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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.101407850382993,

Latest revision as of 12:31, 17 September 2013


Full id: C3704_Eosinophils_Basophils_Mast_CD14_mature_immature_Neutrophils



Phase1 CAGE Peaks

Hg19::chr17:8339189..8339285,+p1@NDEL1
Hg19::chr19:39897478..39897493,+p1@ZFP36
Hg19::chr8:103667935..103667960,-p1@KLF10


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:0000289poly(A) tail shortening0.00339482700640546
GO:0017091AU-rich element binding0.00339482700640546
GO:0050779RNA destabilization0.00339482700640546
GO:0048731system development0.00339482700640546
GO:0048856anatomical structure development0.00529648511130244
GO:0007275multicellular organismal development0.00650898764464172
GO:0000288mRNA catabolic process, deadenylation-dependent decay0.00650898764464172
GO:0043487regulation of RNA stability0.00931831515612074
GO:0043488regulation of mRNA stability0.00931831515612074
GO:0031348negative regulation of defense response0.00931831515612074
GO:0050728negative regulation of inflammatory response0.00931831515612074
GO:0032502developmental process0.0102721473776894
GO:0031124mRNA 3'-end processing0.0122633274630083
GO:0032501multicellular organismal process0.0126504045457779
GO:0045638negative regulation of myeloid cell differentiation0.0126504045457779
GO:0031123RNA 3'-end processing0.0126504045457779
GO:0051252regulation of RNA metabolic process0.0126504045457779
GO:0003727single-stranded RNA binding0.0126504045457779
GO:0031347regulation of defense response0.0142296101213018
GO:0050727regulation of inflammatory response0.0142296101213018
GO:0006402mRNA catabolic process0.0157184797707154
GO:0045637regulation of myeloid cell differentiation0.016401392162261
GO:0003729mRNA binding0.016401392162261
GO:0048583regulation of response to stimulus0.016401392162261
GO:0048523negative regulation of cellular process0.016401392162261
GO:0048513organ development0.016401392162261
GO:0048519negative regulation of biological process0.0169359510998705
GO:0006401RNA catabolic process0.0186902118941852
GO:0007179transforming growth factor beta receptor signaling pathway0.0196126044726536
GO:0045596negative regulation of cell differentiation0.0246356198112062
GO:0007178transmembrane receptor protein serine/threonine kinase signaling pathway0.026074786722757
GO:0030099myeloid cell differentiation0.026074786722757
GO:0051093negative regulation of developmental process0.026074786722757
GO:0005819spindle0.026074786722757
GO:0048869cellular developmental process0.0294175409287247
GO:0030154cell differentiation0.0294175409287247
GO:0000122negative regulation of transcription from RNA polymerase II promoter0.0385264091806844
GO:0005813centrosome0.0385264091806844
GO:0045595regulation of cell differentiation0.0416849547241876
GO:0005815microtubule organizing center0.0416849547241876
GO:0030097hemopoiesis0.0445230348524182
GO:0048534hemopoietic or lymphoid organ development0.0466859166721047
GO:0002520immune system development0.0479597324192457



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 leukocyte1.09e-2372
classical monocyte2.73e-2342
CD14-positive, CD16-negative classical monocyte2.73e-2342
defensive cell1.85e-2248
phagocyte1.85e-2248
leukocyte2.31e-21136
granulocyte monocyte progenitor cell1.92e-2067
macrophage dendritic cell progenitor6.56e-1861
myeloid lineage restricted progenitor cell3.72e-1766
monopoietic cell8.67e-1759
monocyte8.67e-1759
monoblast8.67e-1759
promonocyte8.67e-1759
hematopoietic lineage restricted progenitor cell1.43e-14120
nongranular leukocyte1.12e-13115
stuff accumulating cell9.61e-0987
hematopoietic stem cell1.20e-08168
angioblastic mesenchymal cell1.20e-08168
myeloid cell7.66e-08108
common myeloid progenitor7.66e-08108
hematopoietic cell1.40e-07177
hematopoietic oligopotent progenitor cell1.78e-07161
hematopoietic multipotent progenitor cell1.78e-07161
Uber Anatomy
Ontology termp-valuen
hematopoietic system6.03e-2098
blood island6.03e-2098
bone marrow5.66e-1976
skeletal element3.90e-1890
hemolymphoid system5.57e-18108
bone element1.43e-1782
immune system1.96e-1693
skeletal system9.42e-16100
adult organism2.36e-09114
lateral plate mesoderm4.08e-09203
musculoskeletal system1.56e-07167
organ1.95e-07503


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)
MA0003.13.8806
MA0004.10.826076
MA0006.11.5435
MA0007.10.804807
MA0009.11.3275
MA0014.13.90467
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
MA0055.10.190716
MA0056.10
MA0057.10.886807
MA0058.10.716037
MA0059.10.714521
MA0060.11.23283
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.11.04561
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.18.86238
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
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.846801
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
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.11.31729
MA0145.12.11725
MA0146.12.3244
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.25.50873
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.731309
MA0065.21.39232
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.12.76014
MA0163.10.776149
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.28.812
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
CCNT2#90536.336201576962630.003930750035764890.0189881407486239
E2F6#187635.017155731697390.00791769806886330.0321882626942006
EGR1#195834.988179094810140.008056488137383440.0320403474574536
HMGN3#932438.178547723350590.001827766942164210.0108633138898639
NFKB1#479035.488063424193840.006049381815655430.0269420634305005
NR3C1#290829.982015554115360.01278474365547170.0460390953256262
SIN3A#2594235.408884726815140.006318961977991520.0276463520597988
TAF7#6879311.43306940492390.0006690181981945830.0054243918640823
YY1#752834.911170749853860.008441455341808260.0329059851613583



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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