Personal tools

Coexpression cluster:C1017: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
 
(One intermediate revision by the same user not shown)
Line 1: Line 1:
{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 11:35, 17 September 2013


Full id: C1017_CD14_Macrophage_Monocytederived_Mast_Dendritic_B_splenic



Phase1 CAGE Peaks

Hg19::chr12:51402984..51403042,-p2@SLC11A2
Hg19::chr14:93651635..93651647,+p4@C14orf109
Hg19::chr1:111742738..111742772,-p4@DENND2D
Hg19::chr1:111742778..111742797,-p7@DENND2D
Hg19::chr1:111742809..111742819,-p12@DENND2D
Hg19::chr1:111742823..111742838,-p5@DENND2D
Hg19::chr1:111742942..111742955,+p5@CHI3L2
Hg19::chr1:111743000..111743011,+p8@CHI3L2


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:0005381iron ion transmembrane transporter activity0.0126732839990412
GO:0006032chitin catabolic process0.0126732839990412
GO:0006046N-acetylglucosamine catabolic process0.0126732839990412
GO:0006043glucosamine catabolic process0.0126732839990412
GO:0006030chitin metabolic process0.0126732839990412
GO:0004568chitinase activity0.0126732839990412
GO:0046348amino sugar catabolic process0.0126732839990412
GO:0044247cellular polysaccharide catabolic process0.0137973605797099
GO:0000272polysaccharide catabolic process0.0137973605797099
GO:0046915transition metal ion transmembrane transporter activity0.0172395925919889
GO:0006044N-acetylglucosamine metabolic process0.0172395925919889
GO:0006041glucosamine metabolic process0.0172395925919889
GO:0006040amino sugar metabolic process0.0186382001077193
GO:0015082di-, tri-valent inorganic cation transmembrane transporter activity0.0224461786782998
GO:0006826iron ion transport0.0224461786782998
GO:0044264cellular polysaccharide metabolic process0.0298563934301294
GO:0005976polysaccharide metabolic process0.0298563934301294
GO:0000041transition metal ion transport0.0334280270378697



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 lineage restricted progenitor cell2.45e-57120
leukocyte2.90e-55136
granulocyte monocyte progenitor cell5.41e-5567
nongranular leukocyte6.33e-54115
myeloid lineage restricted progenitor cell1.31e-5266
myeloid leukocyte4.97e-5272
macrophage dendritic cell progenitor1.24e-5061
monopoietic cell1.83e-4959
monocyte1.83e-4959
monoblast1.83e-4959
promonocyte1.83e-4959
defensive cell7.38e-4948
phagocyte7.38e-4948
hematopoietic stem cell7.11e-47168
angioblastic mesenchymal cell7.11e-47168
hematopoietic oligopotent progenitor cell1.02e-46161
hematopoietic multipotent progenitor cell1.02e-46161
hematopoietic cell1.51e-42177
classical monocyte8.27e-4242
CD14-positive, CD16-negative classical monocyte8.27e-4242
myeloid cell6.57e-38108
common myeloid progenitor6.57e-38108
stuff accumulating cell4.77e-2387
lymphoid lineage restricted progenitor cell6.05e-0952
lymphocyte1.30e-0853
common lymphoid progenitor1.30e-0853
intermediate monocyte1.70e-089
CD14-positive, CD16-positive monocyte1.70e-089
macrophage2.53e-086
nucleate cell5.41e-0855
CD8-positive, alpha-beta T cell2.79e-0711
mature alpha-beta T cell3.21e-0718
alpha-beta T cell3.21e-0718
immature T cell3.21e-0718
mature T cell3.21e-0718
immature alpha-beta T cell3.21e-0718
histamine secreting cell8.18e-075
biogenic amine secreting cell8.18e-075
granulocytopoietic cell8.18e-075
mast cell8.18e-075
mast cell progenitor8.18e-075
basophil mast progenitor cell8.18e-075
mesenchymal cell9.23e-07354
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.92e-5498
blood island1.92e-5498
hemolymphoid system7.67e-50108
bone marrow1.77e-4576
immune system1.35e-4493
bone element2.53e-4082
skeletal element1.47e-3490
skeletal system1.04e-28100
adult organism1.32e-19114
lateral plate mesoderm1.53e-16203
musculoskeletal system2.52e-10167


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)
MA0003.10.248189
MA0004.10.455723
MA0006.10.300178
MA0007.10.437331
MA0009.10.918715
MA0014.10.134069
MA0017.13.35603
MA0019.10.602411
MA0024.10.813542
MA0025.11.05265
MA0027.12.5321
MA0028.10.315574
MA0029.10.832916
MA0030.10.821423
MA0031.10.756713
MA0038.10.557409
MA0040.10.838784
MA0041.10.474018
MA0042.10.442535
MA0043.10.919032
MA0046.10.90778
MA0048.10.0955945
MA0050.10.443405
MA0051.10.553205
MA0052.10.842664
MA0055.10.028436
MA0056.10
MA0057.10.0912556
MA0058.10.362328
MA0059.11.69011
MA0060.10.190336
MA0061.10.165998
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.10.133123
MA0069.10.903908
MA0070.10.892666
MA0071.12.22338
MA0072.12.05773
MA0073.19.20286e-05
MA0074.10.552456
MA0076.10.377799
MA0077.10.880402
MA0078.10.652193
MA0081.11.69066
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.10.054222
MA0089.10
MA0090.10.391903
MA0091.10.458301
MA0092.11.07975
MA0093.10.303084
MA0095.10
MA0098.10
MA0100.10.571227
MA0101.10.30624
MA0103.10.291333
MA0105.10.279181
MA0106.10.59853
MA0107.10.236528
MA0108.20.753643
MA0109.10
MA0111.10.405141
MA0113.19.16025
MA0114.12.66555
MA0115.15.98565
MA0116.10.239768
MA0117.10.956472
MA0119.10.345493
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.10.670358
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.12.37243
MA0139.11.46857
MA0140.10.516266
MA0141.10.359385
MA0142.10.724856
MA0143.10.615094
MA0144.10.623945
MA0145.12.92343
MA0146.10.934908
MA0147.10.243042
MA0148.10.480298
MA0149.10.506665
MA0062.20.161302
MA0035.20.515566
MA0039.20.00133745
MA0138.20.653421
MA0002.20.179788
MA0137.20.86081
MA0104.20.189646
MA0047.20.586412
MA0112.21.21228
MA0065.22.95949
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.274121
MA0155.10.197713
MA0156.10.323987
MA0157.10.697424
MA0158.10
MA0159.10.682702
MA0160.10.495355
MA0161.10
MA0162.10.0163939
MA0163.10.0517199
MA0164.10.627336
MA0080.23.13741
MA0018.20.599912
MA0099.20.523145
MA0079.29.66794e-05
MA0102.21.46209
MA0258.10.603127
MA0259.10.25092
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
ATF3#467616.84738089450662.0128920133559e-071.08811816243725e-05
EBF1#187966.679850134926754.58015900243755e-050.000805298360362921
ELF1#199773.72583571395660.0002503412725512720.00269818288585989
FOS#235366.74846648167084.31702653902356e-050.000769921336593376
MAX#414964.839416631755340.0002917504313705360.00309687196888987
MYC#460974.569496637658236.28392411465611e-050.00102657085970682
NFE2#4778657.90319548872181.28513996806255e-101.37660239102036e-08
PAX5#507965.002174148383370.0002416084515475770.00262902115765549
POU2F2#545266.829593043306894.02833503357943e-050.000738356059269923
SP1#666774.986083705873283.46905874958224e-050.000680385026756092
SPI1#668866.153242631392047.3612205654473e-050.00114848896718666
TBP#690862.780078015322290.006390181121263010.0278018798635113
USF1#739175.566311867556961.63553159235289e-050.000377905495517132
USF2#739269.74414803880225.07489102954454e-060.000156531761439634



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C1017&oldid=3068134"