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{{Coexpression_clusters
{
|full_id=C900_CD4_thymus_Hodgkin_CD8_CD34_chronic_CD133
 

Latest revision as of 11:33, 17 September 2013


Full id: C900_CD4_thymus_Hodgkin_CD8_CD34_chronic_CD133



Phase1 CAGE Peaks

Hg19::chr13:30951074..30951122,-p1@LINC00426
Hg19::chr13:30951124..30951135,-p4@LINC00426
Hg19::chr13:30951150..30951161,-p5@LINC00426
Hg19::chr14:22309226..22309237,+p4@uc001wbx.2
p4@uc010tmg.1
Hg19::chr14:81425875..81425889,-p5@CEP128
Hg19::chr2:38830160..38830206,-p3@HNRPLL
Hg19::chr3:133209983..133210005,-p2@AK128281
Hg19::chr4:109087819..109087826,-p45@LEF1
Hg19::chr6:25042231..25042263,-p7@FAM65B


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 development0.00788803686016357
GO:0021766hippocampus development0.00788803686016357
GO:0048341paraxial mesoderm formation0.00788803686016357
GO:0048340paraxial mesoderm morphogenesis0.00788803686016357
GO:0048339paraxial mesoderm development0.00788803686016357
GO:0021543pallium development0.00788803686016357
GO:0021761limbic system development0.00788803686016357
GO:0045843negative regulation of striated muscle development0.00788803686016357
GO:0008301DNA bending activity0.00832491294628465
GO:0021537telencephalon development0.00832491294628465
GO:0016202regulation of striated muscle development0.00832491294628465
GO:0030879mammary gland development0.00832491294628465
GO:0001890placenta development0.00832491294628465
GO:0001707mesoderm formation0.00832491294628465
GO:0048332mesoderm morphogenesis0.00832491294628465
GO:0001704formation of primary germ layer0.00832491294628465
GO:0001756somitogenesis0.00832491294628465
GO:0042475odontogenesis of dentine-containing teeth0.00832491294628465
GO:0042476odontogenesis0.00925727956560874
GO:0007369gastrulation0.00925727956560874
GO:0003705RNA polymerase II transcription factor activity, enhancer binding0.00925727956560874
GO:0035282segmentation0.00925727956560874
GO:0030111regulation of Wnt receptor signaling pathway0.00925727956560874
GO:0030326embryonic limb morphogenesis0.0100597509018366
GO:0035113embryonic appendage morphogenesis0.0100597509018366
GO:0060173limb development0.0100597509018366
GO:0035107appendage morphogenesis0.0100597509018366
GO:0035108limb morphogenesis0.0100597509018366
GO:0048736appendage development0.0100597509018366
GO:0007498mesoderm development0.0113327103941029
GO:0030900forebrain development0.0113327103941029
GO:0048732gland development0.0113327103941029
GO:0009952anterior/posterior pattern formation0.013137632697009
GO:0048729tissue morphogenesis0.0166883415293181
GO:0003002regionalization0.0191898420490159
GO:0014706striated muscle development0.0191898420490159
GO:0048598embryonic morphogenesis0.0191898420490159
GO:0009792embryonic development ending in birth or egg hatching0.0191898420490159
GO:0043009chordate embryonic development0.0191898420490159
GO:0003682chromatin binding0.023232030545665
GO:0007389pattern specification process0.0238101401826761
GO:0000122negative regulation of transcription from RNA polymerase II promoter0.0238101401826761
GO:0007420brain development0.0248709738339615
GO:0045944positive regulation of transcription from RNA polymerase II promoter0.0248709738339615
GO:0016055Wnt receptor signaling pathway0.0253657508702202
GO:0048646anatomical structure formation0.0261802979410705
GO:0007517muscle development0.0287971716144891
GO:0045892negative regulation of transcription, DNA-dependent0.0332640668261998
GO:0005667transcription factor complex0.0337053528466996
GO:0032991macromolecular complex0.0343816716168921
GO:0045893positive regulation of transcription, DNA-dependent0.0343816716168921
GO:0007417central nervous system development0.0348583904248288
GO:0009790embryonic development0.0348583904248288
GO:0016070RNA metabolic process0.0371124061293968
GO:0006397mRNA processing0.0384558457409892
GO:0003702RNA polymerase II transcription factor activity0.0384558457409892
GO:0045941positive regulation of transcription0.0384558457409892
GO:0045935positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0387433320914088
GO:0016481negative regulation of transcription0.0387433320914088
GO:0009888tissue development0.0397803929901879
GO:0016563transcription activator activity0.0397803929901879
GO:0045934negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0403994266050121
GO:0016071mRNA metabolic process0.0426102447334929
GO:0009887organ morphogenesis0.0440615929370697
GO:0031325positive regulation of cellular metabolic process0.0440615929370697
GO:0031324negative regulation of cellular metabolic process0.0452854709956637
GO:0009893positive regulation of metabolic process0.0457736471972898
GO:0006357regulation of transcription from RNA polymerase II promoter0.048768482251992
GO:0009892negative regulation of metabolic process0.0493319114072623
GO:0010467gene expression0.0493319114072623
GO:0044451nucleoplasm part0.049888598166981



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>disease_data<br>

Cell Type
Ontology termp-valuen
lymphocyte9.77e-4953
common lymphoid progenitor9.77e-4953
lymphoid lineage restricted progenitor cell6.63e-4752
T cell9.12e-4725
pro-T cell9.12e-4725
nucleate cell1.42e-4655
mature alpha-beta T cell4.56e-4118
alpha-beta T cell4.56e-4118
immature T cell4.56e-4118
mature T cell4.56e-4118
immature alpha-beta T cell4.56e-4118
nongranular leukocyte5.84e-26115
CD8-positive, alpha-beta T cell1.06e-2511
leukocyte7.56e-23136
hematopoietic lineage restricted progenitor cell4.37e-19120
hematopoietic stem cell2.95e-16168
angioblastic mesenchymal cell2.95e-16168
CD4-positive, alpha-beta T cell4.08e-156
hematopoietic cell7.59e-15177
hematopoietic oligopotent progenitor cell1.93e-13161
hematopoietic multipotent progenitor cell1.93e-13161
naive T cell8.62e-093
natural killer cell1.12e-073
pro-NK cell1.12e-073
single nucleate cell1.95e-073
mononuclear cell1.95e-073
Uber Anatomy
Ontology termp-valuen
blood5.13e-1415
haemolymphatic fluid5.13e-1415
organism substance5.13e-1415
hemopoietic organ2.51e-127
immune organ2.51e-127
thymus6.56e-114
hemolymphoid system gland6.56e-114
thymic region6.56e-114
pharyngeal gland6.56e-114
thymus primordium6.56e-114
pharyngeal epithelium3.12e-076
Disease
Ontology termp-valuen
lymphoma1.39e-0710


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)
MA0003.10.0913842
MA0004.10.415381
MA0006.10.265592
MA0007.10.397529
MA0009.10.870971
MA0014.10.0324647
MA0017.10.301634
MA0019.11.37405
MA0024.10.766783
MA0025.11.00397
MA0027.12.48103
MA0028.11.40203
MA0029.10.785955
MA0030.10.774581
MA0031.10.710608
MA0038.10.514558
MA0040.10.791764
MA0041.10.433167
MA0042.10.402577
MA0043.10.871285
MA0046.10.860127
MA0048.11.41801
MA0050.10.403421
MA0051.10.510444
MA0052.10.795605
MA0055.11.02363
MA0056.10
MA0057.10.0725989
MA0058.10.325084
MA0059.10.323879
MA0060.10.488252
MA0061.10.139804
MA0063.10
MA0066.10.514973
MA0067.11.18766
MA0068.10.109867
MA0069.10.856287
MA0070.10.845142
MA0071.10.47692
MA0072.10.840664
MA0073.10.602377
MA0074.10.509711
MA0076.10.901394
MA0077.10.832987
MA0078.10.607575
MA0081.10.324031
MA0083.10.878452
MA0084.11.37471
MA0087.10.838229
MA0088.10.0408613
MA0089.10
MA0090.10.353576
MA0091.10.417885
MA0092.10.381858
MA0093.10.26836
MA0095.10
MA0098.10
MA0100.10.528088
MA0101.10.271368
MA0103.10.714036
MA0105.10.0643619
MA0106.10.554855
MA0107.10.205358
MA0108.20.707575
MA0109.10
MA0111.10.366362
MA0113.10.57094
MA0114.11.10197
MA0115.11.11137
MA0116.10.599942
MA0117.10.908433
MA0119.10.308914
MA0122.10.934245
MA0124.11.06995
MA0125.10.986127
MA0130.10
MA0131.10.625452
MA0132.10
MA0133.10
MA0135.10.90122
MA0136.10.521435
MA0139.10.406919
MA0140.10.474342
MA0141.10.322254
MA0142.10.679161
MA0143.10.571113
MA0144.10.1885
MA0145.11.08897
MA0146.10.175555
MA0147.10.211483
MA0148.10.439278
MA0149.10.464973
MA0062.20.833414
MA0035.20.473658
MA0039.20.0189957
MA0138.21.4796
MA0002.20.46405
MA0137.20.28622
MA0104.20.161609
MA0047.20.542971
MA0112.20.0433683
MA0065.20.0483532
MA0150.11.64445
MA0151.10
MA0152.10.480711
MA0153.10.969315
MA0154.10.225151
MA0155.10.359913
MA0156.10.288314
MA0157.10.652111
MA0158.10
MA0159.10.60858
MA0160.10.453945
MA0161.10
MA0162.10.502732
MA0163.10.034916
MA0164.10.583138
MA0080.20.268439
MA0018.20.556211
MA0099.20.481058
MA0079.20.00267252
MA0102.21.41188
MA0258.10.180288
MA0259.10.218904
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
ELF1#199762.838731972538360.007207863124148630.0298568998858906
NFKB1#479053.048924124552130.01316873026498510.0466023658222005
PAX5#507953.705314183987680.005616557077719420.0253923035643452
PBX3#509037.304837562248040.006482999615409630.0281470794776041
POU2F2#545266.070749371828350.0001095272295875280.00152376639548313



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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