beta T cell4.64e-1218
alpha-beta T cell4.64e-1218
immature T cell4.64e-1218
mature T cell4.64e-1218
immature alpha-beta T cell4.64e-1218
T cell9.31e-1225
pro-T cell9.31e-1225
lymphocyte of B lineage3.71e-1024
pro-B cell3.71e-1024
CD8-positive, alpha-beta T cell1.23e-0811
B cell4.63e-0814
intermediate monocyte3.09e-079
CD14-positive, CD16-positive monocyte3.09e-079
mesenchymal cell3.36e-07354
Uber Anatomy
Ontology termp-valuen
hemolymphoid system5.07e-30108
hematopoietic system7.31e-3098
blood island7.31e-3098
immune system8.91e-2593
bone marrow2.71e-2376
bone element4.11e-2082
skeletal element1.53e-1590
skeletal system4.70e-12100
lateral plate mesoderm7.25e-10203
adult organism1.45e-07114


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)
MA0003.10.515118
MA0004.11.37419
MA0006.11.01439
MA0007.11.33289
MA0009.11.03681
MA0014.10.788761
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.12.77054
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.10.152639
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.465994
MA0056.10
MA0057.10.450439
MA0058.11.16137
MA0059.10.457555
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.0214749
MA0074.10.660398
MA0076.12.07987
MA0077.10.997832
MA0078.10.763954
MA0081.11.15882
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.32124
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.11.02138
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.10.134725
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.845337
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.10.226048
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.707171
MA0146.10.232472
MA0147.11.57246
MA0148.10.584698
MA0149.10.612449
MA0062.21.90691
MA0035.20.621793
MA0039.20.35955
MA0138.20.765223
MA0002.20.709311
MA0137.20.414885
MA0104.21.35181
MA0047.20.695777
MA0112.20.101413
MA0065.20.718489
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.132326
MA0155.10.65596
MA0156.11.07131
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.10.62636
MA0163.10.273773
MA0164.10.738243
MA0080.21.02158
MA0018.20.709805
MA0099.20.629739
MA0079.20.248693
MA0102.21.58513
MA0258.10.788656
MA0259.10.893594
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
ELF1#199764.258097958807540.0001677224776288830.00205330768269639
POLR2A#543062.147453176558070.01019570676818780.0380513657505277
SRF#672236.89858913108390.00644245168930370.0280036297489986
TAF1#687263.343046285745290.0007162474284635620.00573475660696918



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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