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{{Coexpression_clusters
{
|full_id=C1053_CD19_CD4_Natural_CD8_Peripheral_granulocyte_tonsil
|

Latest revision as of 11:36, 17 September 2013


Full id: C1053_CD19_CD4_Natural_CD8_Peripheral_granulocyte_tonsil



Phase1 CAGE Peaks

Hg19::chr17:56565257..56565283,-p2@HSF5
Hg19::chr3:122296443..122296454,+p3@PARP15
Hg19::chr3:122296465..122296476,+p2@PARP15
Hg19::chr3:122296477..122296503,+p1@PARP15
Hg19::chr4:114683412..114683431,-p10@CAMK2D
Hg19::chr6:157098579..157098634,+p4@ARID1B
Hg19::chr6:91006503..91006517,-p3@BACH2
Hg19::chr7:86848933..86848940,-p5@C7orf23


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:0050794regulation of cellular process0.015938311957429
GO:0048096chromatin-mediated maintenance of transcription0.015938311957429
GO:0005954calcium- and calmodulin-dependent protein kinase complex0.015938311957429
GO:0050789regulation of biological process0.015938311957429
GO:0006355regulation of transcription, DNA-dependent0.015938311957429
GO:0045815positive regulation of gene expression, epigenetic0.015938311957429
GO:0006351transcription, DNA-dependent0.015938311957429
GO:0032774RNA biosynthetic process0.015938311957429
GO:0016514SWI/SNF complex0.015938311957429
GO:0065007biological regulation0.015938311957429
GO:0045449regulation of transcription0.015938311957429
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.015938311957429
GO:0006350transcription0.015938311957429
GO:0010468regulation of gene expression0.015938311957429
GO:0031323regulation of cellular metabolic process0.0164057432460003
GO:0019222regulation of metabolic process0.0178265496741685
GO:0016070RNA metabolic process0.0178265496741685
GO:0043283biopolymer metabolic process0.0207611315204404
GO:0004683calmodulin-dependent protein kinase activity0.0216361309010111
GO:0003950NAD+ ADP-ribosyltransferase activity0.0371470414944187
GO:0016585chromatin remodeling complex0.0381627203013111
GO:0010467gene expression0.0381975373612162
GO:0043565sequence-specific DNA binding0.0444808009532835
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0453126974446688
GO:0006338chromatin remodeling0.0469739915798931
GO:0005634nucleus0.0469739915798931
GO:0040029regulation of gene expression, epigenetic0.0469739915798931



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
leukocyte1.52e-53136
hematopoietic stem cell8.01e-50168
angioblastic mesenchymal cell8.01e-50168
nongranular leukocyte1.07e-49115
hematopoietic lineage restricted progenitor cell1.33e-47120
hematopoietic cell3.91e-46177
hematopoietic oligopotent progenitor cell1.24e-44161
hematopoietic multipotent progenitor cell1.24e-44161
lymphocyte7.45e-3453
common lymphoid progenitor7.45e-3453
lymphoid lineage restricted progenitor cell4.14e-3352
nucleate cell9.22e-3255
lymphocyte of B lineage7.45e-2024
pro-B cell7.45e-2024
granulocyte monocyte progenitor cell8.08e-1867
myeloid leukocyte6.11e-1772
myeloid lineage restricted progenitor cell3.17e-1666
mature alpha-beta T cell3.08e-1518
alpha-beta T cell3.08e-1518
immature T cell3.08e-1518
mature T cell3.08e-1518
immature alpha-beta T cell3.08e-1518
myeloid cell5.66e-15108
common myeloid progenitor5.66e-15108
monopoietic cell7.78e-1559
monocyte7.78e-1559
monoblast7.78e-1559
promonocyte7.78e-1559
macrophage dendritic cell progenitor1.03e-1461
B cell1.03e-1314
classical monocyte8.84e-1342
CD14-positive, CD16-negative classical monocyte8.84e-1342
T cell2.61e-1225
pro-T cell2.61e-1225
defensive cell7.67e-1248
phagocyte7.67e-1248
CD8-positive, alpha-beta T cell4.30e-1011
mesenchymal cell4.32e-08354
connective tissue cell1.74e-07361
CD4-positive, alpha-beta T cell7.29e-076
Uber Anatomy
Ontology termp-valuen
hemolymphoid system2.19e-24108
hematopoietic system1.18e-2398
blood island1.18e-2398
immune system1.39e-1893
bone marrow3.13e-1576
bone element7.62e-1482
skeletal element1.79e-1190
skeletal system5.73e-10100
adult organism7.49e-10114
blood3.56e-0715
haemolymphatic fluid3.56e-0715
organism substance3.56e-0715


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)
MA0003.11.05323
MA0004.10.455723
MA0006.10.812175
MA0007.10.437331
MA0009.10.918715
MA0014.10.727045
MA0017.10.337901
MA0019.10.602411
MA0024.10.813542
MA0025.12.39311
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
MA0048.11.60389
MA0050.10.443405
MA0051.12.33582
MA0052.10.842664
MA0055.17.39156
MA0056.10
MA0057.10.305162
MA0058.10.362328
MA0059.10.361075
MA0060.10.190336
MA0061.10.497495
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.10.415214
MA0069.10.903908
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.10.634172
MA0074.10.552456
MA0076.10.377799
MA0077.10.880402
MA0078.10.652193
MA0081.10.361233
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.10.199853
MA0089.10
MA0090.11.01596
MA0091.11.16006
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
MA0113.10.614917
MA0114.10.231781
MA0115.11.1606
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
MA0136.10.564434
MA0139.10.155155
MA0140.10.516266
MA0141.10.359385
MA0142.10.724856
MA0143.10.615094
MA0144.10.218541
MA0145.11.25866
MA0146.11.26525
MA0147.10.681318
MA0148.10.480298
MA0149.10.506665
MA0062.22.15478
MA0035.20.515566
MA0039.20.881644
MA0138.20.653421
MA0002.20.179788
MA0137.20.321796
MA0104.20.55506
MA0047.21.43258
MA0112.20.208783
MA0065.20.0631316
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.0799828
MA0155.10.764865
MA0156.10.323987
MA0157.10.697424
MA0158.10
MA0159.10.243637
MA0160.10.495355
MA0161.10
MA0162.12.16395
MA0163.10.288263
MA0164.10.627336
MA0080.20.818924
MA0018.20.599912
MA0099.20.523145
MA0079.21.97275
MA0102.21.46209
MA0258.10.209744
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
BCLAF1#9774410.82632380506090.0002738756562691510.00292079032626303
NFKB1#479064.116047568145380.0007299856589784310.00581621698489841
POLR2A#543082.147453176558070.002210725788971910.0127202903792869
TAF1#687272.925165500027130.001265325357915740.00849179508131102
YY1#752863.683378062390390.001360631154992740.00895700959321065



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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