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{{Coexpression_clusters
{
|full_id=C662_Mast_CD8_Natural_Basophils_CD4_Peripheral_Dendritic
 

Latest revision as of 11:28, 17 September 2013


Full id: C662_Mast_CD8_Natural_Basophils_CD4_Peripheral_Dendritic



Phase1 CAGE Peaks

Hg19::chr12:9142131..9142229,+p1@KLRG1
Hg19::chr12:9142239..9142262,+p4@KLRG1
Hg19::chr12:9142310..9142328,+p5@KLRG1
Hg19::chr12:9142330..9142341,+p@chr12:9142330..9142341
+
Hg19::chr12:9144805..9144867,+p3@KLRG1
Hg19::chr15:86126120..86126165,+p3@AKAP13
Hg19::chr16:85588893..85588910,-p@chr16:85588893..85588910
-
Hg19::chr1:23430065..23430077,+p@chr1:23430065..23430077
+
Hg19::chr21:36421147..36421193,-p10@RUNX1
Hg19::chr21:36421347..36421380,-p8@RUNX1
Hg19::chr4:151749436..151749449,-p@chr4:151749436..151749449
-
Hg19::chr4:151749450..151749479,-p@chr4:151749450..151749479
-
Hg19::chr4:151749484..151749504,-p@chr4:151749484..151749504
-


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:0030854positive regulation of granulocyte differentiation0.00596079123984457
GO:0030852regulation of granulocyte differentiation0.00596079123984457
GO:0030851granulocyte differentiation0.0149002234807402
GO:0002763positive regulation of myeloid leukocyte differentiation0.0149002234807402
GO:0004691cAMP-dependent protein kinase activity0.0190706017369349
GO:0045766positive regulation of angiogenesis0.0193657290530936
GO:0004690cyclic nucleotide-dependent protein kinase activity0.0193657290530936
GO:0045639positive regulation of myeloid cell differentiation0.0193657290530936
GO:0002761regulation of myeloid leukocyte differentiation0.0198611167149153
GO:0002573myeloid leukocyte differentiation0.0357342245604695
GO:0045637regulation of myeloid cell differentiation0.0368127436255965
GO:0045765regulation of angiogenesis0.0377105745980246
GO:0045597positive regulation of cell differentiation0.0430427686180983
GO:0019992diacylglycerol binding0.0446283343177092
GO:0031404chloride ion binding0.0446283343177092
GO:0043168anion binding0.0446283343177092
GO:0051094positive regulation of developmental process0.0475867330910966
GO:0006968cellular defense response0.0475867330910966
GO:0030099myeloid cell differentiation0.0482057734703268



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
hematopoietic stem cell2.02e-30168
angioblastic mesenchymal cell2.02e-30168
mature alpha-beta T cell1.62e-2818
alpha-beta T cell1.62e-2818
immature T cell1.62e-2818
mature T cell1.62e-2818
immature alpha-beta T cell1.62e-2818
hematopoietic cell8.58e-28177
leukocyte8.89e-27136
hematopoietic oligopotent progenitor cell1.95e-26161
hematopoietic multipotent progenitor cell1.95e-26161
hematopoietic lineage restricted progenitor cell1.10e-20120
CD8-positive, alpha-beta T cell1.98e-1911
T cell7.73e-1925
pro-T cell7.73e-1925
nongranular leukocyte1.76e-18115
lymphoid lineage restricted progenitor cell3.30e-1552
nucleate cell3.85e-1555
lymphocyte9.08e-1553
common lymphoid progenitor9.08e-1553
myeloid cell2.36e-12108
common myeloid progenitor2.36e-12108
myeloid leukocyte3.40e-1172
histamine secreting cell3.56e-105
biogenic amine secreting cell3.56e-105
granulocytopoietic cell3.56e-105
mast cell3.56e-105
mast cell progenitor3.56e-105
basophil mast progenitor cell3.56e-105
CD4-positive, alpha-beta T cell6.96e-106
myeloid lineage restricted progenitor cell1.01e-0766
granulocyte2.17e-078
granulocyte monocyte progenitor cell8.56e-0767
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.19e-1898
blood island2.19e-1898
hemolymphoid system1.37e-17108
blood2.17e-1415
haemolymphatic fluid2.17e-1415
organism substance2.17e-1415
immune system2.35e-0993
adult organism2.89e-07114
hemopoietic organ6.19e-077
immune organ6.19e-077


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)
MA0003.10.00135586
MA0004.10.297884
MA0006.10.169524
MA0007.10.282081
MA0009.10.724811
MA0014.10.00634684
MA0017.10.199401
MA0019.11.09485
MA0024.10.6245
MA0025.10.854131
MA0027.12.32165
MA0028.10.181601
MA0029.10.642879
MA0030.10.63197
MA0031.10.570886
MA0038.10.387473
MA0040.10.648455
MA0041.13.20459
MA0042.12.1821
MA0043.10.725115
MA0046.10.714324
MA0048.10.0323146
MA0050.12.18586
MA0051.10.383704
MA0052.10.652145
MA0055.10.531463
MA0056.10
MA0057.10.123867
MA0058.10.219229
MA0059.10.218203
MA0060.10.0892161
MA0061.10.542967
MA0063.10
MA0066.10.387854
MA0067.11.03434
MA0068.10.196125
MA0069.10.710614
MA0070.10.69985
MA0071.10.35315
MA0072.10.695528
MA0073.10.0160649
MA0074.10.383033
MA0076.10.231962
MA0077.10.688123
MA0078.10.473657
MA0081.10.623454
MA0083.10.732051
MA0084.11.21913
MA0087.10.693179
MA0088.10.337854
MA0089.10
MA0090.10.243681
MA0091.10.30011
MA0092.10.268302
MA0093.10.171791
MA0095.10
MA0098.10
MA0100.10.399896
MA0101.10.17426
MA0103.10.162663
MA0105.10.26318
MA0106.10.424592
MA0107.10.121572
MA0108.20.568002
MA0109.10
MA0111.10.254772
MA0113.10.439505
MA0114.10.118142
MA0115.10.959312
MA0116.10.123927
MA0117.10.76111
MA0119.10.205526
MA0122.10.786181
MA0124.10.918678
MA0125.10.83671
MA0130.10
MA0131.10.490408
MA0132.10
MA0133.10
MA0135.10.754112
MA0136.10.393782
MA0139.12.39706
MA0140.10.925465
MA0141.10.216821
MA0142.12.29607
MA0143.10.439666
MA0144.10.35188
MA0145.10.0164225
MA0146.10.0045745
MA0147.10.126316
MA0148.10.319209
MA0149.10.342334
MA0062.20.246574
MA0035.20.350194
MA0039.20.000373861
MA0138.20.474787
MA0002.21.4757
MA0137.21.04503
MA0104.20.298328
MA0047.20.413608
MA0112.20.180347
MA0065.20.0171659
MA0150.10.238884
MA0151.10
MA0152.10.356591
MA0153.11.91857
MA0154.10.0246626
MA0155.10.167839
MA0156.11.6604
MA0157.10.515488
MA0158.10
MA0159.10.126752
MA0160.10.332385
MA0161.10
MA0162.10.00205586
MA0163.10.02611
MA0164.11.144
MA0080.20.171855
MA0018.20.425847
MA0099.20.938958
MA0079.20.000154944
MA0102.21.25596
MA0258.10.335505
MA0259.10.132107
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#10538611.24206236567866.38699523402909e-060.000188326198545106
FOS#235353.460752041882460.01011210325939170.0378285676734585
GATA2#262476.862655548836762.05065762260648e-050.000454517469115871
IRF4#366246.742926980536660.002221995594476970.0127759853496796
JUN#372576.737677257411872.31332287642027e-050.000504913537911089
SPI1#668863.786610850087410.002614000338510870.0144530457596345



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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