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{{Coexpression_clusters
{
|full_id=C911_cord_CD8_Natural_mycosis_Basophils_Peripheral_CD4
|

Latest revision as of 11:33, 17 September 2013


Full id: C911_cord_CD8_Natural_mycosis_Basophils_Peripheral_CD4



Phase1 CAGE Peaks

Hg19::chr16:27413488..27413517,+p1@IL21R
Hg19::chr16:27413524..27413547,+p2@IL21R
Hg19::chr16:27413589..27413601,+p5@IL21R
Hg19::chr16:27413815..27413889,+p4@IL21R
Hg19::chr17:45810594..45810608,+p1@TBX21
Hg19::chr17:45810816..45810838,+p2@TBX21
Hg19::chr3:193311668..193311697,-p@chr3:193311668..193311697
-
Hg19::chr6:106968697..106968723,-p@chr6:106968697..106968723
-
Hg19::chr6:90790583..90790604,-p@chr6:90790583..90790604
-


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:0046649lymphocyte activation0.00107147062286589
GO:0045321leukocyte activation0.00107147062286589
GO:0001775cell activation0.00107147062286589
GO:0019977interleukin-21 binding0.00107147062286589
GO:0001532interleukin-21 receptor activity0.00107147062286589
GO:0048304positive regulation of isotype switching to IgG isotypes0.00267855827937379
GO:0048302regulation of isotype switching to IgG isotypes0.00267855827937379
GO:0048291isotype switching to IgG isotypes0.00267855827937379
GO:0045830positive regulation of isotype switching0.00357130590335091
GO:0045191regulation of isotype switching0.00420872932521112
GO:0002208somatic diversification of immunoglobulins during immune response0.00420872932521112
GO:0002381immunoglobulin production during immune response0.00420872932521112
GO:0002204somatic recombination of immunoglobulin genes during immune response0.00420872932521112
GO:0045190isotype switching0.00420872932521112
GO:0016447somatic recombination of immunoglobulin gene segments0.00438219215402637
GO:0016445somatic diversification of immunoglobulins0.00438219215402637
GO:0002562somatic diversification of immune receptors via germline recombination within a single locus0.00438219215402637
GO:0016444somatic cell DNA recombination0.00438219215402637
GO:0002200somatic diversification of immune receptors0.00438219215402637
GO:0030101natural killer cell activation0.00438219215402637
GO:0050871positive regulation of B cell activation0.00438219215402637
GO:0002377immunoglobulin production0.00438219215402637
GO:0050864regulation of B cell activation0.00582115290182016
GO:0002440production of molecular mediator of immune response0.00602471583669748
GO:0002376immune system process0.00605459280668687
GO:0004907interleukin receptor activity0.00700236669613786
GO:0019965interleukin binding0.00793226354335589
GO:0051251positive regulation of lymphocyte activation0.00927910822702546
GO:0016064immunoglobulin mediated immune response0.00927910822702546
GO:0019724B cell mediated immunity0.00927910822702546
GO:0042113B cell activation0.0105325787794911
GO:0004896hematopoietin/interferon-class (D200-domain) cytokine receptor activity0.0112655238259798
GO:0002449lymphocyte mediated immunity0.0112655238259798
GO:0002460adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains0.0112655238259798
GO:0002250adaptive immune response0.0112655238259798
GO:0051249regulation of lymphocyte activation0.0112655238259798
GO:0002443leukocyte mediated immunity0.0112655238259798
GO:0050865regulation of cell activation0.0112655238259798
GO:0050776regulation of immune response0.0130476750734828
GO:0019955cytokine binding0.0130476750734828
GO:0002682regulation of immune system process0.0130476750734828
GO:0002252immune effector process0.0140086525896998
GO:0002520immune system development0.022614900670125
GO:0006310DNA recombination0.0239171348972863
GO:0051239regulation of multicellular organismal process0.0328435206715787



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
leukocyte5.87e-75136
nongranular leukocyte2.39e-64115
hematopoietic stem cell1.07e-59168
angioblastic mesenchymal cell1.07e-59168
hematopoietic cell2.32e-59177
hematopoietic lineage restricted progenitor cell5.67e-59120
hematopoietic oligopotent progenitor cell4.97e-54161
hematopoietic multipotent progenitor cell4.97e-54161
lymphocyte1.33e-4053
common lymphoid progenitor1.33e-4053
lymphoid lineage restricted progenitor cell5.86e-4052
nucleate cell2.27e-3855
myeloid leukocyte6.87e-2572
macrophage dendritic cell progenitor3.16e-2261
T cell3.54e-2225
pro-T cell3.54e-2225
classical monocyte2.81e-2142
CD14-positive, CD16-negative classical monocyte2.81e-2142
monopoietic cell7.72e-2159
monocyte7.72e-2159
monoblast7.72e-2159
promonocyte7.72e-2159
granulocyte monocyte progenitor cell8.99e-2167
defensive cell1.24e-2048
phagocyte1.24e-2048
mature alpha-beta T cell2.15e-1918
alpha-beta T cell2.15e-1918
immature T cell2.15e-1918
mature T cell2.15e-1918
immature alpha-beta T cell2.15e-1918
myeloid lineage restricted progenitor cell6.51e-1966
myeloid cell5.22e-18108
common myeloid progenitor5.22e-18108
lymphocyte of B lineage1.38e-1524
pro-B cell1.38e-1524
CD8-positive, alpha-beta T cell2.61e-1211
mesenchymal cell3.22e-11354
connective tissue cell2.27e-10361
B cell1.25e-0814
CD4-positive, alpha-beta T cell4.26e-086
circulating cell4.26e-086
motile cell4.33e-08386
dendritic cell1.68e-0710
Uber Anatomy
Ontology termp-valuen
hematopoietic system6.73e-3598
blood island6.73e-3598
hemolymphoid system1.03e-31108
immune system2.60e-2093
bone marrow3.83e-1876
bone element3.54e-1782
blood2.61e-1515
haemolymphatic fluid2.61e-1515
organism substance2.61e-1515
skeletal element3.30e-1490
skeletal system7.38e-12100
connective tissue3.06e-09371
lateral plate mesoderm2.20e-08203
adult organism5.02e-07114
hemopoietic organ5.24e-077
immune organ5.24e-077
Disease
Ontology termp-valuen
lymphoma6.03e-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)
MA0003.10.169975
MA0004.10.415381
MA0006.10.733408
MA0007.10.397529
MA0009.10.870971
MA0014.12.31793
MA0017.10.815464
MA0019.10.558663
MA0024.10.766783
MA0025.11.00397
MA0027.12.48103
MA0028.10.767002
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
MA0048.13.21312
MA0050.10.403421
MA0051.10.510444
MA0052.10.795605
MA0055.10.22215
MA0056.10
MA0057.10.0725989
MA0058.10.325084
MA0059.10.323879
MA0060.10.162248
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
MA0073.11.74484
MA0074.10.509711
MA0076.10.339975
MA0077.10.832987
MA0078.10.607575
MA0081.10.865814
MA0083.10.878452
MA0084.11.37471
MA0087.10.838229
MA0088.10.650888
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
MA0105.10.229733
MA0106.10.554855
MA0107.10.205358
MA0108.20.707575
MA0109.10
MA0111.10.366362
MA0113.10.57094
MA0114.10.582067
MA0115.11.11137
MA0116.10.208403
MA0117.10.908433
MA0119.10.83188
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
MA0141.10.861836
MA0142.10.679161
MA0143.10.571113
MA0144.10.1885
MA0145.10.177438
MA0146.10.175555
MA0147.10.211483
MA0148.10.439278
MA0149.10.464973
MA0062.20.135498
MA0035.20.473658
MA0039.21.17223
MA0138.20.608783
MA0002.20.905786
MA0137.20.28622
MA0104.20.486672
MA0047.21.34084
MA0112.20.0433683
MA0065.20.0483532
MA0150.11.64445
MA0151.10
MA0152.10.480711
MA0153.10.969315
MA0154.10.488402
MA0155.10.156896
MA0156.10.288314
MA0157.10.652111
MA0158.10
MA0159.10.60858
MA0160.11.15068
MA0161.10
MA0162.10.502732
MA0163.10.604232
MA0164.11.42569
MA0080.20.268439
MA0018.20.556211
MA0099.20.481058
MA0079.20.289676
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
EBF1#187943.958429709586220.012557390254080.0454176922269658
MEF2A#420548.330324848730690.0008211501430300610.00625483916475214
NFKB1#479063.658708949462560.001850649648602720.010935219159854
PAX5#507964.446377020785220.0006322700088175870.00519132448513364
POU2F2#545277.082540933799745.66141070992737e-060.000170542853514308
TCF12#693855.908036056770230.0006689435531052020.00546494021767477



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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