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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=-0.165240025483351,

Latest revision as of 12:32, 17 September 2013


Full id: C3740_granulocyte_Neutrophils_Eosinophils_immature_acute_CD14_blood



Phase1 CAGE Peaks

Hg19::chr18:74844713..74844724,-p5@MBP
Hg19::chr2:74212029..74212067,+p1@ENST00000441217
Hg19::chr2:74212073..74212109,+p2@ENST00000441217


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:0043209myelin sheath0.00158954433062522
GO:0019911structural constituent of myelin sheath0.00437124690921936
GO:0008366axon ensheathment0.00635817732250088
GO:0007272ensheathment of neurons0.00635817732250088
GO:0001508regulation of action potential0.00635817732250088
GO:0007417central nervous system development0.0311285764747439
GO:0007268synaptic transmission0.0327843518191452
GO:0019226transmission of nerve impulse0.0327843518191452



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 cell7.09e-68168
angioblastic mesenchymal cell7.09e-68168
hematopoietic cell2.46e-64177
hematopoietic oligopotent progenitor cell5.83e-64161
hematopoietic multipotent progenitor cell5.83e-64161
leukocyte3.89e-60136
nongranular leukocyte5.75e-50115
hematopoietic lineage restricted progenitor cell7.00e-50120
myeloid cell1.87e-43108
common myeloid progenitor1.87e-43108
myeloid leukocyte1.44e-3672
granulocyte monocyte progenitor cell3.11e-3367
macrophage dendritic cell progenitor1.58e-3161
myeloid lineage restricted progenitor cell1.52e-3066
monopoietic cell2.99e-3059
monocyte2.99e-3059
monoblast2.99e-3059
promonocyte2.99e-3059
defensive cell2.49e-2748
phagocyte2.49e-2748
classical monocyte7.88e-2542
CD14-positive, CD16-negative classical monocyte7.88e-2542
lymphocyte2.58e-1753
common lymphoid progenitor2.58e-1753
lymphoid lineage restricted progenitor cell4.65e-1752
nucleate cell7.07e-1755
T cell4.00e-0925
pro-T cell4.00e-0925
lymphocyte of B lineage7.25e-0824
pro-B cell7.25e-0824
stuff accumulating cell2.34e-0787
mature alpha-beta T cell4.74e-0718
alpha-beta T cell4.74e-0718
immature T cell4.74e-0718
mature T cell4.74e-0718
immature alpha-beta T cell4.74e-0718
Uber Anatomy
Ontology termp-valuen
hematopoietic system4.46e-3598
blood island4.46e-3598
hemolymphoid system5.78e-31108
bone marrow1.91e-2576
immune system5.22e-2493
bone element1.02e-2382
skeletal element1.58e-1890
skeletal system7.05e-14100
blood4.41e-0815
haemolymphatic fluid4.41e-0815
organism substance4.41e-0815
Disease
Ontology termp-valuen
hematologic cancer1.37e-1051
immune system cancer1.37e-1051
leukemia1.58e-0939
myeloid leukemia2.75e-0731


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)
MA0003.14.57391
MA0004.13.20493
MA0006.11.5435
MA0007.10.804807
MA0009.11.3275
MA0014.11.80735
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.15.8296
MA0056.10
MA0057.11.59304
MA0058.12.8588
MA0059.12.854
MA0060.10.492218
MA0061.14.06645
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.11.36698
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.12.626
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.18.61931
MA0106.10.986396
MA0107.11.36919
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.11.12079
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.13.00132
MA0147.15.9629
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.21.62945
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.25.45805
MA0047.20.973066
MA0112.22.07067
MA0065.21.39232
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.838867
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.11.38935
MA0160.10.871361
MA0161.10
MA0162.14.34338
MA0163.11.84145
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.23.14419
MA0102.21.88331
MA0258.10.519674
MA0259.12.40872
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
BHLHE40#8553229.91454236465160.001467483527106140.00939626706440063
E2F1#186934.907389214879320.008460985347239390.03251966469217
NFKB1#479035.488063424193840.006049381815655430.026951257889482



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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