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{{Coexpression_clusters
{
|full_id=C1361_CD4_cord_mycosis_hairy_CD8_Whole_thymus
 

Latest revision as of 11:43, 17 September 2013


Full id: C1361_CD4_cord_mycosis_hairy_CD8_Whole_thymus



Phase1 CAGE Peaks

Hg19::chr12:48277143..48277154,-p10@VDR
Hg19::chr3:32993065..32993074,+p3@CCR4
Hg19::chr3:32993109..32993124,+p2@CCR4
Hg19::chr3:32993128..32993144,+p1@CCR4
Hg19::chr6:106547062..106547071,+p25@PRDM1
Hg19::chr6:106547079..106547114,+p9@PRDM1


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:0006874cellular calcium ion homeostasis0.00136204756176744
GO:0055074calcium ion homeostasis0.00136204756176744
GO:0006875cellular metal ion homeostasis0.00136204756176744
GO:0055065metal ion homeostasis0.00136204756176744
GO:0030005cellular di-, tri-valent inorganic cation homeostasis0.00148645142072713
GO:0055066di-, tri-valent inorganic cation homeostasis0.00148645142072713
GO:0002507tolerance induction0.00148645142072713
GO:0008434vitamin D3 receptor activity0.00148645142072713
GO:0030003cellular cation homeostasis0.00148645142072713
GO:0055080cation homeostasis0.00148645142072713
GO:0055082cellular chemical homeostasis0.00168846236759857
GO:0006873cellular ion homeostasis0.00168846236759857
GO:0050801ion homeostasis0.00197790247834568
GO:0016481negative regulation of transcription0.00218128597867069
GO:0048878chemical homeostasis0.00219248957442734
GO:0045934negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.00229301767600982
GO:0019725cellular homeostasis0.0029054511865854
GO:0031324negative regulation of cellular metabolic process0.0029054511865854
GO:0009892negative regulation of metabolic process0.00360186242986817
GO:0042592homeostatic process0.00414451130338411
GO:0004945angiotensin type II receptor activity0.00505645008471668
GO:0001595angiotensin receptor activity0.00505645008471668
GO:0050892intestinal absorption0.005373846714639
GO:0022600digestive system process0.00978228687467743
GO:0019957C-C chemokine binding0.0114043882617499
GO:0016493C-C chemokine receptor activity0.0114043882617499
GO:0065008regulation of biological quality0.0120006251142817
GO:0004950chemokine receptor activity0.0146652234547873
GO:0001764neuron migration0.0146652234547873
GO:0001637G-protein chemoattractant receptor activity0.0146652234547873
GO:0048523negative regulation of cellular process0.0146652234547873
GO:0019956chemokine binding0.0146652234547873
GO:0048519negative regulation of biological process0.0150382652472423
GO:0003700transcription factor activity0.0233294294183521
GO:0051480cytosolic calcium ion homeostasis0.0239906100823015
GO:0007204elevation of cytosolic calcium ion concentration0.0239906100823015
GO:0048731system development0.0245253645526278
GO:0065007biological regulation0.0286460422766611
GO:0007586digestion0.0300320435974881
GO:0019955cytokine binding0.0305105407580529
GO:0048856anatomical structure development0.0342634993280422
GO:0003707steroid hormone receptor activity0.034322657953198
GO:0000122negative regulation of transcription from RNA polymerase II promoter0.0363790715162824
GO:0042330taxis0.0382503179965157
GO:0006935chemotaxis0.0382503179965157
GO:0001653peptide receptor activity0.0382503179965157
GO:0008528peptide receptor activity, G-protein coupled0.0382503179965157
GO:0007275multicellular organismal development0.0382503179965157
GO:0004879ligand-dependent nuclear receptor activity0.0384307489624711
GO:0007626locomotory behavior0.0441245460901082
GO:0006816calcium ion transport0.0441245460901082
GO:0045892negative regulation of transcription, DNA-dependent0.0475574799163466
GO:0042277peptide binding0.0475574799163466
GO:0001501skeletal development0.0475574799163466



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>

Uber Anatomy
Ontology termp-valuen
blood8.75e-2115
haemolymphatic fluid8.75e-2115
organism substance8.75e-2115
hemolymphoid system9.16e-12108
hematopoietic system3.28e-1198
blood island3.28e-1198
adult organism1.64e-07114


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)
MA0003.10.00461978
MA0004.10.558729
MA0006.11.01439
MA0007.10.539222
MA0009.11.03681
MA0014.10.0254709
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.11.41501
MA0042.11.3446
MA0043.11.03713
MA0046.11.02569
MA0048.10.152639
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.0586456
MA0056.10
MA0057.10.147053
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.11.24837
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.0214749
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.0971959
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.11.02896
MA0103.10.381434
MA0105.10.419295
MA0106.10.70837
MA0107.10.857383
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.845337
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.10.226048
MA0140.12.5604
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.347815
MA0146.10.0213085
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.658749
MA0035.20.621793
MA0039.20.00570825
MA0138.20.765223
MA0002.20.255126
MA0137.20.414885
MA0104.20.26661
MA0047.20.695777
MA0112.20.101413
MA0065.20.109623
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.132326
MA0155.10.0961854
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.10.0383129
MA0163.10.0270301
MA0164.10.738243
MA0080.21.02158
MA0018.20.709805
MA0099.20.629739
MA0079.27.22997e-05
MA0102.21.58513
MA0258.10.289793
MA0259.10.336472
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
BATF#10538312.17890089615180.00125981487125340.00846188213639677
GATA1#262336.780154071900220.006765763983348560.0287485098928736
GATA2#262436.3724658667770.008058821308742550.0318857114208124
MEF2A#4205412.4954872730960.0001113336277199790.001545808660655
STAT2#6773332.63188559322036.94270331437341e-050.00110112223454798
TAL1#6886314.93430833872010.0006952184405921510.005598143308944



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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