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{{Coexpression_clusters
{
|full_id=C2141_Neutrophils_Macrophage_CD14_Monocytederived_Eosinophils_Dendritic_CD14CD16
|

Latest revision as of 11:59, 17 September 2013


Full id: C2141_Neutrophils_Macrophage_CD14_Monocytederived_Eosinophils_Dendritic_CD14CD16



Phase1 CAGE Peaks

Hg19::chr11:60719607..60719659,-p1@SLC15A3
Hg19::chr14:93118813..93118870,+p5@RIN3
Hg19::chr5:179498703..179498784,-p1@RNF130
Hg19::chr8:74903580..74903661,+p1@LY96


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:0015198oligopeptide transporter activity0.0376664433950366
GO:0015197peptide transporter activity0.0376664433950366
GO:0015026coreceptor activity0.0400046939624358
GO:0006857oligopeptide transport0.0400046939624358



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
myeloid leukocyte9.31e-4072
granulocyte monocyte progenitor cell1.04e-3367
monopoietic cell4.66e-3259
monocyte4.66e-3259
monoblast4.66e-3259
promonocyte4.66e-3259
myeloid lineage restricted progenitor cell9.16e-3266
macrophage dendritic cell progenitor4.95e-3161
defensive cell7.53e-3048
phagocyte7.53e-3048
myeloid cell9.27e-30108
common myeloid progenitor9.27e-30108
leukocyte1.07e-29136
classical monocyte1.10e-2542
CD14-positive, CD16-negative classical monocyte1.10e-2542
hematopoietic stem cell1.87e-25168
angioblastic mesenchymal cell1.87e-25168
hematopoietic oligopotent progenitor cell1.17e-23161
hematopoietic multipotent progenitor cell1.17e-23161
nongranular leukocyte3.57e-22115
hematopoietic cell6.92e-22177
hematopoietic lineage restricted progenitor cell5.43e-21120
stuff accumulating cell1.59e-1587
mesenchymal cell3.51e-09354
connective tissue cell1.35e-08361
motile cell1.20e-07386
intermediate monocyte6.61e-079
CD14-positive, CD16-positive monocyte6.61e-079
Uber Anatomy
Ontology termp-valuen
hematopoietic system4.70e-3498
blood island4.70e-3498
hemolymphoid system2.42e-33108
adult organism9.54e-31114
bone marrow5.11e-3076
immune system2.42e-2993
bone element2.67e-2682
skeletal element4.29e-2290
skeletal system5.65e-20100
lateral plate mesoderm7.89e-17203
musculoskeletal system1.12e-10167
neural tube6.46e-0956
neural rod6.46e-0956
future spinal cord6.46e-0956
neural keel6.46e-0956
mesoderm8.09e-09315
mesoderm-derived structure8.09e-09315
presumptive mesoderm8.09e-09315
regional part of nervous system6.47e-0853
regional part of brain6.47e-0853
connective tissue7.73e-08371
central nervous system8.87e-0781


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
MA0014.10.524262
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
MA0050.11.66718
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
MA0073.10.214613
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.536981
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
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.11.09982
MA0145.10.195821
MA0146.10.8309
MA0147.11.16748
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.257871
MA0138.20.928035
MA0002.20.379056
MA0137.21.37305
MA0104.21.01696
MA0047.20.856092
MA0112.21.05083
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.649108
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.11.1691
MA0160.10.756582
MA0161.10
MA0162.10.640035
MA0163.10.539587
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.657636
MA0102.21.75932
MA0258.11.07498
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
SPI1#668848.204323508522730.000220661881527680.00249035079369671



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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