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Coexpression cluster:C2440: Difference between revisions

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{{Coexpression_clusters
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|full_id=C2440_CD14_lymphoma_migratory_CD19_b_splenic_immature
|id=C2440
|ontology_enrichment_celltype=CL:0000738!3.29e-44!140;CL:0002087!6.56e-35!119;CL:0000037!6.59e-35!172;CL:0000566!6.59e-35!172;CL:0002031!1.45e-34!124;CL:0000988!3.99e-33!182;CL:0002032!5.36e-33!165;CL:0000837!5.36e-33!165;CL:0000766!6.01e-24!76;CL:0002057!4.44e-22!42;CL:0000557!1.99e-21!71;CL:0000860!1.07e-20!45;CL:0002009!4.03e-20!65;CL:0002194!5.41e-19!63;CL:0000576!5.41e-19!63;CL:0000040!5.41e-19!63;CL:0000559!5.41e-19!63;CL:0000839!7.89e-19!70;CL:0000763!4.30e-18!112;CL:0000049!4.30e-18!112;CL:0000542!2.91e-14!53;CL:0000051!2.91e-14!53;CL:0000838!3.89e-14!52;CL:0000945!1.27e-10!24;CL:0000826!1.27e-10!24;CL:0000236!1.31e-07!14
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002390!9.57e-26!102;UBERON:0003061!9.57e-26!102;UBERON:0002193!9.34e-25!112;UBERON:0002371!5.73e-18!80;UBERON:0001474!1.19e-13!86;UBERON:0002405!1.28e-11!115;UBERON:0004765!2.68e-10!101;UBERON:0001434!2.68e-10!101;UBERON:0003081!4.10e-09!216;UBERON:0007023!4.42e-07!115
}}

Latest revision as of 12:05, 17 September 2013


Full id: C2440_CD14_lymphoma_migratory_CD19_b_splenic_immature



Phase1 CAGE Peaks

Hg19::chr17:76732851..76732873,-p4@CYTH1
Hg19::chr17:76732876..76732900,-p5@CYTH1
Hg19::chr17:76732909..76732922,-p7@CYTH1
Hg19::chr17:76732928..76732991,-p2@CYTH1


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

No GOStat results

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
leukocyte7.50e-44136
nongranular leukocyte1.04e-34115
hematopoietic lineage restricted progenitor cell2.82e-34120
hematopoietic stem cell4.29e-34168
angioblastic mesenchymal cell4.29e-34168
hematopoietic oligopotent progenitor cell2.57e-32161
hematopoietic multipotent progenitor cell2.57e-32161
hematopoietic cell9.21e-32177
myeloid leukocyte1.32e-2372
granulocyte monocyte progenitor cell6.67e-2167
classical monocyte1.51e-2042
CD14-positive, CD16-negative classical monocyte1.51e-2042
defensive cell2.31e-2048
phagocyte2.31e-2048
macrophage dendritic cell progenitor8.69e-2061
monopoietic cell1.23e-1859
monocyte1.23e-1859
monoblast1.23e-1859
promonocyte1.23e-1859
myeloid lineage restricted progenitor cell2.64e-1866
myeloid cell2.68e-17108
common myeloid progenitor2.68e-17108
lymphocyte1.55e-1453
common lymphoid progenitor1.55e-1453
lymphoid lineage restricted progenitor cell1.94e-1452
nucleate cell1.91e-1355
lymphocyte of B lineage8.26e-1124
pro-B cell8.26e-1124
B cell1.20e-0714
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.90e-2498
blood island1.90e-2498
hemolymphoid system6.33e-24108
immune system4.84e-1993
bone marrow2.40e-1776
bone element3.47e-1382
skeletal element5.42e-1290
lateral plate mesoderm1.32e-08203
skeletal system2.12e-08100


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)
MA0003.10.0214529
MA0004.10.71247
MA0006.10.532262
MA0007.11.65296
MA0009.11.20602
MA0014.10.0695829
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.11.80156
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.00636811
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.11.02755
MA0089.10
MA0090.10.640115
MA0091.14.13319
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.12.05499
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.11.09982
MA0145.12.41215
MA0146.10.061409
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.931615
MA0035.20.778873
MA0039.20.483275
MA0138.20.928035
MA0002.20.379056
MA0137.22.35208
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.533581
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.122011
MA0102.21.75932
MA0258.10.418966
MA0259.11.1888
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
CTCF#1066445.360256373075030.001211145381643620.00817229697076356
E2F1#186944.907389214879320.001724022357361790.0106491111296728
EBF1#187948.9064668465690.00015887907472010.00199557085805082
ELF1#199744.258097958807540.003041525565781240.0160869993195901
MYC#460945.22228187160940.001344309395272740.00887585844815333
NFKB1#479045.488063424193840.001102199566301980.00767826977754884
NFYB#4801416.75979325353651.26678572070404e-050.00031122520321009
REST#597849.650028716128020.0001152825614219170.00156995637401794
RFX5#5993412.04791082719514.74457429336527e-050.00082641526788655
SMARCB1#6598418.25271578115749.00423392720929e-060.000241435991559387
SP1#666745.69838137814090.0009482606065333980.00684040540722072
TAF1#687243.343046285745290.008005664898701650.0322123453673718
TCF7L2#6934410.77017656313737.42969445082454e-050.00115434373512297
YY1#752844.911170749853860.00171871838055440.0106833251366933
ZEB1#6935416.88843201754391.22862303393937e-050.000304138803132482
ZNF263#1012736.166381227758010.006539814347975980.0279727923450163



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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