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Coexpression cluster:C1137: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:38, 17 September 2013


Full id: C1137_CD4_CD8_thymus_Natural_blood_Whole_Peripheral



Phase1 CAGE Peaks

Hg19::chr11:14671615..14671618,+p@chr11:14671615..14671618
+
Hg19::chr14:105944163..105944184,+p@chr14:105944163..105944184
+
Hg19::chr14:22265481..22265487,+p5@TRAV8-1
Hg19::chr4:109088233..109088240,-p62@LEF1
Hg19::chr5:133449741..133449744,-p@chr5:133449741..133449744
-
Hg19::chr7:142021271..142021284,+p1@AF020656
p1@AF325867
p1@AF395795
p1@AY611551
p1@AY751843
p1@AY751887
p1@AY751915
p1@EF592002
p1@GQ502881
p1@GQ502883
p1@HM236508
p1@HM236510
p1@HM236512
p1@HM236514
p1@HM236515
p1@HM236544
p1@HM236615
p1@HM236635
p1@HM236642
p1@HM236659
p1@HM236662
p1@HM236673
p1@HM236674
p1@HM236676
p1@HM236718
p1@HM236776
p1@HM236777
p1@HM236807
p1@HM467843
p1@HM467856
p1@HM467875
p1@HM467876
p1@HM467877
p1@HM467878
p1@JF731146
p1@JF731148
p1@JF731150
Hg19::chrX:11776810..11776821,+p17@MSL3


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:0021542dentate gyrus development0.00376780878370423
GO:0021766hippocampus development0.00376780878370423
GO:0048341paraxial mesoderm formation0.00376780878370423
GO:0048340paraxial mesoderm morphogenesis0.00376780878370423
GO:0048339paraxial mesoderm development0.00376780878370423
GO:0021543pallium development0.00376780878370423
GO:0021761limbic system development0.00376780878370423
GO:0045843negative regulation of striated muscle development0.00376780878370423
GO:0008301DNA bending activity0.00397713149391001
GO:0021537telencephalon development0.00397713149391001
GO:0016202regulation of striated muscle development0.00397713149391001
GO:0030879mammary gland development0.00397713149391001
GO:0001890placenta development0.00397713149391001
GO:0001707mesoderm formation0.00397713149391001
GO:0048332mesoderm morphogenesis0.00397713149391001
GO:0001704formation of primary germ layer0.00397713149391001
GO:0001756somitogenesis0.00397713149391001
GO:0042475odontogenesis of dentine-containing teeth0.00397713149391001
GO:0042476odontogenesis0.00442307987652235
GO:0007369gastrulation0.00442307987652235
GO:0035282segmentation0.00442307987652235
GO:0003705RNA polymerase II transcription factor activity, enhancer binding0.00442307987652235
GO:0030111regulation of Wnt receptor signaling pathway0.00442307987652235
GO:0030326embryonic limb morphogenesis0.00480720431024332
GO:0035113embryonic appendage morphogenesis0.00480720431024332
GO:0060173limb development0.00480720431024332
GO:0035107appendage morphogenesis0.00480720431024332
GO:0035108limb morphogenesis0.00480720431024332
GO:0048736appendage development0.00480720431024332
GO:0007498mesoderm development0.00541622512657482
GO:0030900forebrain development0.00541622512657482
GO:0048732gland development0.00541622512657482
GO:0009952anterior/posterior pattern formation0.00627968130617371
GO:0048729tissue morphogenesis0.00797888918902071
GO:0003002regionalization0.00917799575517696
GO:0014706striated muscle development0.00917799575517696
GO:0048598embryonic morphogenesis0.00917799575517696
GO:0009792embryonic development ending in birth or egg hatching0.00917799575517696
GO:0043009chordate embryonic development0.00917799575517696
GO:0003682chromatin binding0.0111150359119275
GO:0007389pattern specification process0.011393136084058
GO:0000122negative regulation of transcription from RNA polymerase II promoter0.011393136084058
GO:0007420brain development0.0119028504757929
GO:0045944positive regulation of transcription from RNA polymerase II promoter0.0119028504757929
GO:0016055Wnt receptor signaling pathway0.0121407171919358
GO:0048646anatomical structure formation0.0125320596501467
GO:0007517muscle development0.0137885768254708
GO:0045892negative regulation of transcription, DNA-dependent0.0159346913144158
GO:0005667transcription factor complex0.016147751930161
GO:0045893positive regulation of transcription, DNA-dependent0.0168044271753208
GO:0007417central nervous system development0.0170275973878941
GO:0009790embryonic development0.0170275973878941
GO:0003702RNA polymerase II transcription factor activity0.0194670120491385
GO:0045941positive regulation of transcription0.0194670120491385
GO:0045935positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0195791492153202
GO:0016481negative regulation of transcription0.0195791492153202
GO:0009888tissue development0.0200733261062863
GO:0016563transcription activator activity0.0200733261062863
GO:0045934negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.020371711898333
GO:0009887organ morphogenesis0.0225450853451154
GO:0031325positive regulation of cellular metabolic process0.0225450853451154
GO:0031324negative regulation of cellular metabolic process0.0231537926869566
GO:0009893positive regulation of metabolic process0.0233843370544183
GO:0006357regulation of transcription from RNA polymerase II promoter0.0249028611797951
GO:0009892negative regulation of metabolic process0.0252733019953083
GO:0044451nucleoplasm part0.0258037813671865
GO:0005654nucleoplasm0.0291864590857088
GO:0006366transcription from RNA polymerase II promoter0.0354617297289809
GO:0031981nuclear lumen0.0376780878370422
GO:0007399nervous system development0.0385393012733175
GO:0009966regulation of signal transduction0.0424541834783575
GO:0043565sequence-specific DNA binding0.0456323508248623
GO:0048522positive regulation of cellular process0.0487805643863574
GO:0031974membrane-enclosed lumen0.0487805643863574
GO:0043233organelle lumen0.0487805643863574



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
mature alpha-beta T cell3.14e-4618
alpha-beta T cell3.14e-4618
immature T cell3.14e-4618
mature T cell3.14e-4618
immature alpha-beta T cell3.14e-4618
T cell4.82e-3725
pro-T cell4.82e-3725
CD4-positive, alpha-beta T cell4.46e-276
CD8-positive, alpha-beta T cell5.27e-2511
lymphoid lineage restricted progenitor cell8.81e-2452
lymphocyte2.99e-2353
common lymphoid progenitor2.99e-2353
nucleate cell3.00e-2255
natural killer cell2.20e-143
pro-NK cell2.20e-143
naive T cell3.60e-143
single nucleate cell2.00e-133
mononuclear cell2.00e-133
nongranular leukocyte2.47e-13115
leukocyte5.98e-13136
regulatory T cell6.88e-102
CD4-positive, CD25-positive, alpha-beta regulatory T cell6.88e-102
naive regulatory T cell6.88e-102
hematopoietic stem cell1.82e-09168
angioblastic mesenchymal cell1.82e-09168
hematopoietic lineage restricted progenitor cell6.40e-09120
hematopoietic cell1.02e-08177
hematopoietic oligopotent progenitor cell3.05e-07161
hematopoietic multipotent progenitor cell3.05e-07161
circulating cell6.10e-076
Uber Anatomy
Ontology termp-valuen
thymus5.61e-114
hemolymphoid system gland5.61e-114
thymic region5.61e-114
pharyngeal gland5.61e-114
thymus primordium5.61e-114
pharyngeal epithelium1.88e-076
chordate pharynx2.69e-0710
pharyngeal region of foregut2.69e-0710
blood5.79e-0715
haemolymphatic fluid5.79e-0715
organism substance5.79e-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)
MA0003.10.110456
MA0004.10.502801
MA0006.10.341337
MA0007.11.21493
MA0009.10.973289
MA0014.10.187674
MA0017.10.380797
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.35747
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.10.120314
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.10.158296
MA0056.10
MA0057.10.115382
MA0058.10.406232
MA0059.10.404929
MA0060.10.224688
MA0061.10.575931
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.946606
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.14.49289
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.538456
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.10.467172
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.347695
MA0103.11.58817
MA0105.10.104569
MA0106.10.648997
MA0107.10.274127
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.10.665691
MA0114.10.269076
MA0115.11.21667
MA0116.10.277571
MA0117.11.01134
MA0119.10.388712
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.10.547495
MA0140.10.564957
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.10.254954
MA0145.10.0807715
MA0146.10.162729
MA0147.10.281049
MA0148.10.528066
MA0149.10.555119
MA0062.20.193221
MA0035.20.564239
MA0039.20.128723
MA0138.20.704862
MA0002.20.611548
MA0137.20.36398
MA0104.20.223944
MA0047.20.636643
MA0112.20.556641
MA0065.20.0828768
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.102476
MA0155.10.250175
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.11.55314
MA0163.10.0167306
MA0164.10.678332
MA0080.20.911393
MA0018.20.650405
MA0099.20.572
MA0079.20.478894
MA0102.21.51913
MA0258.10.245543
MA0259.10.289405
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

No analysis results for this cluster

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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