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Coexpression cluster:C2737: Difference between revisions

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{{Coexpression_clusters
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|full_id=C2737_Monocytederived_granulocyte_chronic_Dendritic_Basophils_Macrophage_CD14
|id=C2737
|ontology_enrichment_celltype=CL:0000037!3.84e-70!172;CL:0000566!3.84e-70!172;CL:0000988!4.79e-67!182;CL:0002032!8.23e-66!165;CL:0000837!8.23e-66!165;CL:0000738!1.46e-51!140;CL:0000763!2.67e-46!112;CL:0000049!2.67e-46!112;CL:0002031!9.95e-44!124;CL:0002087!5.56e-42!119;CL:0000766!3.66e-28!76;CL:0000557!2.85e-27!71;CL:0000839!3.56e-26!70;CL:0002009!2.65e-24!65;CL:0002194!1.69e-23!63;CL:0000576!1.69e-23!63;CL:0000040!1.69e-23!63;CL:0000559!1.69e-23!63;CL:0002057!1.15e-20!42;CL:0000860!2.77e-17!45;CL:0000542!2.66e-16!53;CL:0000051!2.66e-16!53;CL:0000838!8.78e-16!52;CL:0000134!3.50e-12!358;CL:0002320!1.13e-10!365;CL:0000219!1.53e-09!390;CL:0000945!2.49e-08!24;CL:0000826!2.49e-08!24;CL:0000034!3.13e-08!444;CL:0000048!4.67e-08!430;CL:0000084!6.55e-08!25;CL:0000827!6.55e-08!25;CL:0000723!4.62e-07!436;CL:0002393!7.24e-07!9;CL:0002397!7.24e-07!9;CL:0000451!8.68e-07!10
|ontology_enrichment_disease=DOID:1240!1.44e-19!39;DOID:2531!1.80e-19!51;DOID:0060083!1.80e-19!51;DOID:8692!7.15e-16!31
|ontology_enrichment_uberon=UBERON:0002390!9.53e-33!102;UBERON:0003061!9.53e-33!102;UBERON:0002193!1.83e-32!112;UBERON:0002371!4.13e-24!80;UBERON:0001474!1.20e-19!86;UBERON:0002405!7.34e-19!115;UBERON:0003081!3.83e-17!216;UBERON:0004765!1.45e-13!101;UBERON:0001434!1.45e-13!101;UBERON:0007023!1.87e-09!115;UBERON:0002384!2.00e-09!375
}}

Latest revision as of 12:11, 17 September 2013


Full id: C2737_Monocytederived_granulocyte_chronic_Dendritic_Basophils_Macrophage_CD14



Phase1 CAGE Peaks

Hg19::chr3:196366555..196366572,+p2@LRRC33
Hg19::chr3:196366587..196366604,+p3@LRRC33
Hg19::chr3:196366616..196366690,+p1@LRRC33
p2@PIGX
Hg19::chr3:196366873..196366890,-p@chr3:196366873..196366890
-


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>disease_data<br>

Cell Type
Ontology termp-valuen
hematopoietic stem cell2.21e-77168
angioblastic mesenchymal cell2.21e-77168
hematopoietic cell7.46e-74177
hematopoietic oligopotent progenitor cell7.98e-73161
hematopoietic multipotent progenitor cell7.98e-73161
leukocyte1.22e-57136
myeloid cell2.38e-51108
common myeloid progenitor2.38e-51108
hematopoietic lineage restricted progenitor cell9.99e-50120
nongranular leukocyte4.77e-48115
myeloid leukocyte4.59e-3272
granulocyte monocyte progenitor cell1.67e-3167
myeloid lineage restricted progenitor cell1.98e-3066
macrophage dendritic cell progenitor1.09e-2861
monopoietic cell8.06e-2859
monocyte8.06e-2859
monoblast8.06e-2859
promonocyte8.06e-2859
defensive cell5.61e-2448
phagocyte5.61e-2448
classical monocyte4.52e-2042
CD14-positive, CD16-negative classical monocyte4.52e-2042
nucleate cell1.88e-1855
lymphocyte6.37e-1853
common lymphoid progenitor6.37e-1853
lymphoid lineage restricted progenitor cell2.41e-1752
mesenchymal cell3.14e-12354
connective tissue cell7.56e-11361
stuff accumulating cell1.57e-1087
motile cell1.08e-09386
lymphocyte of B lineage5.33e-0924
pro-B cell5.33e-0924
T cell8.95e-0925
pro-T cell8.95e-0925
stem cell1.34e-07441
multi fate stem cell2.70e-07427
dendritic cell4.15e-0710
Uber Anatomy
Ontology termp-valuen
hematopoietic system6.22e-3698
blood island6.22e-3698
hemolymphoid system3.83e-34108
immune system5.92e-2893
bone marrow8.43e-2776
bone element2.35e-2282
skeletal element2.52e-1790
lateral plate mesoderm2.50e-16203
skeletal system9.92e-14100
connective tissue8.43e-10371
adult organism2.93e-08114
blood5.79e-0715
haemolymphatic fluid5.79e-0715
organism substance5.79e-0715
Disease
Ontology termp-valuen
hematologic cancer4.32e-2151
immune system cancer4.32e-2151
leukemia1.22e-2039
myeloid leukemia1.25e-1631


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)
MA0003.10.443649
MA0004.10.71247
MA0006.10.532262
MA0007.11.65296
MA0009.11.20602
MA0014.13.76953
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
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.11.8408
MA0072.11.1744
MA0073.13.33774
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.11.4709
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.536981
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.11.29536
MA0105.10.656404
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
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
MA0144.10.430413
MA0145.10.195821
MA0146.10.8309
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.21.5472
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.23.12566
MA0065.20.199162
MA0150.11.53138
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.11.02191
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.11.57817
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.22.00408
MA0102.21.75932
MA0258.11.88931
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
GABPB1#255335.300762877136630.01012678824234270.0378753630297247
GATA1#2623413.56030814380042.95627390049268e-050.000614917924504192
GATA2#2624412.7449317335543.78864877853583e-050.000723236501154275
MAX#414934.839416631755340.01315737137836840.0466411889683461
MEF2A#4205314.0574231822330.0005830038854186610.00488905916085109
NFKB1#479045.488063424193840.001102199566301980.00768801312395728
PAX5#507946.669565531177830.0005052774169483260.00444534311756939
POU2F2#545236.829593043306890.004860473775203740.0227705118471495
USF1#739134.771124457905970.01370465887188020.0483253720008202
USF2#739239.74414803880220.001718341848410070.010724387731929



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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