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Coexpression cluster:C1638: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 11:49, 17 September 2013


Full id: C1638_Dendritic_CD14_CD19_granulocyte_immature_acute_xeroderma



Phase1 CAGE Peaks

Hg19::chr11:615942..615957,-p1@IRF7
Hg19::chr16:85932760..85932775,+p1@IRF8
Hg19::chr3:150996176..150996198,-p5@P2RY14
Hg19::chr3:150996239..150996276,-p3@P2RY14
Hg19::chr3:150996322..150996336,-p2@P2RY14


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:0000122negative regulation of transcription from RNA polymerase II promoter0.0031410574327759
GO:0045892negative regulation of transcription, DNA-dependent0.0031410574327759
GO:0045029UDP-activated nucleotide receptor activity0.0031410574327759
GO:0003702RNA polymerase II transcription factor activity0.0031410574327759
GO:0016481negative regulation of transcription0.0031410574327759
GO:0045934negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0031410574327759
GO:0015065uridine nucleotide receptor activity0.0031410574327759
GO:0031324negative regulation of cellular metabolic process0.00387566435067731
GO:0006357regulation of transcription from RNA polymerase II promoter0.00405724075135865
GO:0009892negative regulation of metabolic process0.00405724075135865
GO:0006366transcription from RNA polymerase II promoter0.00792110884661063
GO:0003705RNA polymerase II transcription factor activity, enhancer binding0.016104641718451
GO:0048523negative regulation of cellular process0.016104641718451
GO:0003704specific RNA polymerase II transcription factor activity0.016104641718451
GO:0048519negative regulation of biological process0.016104641718451
GO:0006955immune response0.016104641718451
GO:0001608nucleotide receptor activity, G-protein coupled0.016104641718451
GO:0045028purinergic nucleotide receptor activity, G-protein coupled0.016104641718451
GO:0016502nucleotide receptor activity0.016104641718451
GO:0001614purinergic nucleotide receptor activity0.016104641718451
GO:0002376immune system process0.0191868854807885
GO:0003700transcription factor activity0.0213752109800616
GO:0030099myeloid cell differentiation0.024483254351918
GO:0009615response to virus0.0298436809913163
GO:0030097hemopoiesis0.0469804302644277
GO:0048534hemopoietic or lymphoid organ development0.0485232872745847
GO:0002520immune system development0.0491439233431777



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
leukocyte9.16e-22136
hematopoietic stem cell5.72e-16168
angioblastic mesenchymal cell5.72e-16168
hematopoietic lineage restricted progenitor cell1.50e-15120
nongranular leukocyte1.81e-14115
hematopoietic cell6.11e-14177
hematopoietic oligopotent progenitor cell2.62e-13161
hematopoietic multipotent progenitor cell2.62e-13161
myeloid leukocyte3.79e-1172
granulocyte monocyte progenitor cell1.21e-0967
B cell2.65e-0914
lymphoid lineage restricted progenitor cell9.69e-0852
macrophage dendritic cell progenitor1.06e-0761
lymphocyte1.92e-0753
common lymphoid progenitor1.92e-0753
myeloid lineage restricted progenitor cell1.97e-0766
classical monocyte5.03e-0742
CD14-positive, CD16-negative classical monocyte5.03e-0742
myeloid cell6.77e-07108
common myeloid progenitor6.77e-07108
nucleate cell6.94e-0755
Uber Anatomy
Ontology termp-valuen
adult organism3.03e-61114
neural tube1.64e-1556
neural rod1.64e-1556
future spinal cord1.64e-1556
neural keel1.64e-1556
hematopoietic system2.22e-1498
blood island2.22e-1498
regional part of nervous system6.06e-1453
regional part of brain6.06e-1453
hemolymphoid system5.62e-13108
regional part of forebrain1.05e-1141
forebrain1.05e-1141
anterior neural tube1.05e-1141
future forebrain1.05e-1141
neural plate1.89e-1082
presumptive neural plate1.89e-1082
brain grey matter4.73e-1034
gray matter4.73e-1034
telencephalon4.97e-1034
neurectoderm2.19e-0986
cerebral hemisphere4.59e-0932
regional part of telencephalon5.52e-0932
brain6.77e-0968
future brain6.77e-0968
central nervous system9.57e-0981
immune system2.24e-0893
bone marrow6.54e-0876
blood2.15e-0715
haemolymphatic fluid2.15e-0715
organism substance2.15e-0715
nervous system3.28e-0789
neural nucleus3.33e-079
nucleus of brain3.33e-079


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)
MA0003.10.280184
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.10.161847
MA0017.11.24112
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.195817
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.11.01397
MA0056.10
MA0057.10.189508
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.11.44118
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.00220137
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.11.95181
MA0081.11.2972
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.818263
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.11.16366
MA0103.10.442769
MA0105.10.520776
MA0106.10.779931
MA0107.10.985964
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.973423
MA0115.11.35895
MA0116.10.994489
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.277033
MA0140.11.65391
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.938075
MA0145.10.143698
MA0146.10.6031
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.20.15493
MA0138.20.837782
MA0002.21.50443
MA0137.22.08722
MA0104.20.320919
MA0047.20.767096
MA0112.20.425004
MA0065.20.880827
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.10.130813
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.11.00463
MA0160.10.669748
MA0161.10
MA0162.10.21472
MA0163.10.382496
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.20.0198381
MA0102.21.66336
MA0258.10.914277
MA0259.11.02361
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

No analysis results for this cluster

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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