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{{Coexpression_clusters
{
|full_id=C1121_Hodgkin_CD4_acute_CD8_thymus_Natural_chronic
 

Latest revision as of 11:38, 17 September 2013


Full id: C1121_Hodgkin_CD4_acute_CD8_thymus_Natural_chronic



Phase1 CAGE Peaks

Hg19::chr10:73975408..73975422,+p5@ANAPC16
Hg19::chr2:240220167..240220189,-p11@HDAC4
Hg19::chr2:240220194..240220214,-p9@HDAC4
Hg19::chr2:240220219..240220235,-p8@HDAC4
Hg19::chr2:98330032..98330054,+p1@ZAP70
Hg19::chr5:133485552..133485556,+p@chr5:133485552..133485556
+
Hg19::chr7:142511881..142511883,+p@chr7:142511881..142511883
+


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:0030098lymphocyte differentiation0.000537903997551219
GO:0002521leukocyte differentiation0.000537903997551219
GO:0046649lymphocyte activation0.000632053985636964
GO:0030097hemopoiesis0.000632053985636964
GO:0048534hemopoietic or lymphoid organ development0.000632053985636964
GO:0045321leukocyte activation0.000632053985636964
GO:0002520immune system development0.000632053985636964
GO:0001775cell activation0.000729830292807322
GO:0045059positive thymic T cell selection0.00182500551798389
GO:0043368positive T cell selection0.00182500551798389
GO:0045582positive regulation of T cell differentiation0.00331809417225125
GO:0045061thymic T cell selection0.0038019269439903
GO:0045621positive regulation of lymphocyte differentiation0.00491311479580289
GO:0045843negative regulation of striated muscle development0.00513229918112986
GO:0045058T cell selection0.00513229918112986
GO:0033077T cell differentiation in the thymus0.00513229918112986
GO:0045580regulation of T cell differentiation0.00536703125000323
GO:0042101T cell receptor complex0.00608245633918467
GO:0016202regulation of striated muscle development0.00624242908466399
GO:0045619regulation of lymphocyte differentiation0.007298517821056
GO:0001772immunological synapse0.00738529621235706
GO:0048513organ development0.00794090620559271
GO:0000118histone deacetylase complex0.00912220711952032
GO:0002376immune system process0.0105808254741684
GO:0030183B cell differentiation0.0105808254741684
GO:0004407histone deacetylase activity0.0119695475357714
GO:0048731system development0.0119695475357714
GO:0033558protein deacetylase activity0.0119695475357714
GO:0004715non-membrane spanning protein tyrosine kinase activity0.0119695475357714
GO:0050870positive regulation of T cell activation0.0119695475357714
GO:0030217T cell differentiation0.0119695475357714
GO:0019213deacetylase activity0.0119695475357714
GO:0048869cellular developmental process0.0129342269232722
GO:0030154cell differentiation0.0129342269232722
GO:0051251positive regulation of lymphocyte activation0.0132868791745255
GO:0050863regulation of T cell activation0.0145852078161808
GO:0048856anatomical structure development0.0145852078161808
GO:0042113B cell activation0.0146353502126821
GO:0051249regulation of lymphocyte activation0.0177390866745995
GO:0007275multicellular organismal development0.0177390866745995
GO:0050865regulation of cell activation0.0177844908429431
GO:0014706striated muscle development0.0188625001807961
GO:0016811hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides0.0188625001807961
GO:0042110T cell activation0.0202952075698475
GO:0043235receptor complex0.0222701656554202
GO:0043234protein complex0.0242595666410333
GO:0000122negative regulation of transcription from RNA polymerase II promoter0.0246116247363006
GO:0032502developmental process0.0313359353861005
GO:0007517muscle development0.0319505627797065
GO:0016810hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds0.033853171416462
GO:0045892negative regulation of transcription, DNA-dependent0.035282625829304
GO:0001501skeletal development0.035282625829304
GO:0005667transcription factor complex0.035282625829304
GO:0016564transcription repressor activity0.035282625829304
GO:0032501multicellular organismal process0.035282625829304
GO:0016568chromatin modification0.035282625829304
GO:0032991macromolecular complex0.035282625829304
GO:0008285negative regulation of cell proliferation0.035282625829304
GO:0051239regulation of multicellular organismal process0.0426678257933063
GO:0006954inflammatory response0.043345702468306
GO:0016481negative regulation of transcription0.043345702468306
GO:0004713protein-tyrosine kinase activity0.0449807666101281
GO:0045934negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0459889232023415



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
T cell5.98e-5425
pro-T cell5.98e-5425
mature alpha-beta T cell2.66e-4318
alpha-beta T cell2.66e-4318
immature T cell2.66e-4318
mature T cell2.66e-4318
immature alpha-beta T cell2.66e-4318
lymphoid lineage restricted progenitor cell1.53e-3152
lymphocyte8.67e-3153
common lymphoid progenitor8.67e-3153
nucleate cell2.29e-2955
CD8-positive, alpha-beta T cell8.63e-2711
leukocyte2.49e-21136
nongranular leukocyte2.79e-21115
hematopoietic lineage restricted progenitor cell5.46e-16120
CD4-positive, alpha-beta T cell7.13e-166
hematopoietic stem cell3.72e-15168
angioblastic mesenchymal cell3.72e-15168
hematopoietic cell9.86e-15177
hematopoietic oligopotent progenitor cell4.04e-12161
hematopoietic multipotent progenitor cell4.04e-12161
single nucleate cell6.28e-093
mononuclear cell6.28e-093
natural killer cell9.74e-093
pro-NK cell9.74e-093
naive T cell3.11e-083
basophil1.02e-073
circulating cell3.60e-076
Uber Anatomy
Ontology termp-valuen
blood3.65e-1815
haemolymphatic fluid3.65e-1815
organism substance3.65e-1815
hemopoietic organ2.54e-127
immune organ2.54e-127
thymus8.96e-114
hemolymphoid system gland8.96e-114
thymic region8.96e-114
pharyngeal gland8.96e-114
thymus primordium8.96e-114
neck2.57e-0810
hemolymphoid system3.86e-08108
hematopoietic system7.37e-0898
blood island7.37e-0898
pharyngeal epithelium3.72e-076


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)
MA0003.10.0137961
MA0004.10.502801
MA0006.10.341337
MA0007.10.483857
MA0009.10.973289
MA0014.10.367415
MA0017.10.380797
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.940207
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.12.23229
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.10.382278
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.10.362619
MA0056.10
MA0057.10.115382
MA0058.11.04727
MA0059.12.75581
MA0060.10.224688
MA0061.10.575931
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.162298
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.10.0022316
MA0074.10.60198
MA0076.11.90063
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.252594
MA0089.10
MA0090.11.95014
MA0091.10.505453
MA0092.10.467172
MA0093.10.9112
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.347695
MA0103.10.332048
MA0105.10.340955
MA0106.10.648997
MA0107.10.274127
MA0108.20.806528
MA0109.10
MA0111.11.14351
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
MA0139.10.186511
MA0140.10.564957
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.11.30855
MA0145.10.276317
MA0146.10.0610556
MA0147.10.281049
MA0148.10.528066
MA0149.10.555119
MA0062.20.563664
MA0035.20.564239
MA0039.20.00276064
MA0138.20.704862
MA0002.20.611548
MA0137.20.36398
MA0104.20.223944
MA0047.20.636643
MA0112.20.0758925
MA0065.20.282161
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.102476
MA0155.10.071478
MA0156.10.959643
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.10.0249953
MA0163.10.0765396
MA0164.10.678332
MA0080.20.344472
MA0018.20.650405
MA0099.20.572
MA0079.29.15802e-07
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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