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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.0724992894770213,

Latest revision as of 12:33, 17 September 2013


Full id: C3811_Neutrophils_CD19_CD14CD16_CD14_migratory_Eosinophils_Peripheral



Phase1 CAGE Peaks

Hg19::chr19:49842010..49842054,+p@chr19:49842010..49842054
+
Hg19::chr2:158300517..158300544,-p2@CYTIP
Hg19::chr7:135662021..135662051,-p2@MTPN


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:0021697cerebellar cortex formation0.000863456179598885
GO:0021533cell differentiation in hindbrain0.000863456179598885
GO:0021684cerebellar granular layer formation0.000863456179598885
GO:0021683cerebellar granular layer morphogenesis0.000863456179598885
GO:0021681cerebellar granular layer development0.000863456179598885
GO:0021707cerebellar granule cell differentiation0.000863456179598885
GO:0043403skeletal muscle regeneration0.00129518426939833
GO:0021575hindbrain morphogenesis0.00129518426939833
GO:0021587cerebellum morphogenesis0.00129518426939833
GO:0021696cerebellar cortex morphogenesis0.00129518426939833
GO:0021695cerebellar cortex development0.00141292829388908
GO:0022037metencephalon development0.00159407294695179
GO:0021549cerebellum development0.00159407294695179
GO:0016202regulation of striated muscle development0.00240534221459689
GO:0051146striated muscle cell differentiation0.00259036853879666
GO:0042246tissue regeneration0.00259036853879666
GO:0031099regeneration0.00274274315872587
GO:0030902hindbrain development0.00330991535512906
GO:0006584catecholamine metabolic process0.00349699752737549
GO:0018958phenol metabolic process0.00349699752737549
GO:0030424axon0.00419393001519459
GO:0048589developmental growth0.00435652890615801
GO:0042692muscle cell differentiation0.00518073707759331
GO:0006576biogenic amine metabolic process0.00798696966128969
GO:0043005neuron projection0.00839279406570117
GO:0014706striated muscle development0.00863456179598885
GO:0006575amino acid derivative metabolic process0.00863456179598885
GO:0042060wound healing0.0121192242350843
GO:0007420brain development0.0124159043756116
GO:0048646anatomical structure formation0.0132108795478629
GO:0007517muscle development0.0143723673765492
GO:0006725aromatic compound metabolic process0.0144432670041995
GO:0006417regulation of translation0.0144432670041995
GO:0031326regulation of cellular biosynthetic process0.0147020917066837
GO:0016049cell growth0.0147020917066837
GO:0008361regulation of cell size0.0147020917066837
GO:0030182neuron differentiation0.0147020917066837
GO:0009889regulation of biosynthetic process0.0147923677083914
GO:0007417central nervous system development0.0156086309389029
GO:0048699generation of neurons0.0156717296597198
GO:0022008neurogenesis0.0165530867601152
GO:0009888tissue development0.0188110096269757
GO:0042995cell projection0.0188554733172873
GO:0051246regulation of protein metabolic process0.0243494642646886
GO:0009611response to wounding0.0243494642646886
GO:0006066alcohol metabolic process0.0250589999948807
GO:0000902cell morphogenesis0.0257957533655167
GO:0032989cellular structure morphogenesis0.0257957533655167
GO:0006519amino acid and derivative metabolic process0.0289698359032769
GO:0009605response to external stimulus0.0323034194249936
GO:0009308amine metabolic process0.0323034194249936
GO:0006807nitrogen compound metabolic process0.033774420563541
GO:0007399nervous system development0.0349944127128001
GO:0065008regulation of biological quality0.0457152077309854
GO:0009653anatomical structure morphogenesis0.0493111974567291



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 cell2.54e-92168
angioblastic mesenchymal cell2.54e-92168
leukocyte7.05e-89136
hematopoietic oligopotent progenitor cell2.71e-88161
hematopoietic multipotent progenitor cell2.71e-88161
hematopoietic cell1.55e-84177
nongranular leukocyte1.79e-75115
hematopoietic lineage restricted progenitor cell6.33e-75120
myeloid cell2.84e-53108
common myeloid progenitor2.84e-53108
myeloid leukocyte3.92e-5072
granulocyte monocyte progenitor cell9.63e-4567
myeloid lineage restricted progenitor cell3.85e-4266
macrophage dendritic cell progenitor6.30e-4261
monopoietic cell7.65e-4159
monocyte7.65e-4159
monoblast7.65e-4159
promonocyte7.65e-4159
defensive cell7.47e-3948
phagocyte7.47e-3948
classical monocyte2.91e-3542
CD14-positive, CD16-negative classical monocyte2.91e-3542
lymphocyte2.05e-2953
common lymphoid progenitor2.05e-2953
lymphoid lineage restricted progenitor cell1.19e-2852
nucleate cell1.47e-2855
mesenchymal cell4.69e-18354
lymphocyte of B lineage4.10e-1724
pro-B cell4.10e-1724
connective tissue cell8.93e-17361
stuff accumulating cell5.67e-1387
motile cell9.08e-13386
B cell3.86e-1214
T cell3.07e-1125
pro-T cell3.07e-1125
mature alpha-beta T cell2.16e-1018
alpha-beta T cell2.16e-1018
immature T cell2.16e-1018
mature T cell2.16e-1018
immature alpha-beta T cell2.16e-1018
intermediate monocyte3.31e-099
CD14-positive, CD16-positive monocyte3.31e-099
granulocyte5.63e-088
multi fate stem cell7.31e-08427
stem cell2.13e-07441
somatic stem cell3.07e-07433
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.71e-5098
blood island2.71e-5098
hemolymphoid system3.33e-45108
bone marrow6.78e-3976
immune system1.41e-3793
bone element5.34e-3482
skeletal element1.48e-2890
skeletal system8.64e-24100
connective tissue1.61e-15371
lateral plate mesoderm8.01e-13203
adult organism4.18e-10114
blood4.51e-0815
haemolymphatic fluid4.51e-0815
organism substance4.51e-0815
Disease
Ontology termp-valuen
hematologic cancer1.36e-0951
immune system cancer1.36e-0951
leukemia3.29e-0739


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)
MA0003.10.0471418
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
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
MA0048.10.904546
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.557638
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.11.70014
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.12.1667
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.211629
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
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.11.80901
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
MA0141.11.6959
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.107247
MA0147.11.38767
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
MA0112.22.07067
MA0065.20.277623
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
MA0159.11.38935
MA0160.12.02335
MA0161.10
MA0162.10.149099
MA0163.10.387745
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.181755
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
MYC#460935.22228187160940.007020843755740150.0294489698785391



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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