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{{Coexpression_clusters
{
|full_id=C2369_CD14CD16_Natural_CD8_CD14_Basophils_CD4_Whole
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Latest revision as of 12:04, 17 September 2013


Full id: C2369_CD14CD16_Natural_CD8_CD14_Basophils_CD4_Whole



Phase1 CAGE Peaks

Hg19::chr16:30484054..30484084,+p1@ITGAL
Hg19::chr8:21771173..21771178,-p2@DOK2
Hg19::chr8:21771182..21771208,-p1@DOK2
Hg19::chr8:21771214..21771223,-p4@DOK2


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:0005069transmembrane receptor protein tyrosine kinase docking protein activity0.00847732021019322
GO:0005066transmembrane receptor protein tyrosine kinase signaling protein activity0.012714857326154
GO:0005158insulin receptor binding0.021657885290216
GO:0008305integrin complex0.038793191786861
GO:0007229integrin-mediated signaling pathway0.038793191786861
GO:0007166cell surface receptor linked signal transduction0.038793191786861
GO:0032403protein complex binding0.038793191786861
GO:0043235receptor complex0.038793191786861
GO:0005057receptor signaling protein activity0.0493003668503964
GO:0004871signal transducer activity0.0493003668503964
GO:0060089molecular transducer activity0.0493003668503964
GO:0007169transmembrane receptor protein tyrosine kinase signaling pathway0.0493003668503964



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 cell1.87e-81168
angioblastic mesenchymal cell1.87e-81168
hematopoietic cell1.41e-77177
hematopoietic oligopotent progenitor cell6.35e-77161
hematopoietic multipotent progenitor cell6.35e-77161
leukocyte5.47e-72136
nongranular leukocyte5.57e-62115
hematopoietic lineage restricted progenitor cell2.71e-61120
myeloid cell2.73e-51108
common myeloid progenitor2.73e-51108
myeloid leukocyte6.49e-4472
myeloid lineage restricted progenitor cell4.22e-3966
granulocyte monocyte progenitor cell3.30e-3867
monopoietic cell6.47e-3759
monocyte6.47e-3759
monoblast6.47e-3759
promonocyte6.47e-3759
macrophage dendritic cell progenitor2.88e-3661
defensive cell1.62e-3348
phagocyte1.62e-3348
classical monocyte3.27e-3042
CD14-positive, CD16-negative classical monocyte3.27e-3042
nucleate cell8.57e-2255
lymphocyte2.77e-2153
common lymphoid progenitor2.77e-2153
lymphoid lineage restricted progenitor cell4.77e-2152
T cell5.77e-1825
pro-T cell5.77e-1825
mature alpha-beta T cell4.40e-1518
alpha-beta T cell4.40e-1518
immature T cell4.40e-1518
mature T cell4.40e-1518
immature alpha-beta T cell4.40e-1518
mesenchymal cell1.09e-14354
connective tissue cell1.73e-13361
stuff accumulating cell1.34e-1187
CD8-positive, alpha-beta T cell7.11e-1011
motile cell1.00e-09386
intermediate monocyte2.63e-099
CD14-positive, CD16-positive monocyte2.63e-099
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.19e-4798
blood island1.19e-4798
hemolymphoid system2.64e-42108
bone marrow1.66e-3276
immune system7.85e-3293
bone element4.19e-2882
skeletal element3.09e-2390
skeletal system1.63e-19100
adult organism5.26e-16114
lateral plate mesoderm8.98e-13203
connective tissue2.63e-12371
blood1.12e-1115
haemolymphatic fluid1.12e-1115
organism substance1.12e-1115
Disease
Ontology termp-valuen
leukemia3.06e-1139
hematologic cancer2.49e-0951
immune system cancer2.49e-0951
myeloid leukemia7.44e-0931


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)
MA0003.10.720743
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
MA0017.11.41335
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
MA0071.10.782546
MA0072.11.1744
MA0073.10.00636811
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
MA0103.10.521546
MA0105.10.232357
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
MA0139.10.912459
MA0140.10.779643
MA0141.11.46638
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.061409
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.0247757
MA0138.20.928035
MA0002.20.98779
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.21.09513
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.253219
MA0164.12.08227
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.00910927
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
MEF2A#4205418.74323090964418.0978922767748e-060.000224392616474949
SPI1#668848.204323508522730.000220661881527680.00249385415483924
TAF1#687243.343046285745290.008005664898701650.0321850656846371
TBP#690843.706770687096390.005296377814784350.0243914102918363
ZEB1#6935312.66632401315790.000793336075912850.00613151975373804



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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