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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 12:23, 17 September 2013


Full id: C3297_Monocytederived_CD14CD16_CD14_Macrophage_Dendritic_migratory_splenic



Phase1 CAGE Peaks

Hg19::chr12:54891528..54891570,+p1@NCKAP1L
Hg19::chr17:25958204..25958254,+p1@LGALS9
Hg19::chr17:25958269..25958280,+p2@LGALS9


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:0005534galactose binding0.0060047684822202
GO:0048029monosaccharide binding0.0170100048245901



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 cell1.13e-76168
angioblastic mesenchymal cell1.13e-76168
hematopoietic oligopotent progenitor cell4.23e-72161
hematopoietic multipotent progenitor cell4.23e-72161
hematopoietic cell8.64e-69177
leukocyte4.28e-66136
myeloid cell8.25e-58108
common myeloid progenitor8.25e-58108
hematopoietic lineage restricted progenitor cell1.71e-55120
nongranular leukocyte2.94e-53115
myeloid leukocyte1.17e-4772
granulocyte monocyte progenitor cell1.68e-4467
myeloid lineage restricted progenitor cell2.67e-4366
macrophage dendritic cell progenitor1.11e-4161
monopoietic cell1.26e-4059
monocyte1.26e-4059
monoblast1.26e-4059
promonocyte1.26e-4059
defensive cell2.46e-3648
phagocyte2.46e-3648
classical monocyte2.34e-3142
CD14-positive, CD16-negative classical monocyte2.34e-3142
nucleate cell3.69e-1355
lymphocyte7.65e-1353
common lymphoid progenitor7.65e-1353
lymphoid lineage restricted progenitor cell1.40e-1252
stuff accumulating cell7.79e-1087
mesenchymal cell3.23e-09354
lymphocyte of B lineage1.49e-0824
pro-B cell1.49e-0824
connective tissue cell3.79e-08361
intermediate monocyte4.46e-089
CD14-positive, CD16-positive monocyte4.46e-089
dendritic cell1.06e-0710
Uber Anatomy
Ontology termp-valuen
hemolymphoid system3.52e-45108
hematopoietic system6.18e-4498
blood island6.18e-4498
immune system3.32e-4193
bone marrow8.19e-3876
bone element2.41e-3282
skeletal element2.52e-2690
skeletal system6.03e-22100
adult organism1.78e-20114
lateral plate mesoderm5.77e-17203
connective tissue2.78e-07371
Disease
Ontology termp-valuen
myeloid leukemia1.56e-0931
leukemia2.84e-0939
hematologic cancer8.76e-0951
immune system cancer8.76e-0951


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)
MA0003.10.178364
MA0004.10.826076
MA0006.10.639288
MA0007.11.88666
MA0009.12.94911
MA0014.10.377374
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
MA0042.11.89908
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.12.91799
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0834661
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
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
MA0141.11.6959
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.195278
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.11.38935
MA0160.12.02335
MA0161.10
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.23.82238
MA0018.20.987913
MA0099.20.902716
MA0079.20.311277
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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
ELF1#199734.258097958807540.01295179875054610.0460641208822845
NFKB1#479035.488063424193840.006049381815655430.0268904612660242
SPI1#668838.204323508522730.001810593189410520.0108907759090506
STAT2#6773243.50918079096040.0006968990898868230.00560648929661762



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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