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{{Coexpression_clusters
{
|full_id=C1218_hairy_plasma_lymphoma_xeroderma_hereditary_mycosis_splenic
|

Latest revision as of 11:40, 17 September 2013


Full id: C1218_hairy_plasma_lymphoma_xeroderma_hereditary_mycosis_splenic



Phase1 CAGE Peaks

Hg19::chr16:29656517..29656522,-p@chr16:29656517..29656522
-
Hg19::chr1:32716592..32716596,+p5@LCK
Hg19::chr20:52675557..52675561,-p4@BCAS1
Hg19::chr4:36334205..36334210,-p@chr4:36334205..36334210
-
Hg19::chr6:109196481..109196488,+p@chr6:109196481..109196488
+
Hg19::chr6:160351875..160351879,-p@chr6:160351875..160351879
-
Hg19::chr8:101512336..101512341,-p@chr8:101512336..101512341
-


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:0042610CD8 receptor binding0.00549074903622083
GO:0050862positive regulation of T cell receptor signaling pathway0.00549074903622083
GO:0042609CD4 receptor binding0.00549074903622083
GO:0051117ATPase binding0.00549074903622083
GO:0006882cellular zinc ion homeostasis0.00549074903622083
GO:0055069zinc ion homeostasis0.00549074903622083
GO:0043548phosphoinositide 3-kinase binding0.00549074903622083
GO:0001948glycoprotein binding0.00549074903622083
GO:0050857positive regulation of antigen receptor-mediated signaling pathway0.00549074903622083
GO:0000242pericentriolar material0.00549074903622083
GO:0050856regulation of T cell receptor signaling pathway0.00549074903622083
GO:0051283negative regulation of sequestering of calcium ion0.00575204393640925
GO:0051282regulation of sequestering of calcium ion0.00575204393640925
GO:0051209release of sequestered calcium ion into cytosol0.00575204393640925
GO:0051208sequestering of calcium ion0.00629111284022556
GO:0050854regulation of antigen receptor-mediated signaling pathway0.00629111284022556
GO:0051238sequestering of metal ion0.00769702166833902
GO:0050852T cell receptor signaling pathway0.0095055909313886
GO:0042169SH2 domain binding0.00953487963183759
GO:0044450microtubule organizing center part0.0115734324519592
GO:0050851antigen receptor-mediated signaling pathway0.0129384792222954
GO:0002429immune response-activating cell surface receptor signaling pathway0.0132823318112429
GO:0002768immune response-regulating cell surface receptor signaling pathway0.0132823318112429
GO:0002757immune response-activating signal transduction0.0132823318112429
GO:0002764immune response-regulating signal transduction0.0132823318112429
GO:0004715non-membrane spanning protein tyrosine kinase activity0.0142244370855518
GO:0050870positive regulation of T cell activation0.0142244370855518
GO:0030217T cell differentiation0.0142244370855518
GO:0051235maintenance of localization0.0142244370855518
GO:0006919caspase activation0.0149284042553036
GO:0045121lipid raft0.0149284042553036
GO:0043280positive regulation of caspase activity0.0155468175678466
GO:0051251positive regulation of lymphocyte activation0.0155468175678466
GO:0050863regulation of T cell activation0.0172038426275883
GO:0043281regulation of caspase activity0.0172038426275883
GO:0042493response to drug0.0172038426275883
GO:0030098lymphocyte differentiation0.0172038426275883
GO:0004722protein serine/threonine phosphatase activity0.0172038426275883
GO:0051480cytosolic calcium ion homeostasis0.0173694565847348
GO:0007204elevation of cytosolic calcium ion concentration0.0173694565847348
GO:0002253activation of immune response0.0173694565847348
GO:0008022protein C-terminus binding0.0173694565847348
GO:0051345positive regulation of hydrolase activity0.0173694565847348
GO:0051249regulation of lymphocyte activation0.0173694565847348
GO:0050865regulation of cell activation0.0178762817634228
GO:0019901protein kinase binding0.0180143473637898
GO:0050778positive regulation of immune response0.0180143473637898
GO:0002684positive regulation of immune system process0.0180143473637898
GO:0008632apoptotic program0.0180970681862679
GO:0002521leukocyte differentiation0.0180970681862679
GO:0050776regulation of immune response0.0186156389784673
GO:0042110T cell activation0.0186156389784673
GO:0019900kinase binding0.0186156389784673
GO:0002682regulation of immune system process0.0186156389784673
GO:0051240positive regulation of multicellular organismal process0.0191896170851969
GO:0006874cellular calcium ion homeostasis0.0204527827727977
GO:0055074calcium ion homeostasis0.0204527827727977
GO:0006875cellular metal ion homeostasis0.0209496874891393
GO:0055065metal ion homeostasis0.0209496874891393
GO:0019904protein domain specific binding0.0212493622807121
GO:0005813centrosome0.0212493622807121
GO:0005815microtubule organizing center0.0238175112989571
GO:0046649lymphocyte activation0.0247121557886227
GO:0030097hemopoiesis0.025265444591113
GO:0048534hemopoietic or lymphoid organ development0.0266282153137071
GO:0045321leukocyte activation0.0266282153137071
GO:0030005cellular di-, tri-valent inorganic cation homeostasis0.0266282153137071
GO:0002520immune system development0.0266282153137071
GO:0055066di-, tri-valent inorganic cation homeostasis0.0266282153137071
GO:0030003cellular cation homeostasis0.0286789366588777
GO:0055080cation homeostasis0.0286978621515081
GO:0001775cell activation0.0288865464751273
GO:0006917induction of apoptosis0.0288865464751273
GO:0012502induction of programmed cell death0.0288865464751273
GO:0055082cellular chemical homeostasis0.0312844536056327
GO:0006873cellular ion homeostasis0.0312844536056327
GO:0043085positive regulation of catalytic activity0.0327530472383582
GO:0043065positive regulation of apoptosis0.0327530472383582
GO:0043068positive regulation of programmed cell death0.0327530472383582
GO:0050801ion homeostasis0.0334674497335767
GO:0051239regulation of multicellular organismal process0.0342871919098899
GO:0048878chemical homeostasis0.0361962874839148
GO:0019899enzyme binding0.0361962874839148
GO:0004713protein-tyrosine kinase activity0.0361962874839148
GO:0051336regulation of hydrolase activity0.0361962874839148
GO:0004721phosphoprotein phosphatase activity0.0364713582468456
GO:0019725cellular homeostasis0.0431538693944755
GO:0007265Ras protein signal transduction0.0491068728919253
GO:0016791phosphoric monoester hydrolase activity0.0492251115653811



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
lymphocyte of B lineage4.79e-3324
pro-B cell4.79e-3324
lymphocyte5.12e-2553
common lymphoid progenitor5.12e-2553
nucleate cell5.55e-2455
lymphoid lineage restricted progenitor cell2.37e-2252
precursor B cell1.87e-183
mature B cell3.28e-132
pre-B-II cell3.28e-132
transitional stage B cell3.28e-132
small pre-B-II cell3.28e-132
immature B cell3.28e-132
hematopoietic cell3.27e-11177
nongranular leukocyte1.37e-09115
circulating cell4.27e-096
leukocyte9.47e-09136
hematopoietic stem cell1.79e-08168
angioblastic mesenchymal cell1.79e-08168
hematopoietic oligopotent progenitor cell6.61e-08161
hematopoietic multipotent progenitor cell6.61e-08161
hematopoietic lineage restricted progenitor cell7.95e-08120
antibody secreting cell1.55e-071
plasma cell1.55e-071
plasmablast1.55e-071
B-1 B cell2.37e-071
CD34-positive, CD38-negative hematopoietic stem cell3.60e-071
Uber Anatomy
Ontology termp-valuen
lymph node2.52e-071
Disease
Ontology termp-valuen
lymphoma1.41e-3610
hematologic cancer3.07e-1451
immune system cancer3.07e-1451
anemia1.65e-071
non-Hodgkin lymphoma1.75e-071
cutaneous T cell lymphoma1.75e-071
mycosis fungoides1.75e-071
lymphatic system cancer2.37e-071
lymphosarcoma2.37e-071
genetic disease3.01e-071
monogenic disease3.01e-071
xeroderma pigmentosum3.01e-071
acute leukemia4.57e-071
papillary adenocarcinoma4.85e-071


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)
MA0003.10.00215847
MA0004.10.502801
MA0006.10.341337
MA0007.10.483857
MA0009.10.973289
MA0014.10.0156227
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
MA0051.11.46692
MA0052.10.896548
MA0055.10.0407081
MA0056.10
MA0057.10.115382
MA0058.10.406232
MA0059.10.404929
MA0060.10.224688
MA0061.10.198335
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.162298
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.10.000265001
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.11.67751
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.0723293
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.11.17914
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.347695
MA0103.10.332048
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
MA0116.10.760835
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
MA0141.11.04059
MA0142.10.777365
MA0143.10.66587
MA0144.10.254954
MA0145.10.0807715
MA0146.10.0610556
MA0147.10.281049
MA0148.10.528066
MA0149.10.555119
MA0062.20.193221
MA0035.21.38583
MA0039.20.0170091
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
MA0154.10.335384
MA0155.10.250175
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.10.25944
MA0163.10.0167306
MA0164.10.678332
MA0080.20.344472
MA0018.20.650405
MA0099.20.572
MA0079.29.11084e-05
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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
BATF#10538310.43905791098730.00213725079298980.0123499134430155
IRF4#366239.391934008604630.002893813688341480.0156456493139046
MEF2A#420538.032813246990310.004516397834675020.0213549471865096



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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