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Coexpression cluster:C2621: Difference between revisions

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{{Coexpression_clusters
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|full_id=C2621_migratory_Eosinophils_Neutrophils_CD14_hairy_immature_Mast
|id=C2621
|ontology_enrichment_celltype=CL:0000738!1.32e-70!140;CL:0000037!1.81e-68!172;CL:0000566!1.81e-68!172;CL:0000988!1.20e-64!182;CL:0002032!4.51e-64!165;CL:0000837!4.51e-64!165;CL:0002031!5.24e-55!124;CL:0002087!1.58e-53!119;CL:0000763!4.37e-41!112;CL:0000049!4.37e-41!112;CL:0000766!1.40e-40!76;CL:0000557!6.21e-36!71;CL:0000839!4.46e-33!70;CL:0002057!1.83e-32!42;CL:0002009!2.11e-32!65;CL:0002194!7.42e-31!63;CL:0000576!7.42e-31!63;CL:0000040!7.42e-31!63;CL:0000559!7.42e-31!63;CL:0000860!8.29e-29!45;CL:0000542!2.06e-19!53;CL:0000051!2.06e-19!53;CL:0000838!8.18e-19!52;CL:0000945!3.74e-14!24;CL:0000826!3.74e-14!24;CL:0000134!3.47e-09!358;CL:0000451!7.80e-09!10;CL:0002320!3.13e-08!365;CL:0002393!3.15e-08!9;CL:0002397!3.15e-08!9;CL:0000094!3.29e-08!8;CL:0000236!9.44e-08!14;CL:0000990!1.67e-07!8
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002390!2.24e-42!102;UBERON:0003061!2.24e-42!102;UBERON:0002193!2.93e-39!112;UBERON:0002371!8.92e-32!80;UBERON:0001474!1.99e-27!86;UBERON:0002405!1.70e-22!115;UBERON:0007023!6.19e-22!115;UBERON:0004765!5.31e-20!101;UBERON:0001434!5.31e-20!101;UBERON:0001049!2.49e-14!57;UBERON:0005068!2.49e-14!57;UBERON:0006241!2.49e-14!57;UBERON:0007135!2.49e-14!57;UBERON:0002780!2.00e-13!41;UBERON:0001890!2.00e-13!41;UBERON:0006240!2.00e-13!41;UBERON:0003080!8.61e-13!42;UBERON:0002616!6.18e-11!59;UBERON:0002020!6.26e-11!34;UBERON:0003528!6.26e-11!34;UBERON:0001893!6.61e-11!34;UBERON:0002791!1.83e-10!33;UBERON:0001869!3.19e-10!32;UBERON:0002619!3.01e-09!22;UBERON:0003081!5.77e-09!216;UBERON:0001950!2.54e-08!20;UBERON:0000955!3.79e-08!69;UBERON:0006238!3.79e-08!69;UBERON:0000178!5.99e-08!15;UBERON:0000179!5.99e-08!15;UBERON:0000463!5.99e-08!15;UBERON:0003075!6.26e-08!86;UBERON:0007284!6.26e-08!86;UBERON:0000956!6.36e-08!25;UBERON:0000203!6.36e-08!25;UBERON:0001017!1.38e-07!82;UBERON:0002384!1.88e-07!375;UBERON:0005743!4.44e-07!86;UBERON:0002346!6.39e-07!90
}}

Latest revision as of 12:09, 17 September 2013


Full id: C2621_migratory_Eosinophils_Neutrophils_CD14_hairy_immature_Mast



Phase1 CAGE Peaks

Hg19::chr20:4803297..4803323,-p@chr20:4803297..4803323
-
Hg19::chr22:35806477..35806519,+p3@MCM5
Hg19::chr22:35806599..35806615,+p8@MCM5
Hg19::chr6:12061235..12061270,+p@chr6:12061235..12061270
+


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
leukocyte1.70e-82136
nongranular leukocyte6.02e-69115
hematopoietic stem cell1.57e-63168
angioblastic mesenchymal cell1.57e-63168
hematopoietic lineage restricted progenitor cell1.67e-62120
hematopoietic cell8.02e-62177
hematopoietic oligopotent progenitor cell7.11e-59161
hematopoietic multipotent progenitor cell7.11e-59161
myeloid leukocyte1.83e-4672
macrophage dendritic cell progenitor1.73e-4361
defensive cell1.22e-4248
phagocyte1.22e-4248
classical monocyte1.58e-4242
CD14-positive, CD16-negative classical monocyte1.58e-4242
monopoietic cell2.31e-4159
monocyte2.31e-4159
monoblast2.31e-4159
promonocyte2.31e-4159
granulocyte monocyte progenitor cell6.37e-3967
myeloid lineage restricted progenitor cell5.21e-3666
myeloid cell8.40e-33108
common myeloid progenitor8.40e-33108
lymphocyte2.99e-2353
common lymphoid progenitor2.99e-2353
lymphoid lineage restricted progenitor cell1.82e-2252
nucleate cell7.33e-2255
lymphocyte of B lineage2.23e-1924
pro-B cell2.23e-1924
stuff accumulating cell1.52e-1587
dendritic cell9.35e-1210
B cell1.74e-1014
mesenchymal cell1.86e-10354
intermediate monocyte2.45e-109
CD14-positive, CD16-positive monocyte2.45e-109
granulocyte2.84e-108
conventional dendritic cell5.92e-108
connective tissue cell1.14e-09361
blood cell3.66e-0811
Langerhans cell3.33e-075
motile cell5.06e-07386
Uber Anatomy
Ontology termp-valuen
hematopoietic system5.61e-4798
blood island5.61e-4798
hemolymphoid system6.33e-43108
bone marrow1.23e-3476
immune system1.73e-3493
bone element1.61e-3082
skeletal element6.29e-2690
skeletal system4.38e-22100
adult organism2.28e-16114
neural tube3.14e-1356
neural rod3.14e-1356
future spinal cord3.14e-1356
neural keel3.14e-1356
regional part of nervous system1.34e-1253
regional part of brain1.34e-1253
lateral plate mesoderm1.48e-11203
brain grey matter7.72e-1134
gray matter7.72e-1134
telencephalon1.03e-1034
regional part of forebrain2.73e-1041
forebrain2.73e-1041
anterior neural tube2.73e-1041
future forebrain2.73e-1041
regional part of telencephalon1.03e-0932
cerebral hemisphere1.23e-0932
blood4.73e-0915
haemolymphatic fluid4.73e-0915
organism substance4.73e-0915
regional part of cerebral cortex5.94e-0922
connective tissue6.34e-09371
brain4.01e-0868
future brain4.01e-0868
neocortex7.23e-0820
central nervous system1.86e-0781
cerebral cortex2.39e-0725
pallium2.39e-0725
neural plate7.08e-0782
presumptive neural plate7.08e-0782


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)
MA0003.10.233555
MA0004.11.69588
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.896009
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
MA0048.11.30988
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.11.28887
MA0056.10
MA0057.10.248209
MA0058.11.47358
MA0059.11.47051
MA0060.10.393285
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
MA0074.11.91637
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.12.27878
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.11.29536
MA0105.11.22348
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.11.13665
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
MA0145.10.195821
MA0146.10.221129
MA0147.11.16748
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.10559
MA0138.20.928035
MA0002.21.75253
MA0137.20.558189
MA0104.21.01696
MA0047.20.856092
MA0112.21.65877
MA0065.20.577908
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.649108
MA0155.10.533581
MA0156.11.37856
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.309472
MA0163.10.0725493
MA0164.10.90014
MA0080.21.32578
MA0018.20.870662
MA0099.20.7872
MA0079.20.20937
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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#10538212.17890089615180.009566758805047810.0360233170911591
EBF1#187936.679850134926750.005184294118278910.024052351891028
IRF4#3662316.43588451505810.0003669431395554610.00365888624709116
MAX#414934.839416631755340.01315737137836840.046634857441981
NFKB1#479045.488063424193840.001102199566301980.00768390765002418
PAX5#507946.669565531177830.0005052774169483260.00444234936852144
PBX3#5090210.95725634337210.01174530180688030.0428545128356895
SPI1#668836.153242631392040.006580387113059030.0281048971373971
TCF12#693837.975848676639820.003090920396013070.0162822876646428
USF1#739134.771124457905970.01370465887188020.0483123225518225



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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