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Coexpression cluster:C3091: Difference between revisions

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{{Coexpression_clusters
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|full_id=C3091_granulocyte_Neutrophils_optic_skeletal_Eosinophils_immature_CD4
|id=C3091
}}

Latest revision as of 12:19, 17 September 2013


Full id: C3091_granulocyte_Neutrophils_optic_skeletal_Eosinophils_immature_CD4



Phase1 CAGE Peaks

Hg19::chr11:11863500..11863576,+p1@USP47
Hg19::chr1:179923875..179923954,+p1@CEP350
Hg19::chr8:42752053..42752154,+p1@HOOK3


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:0031122cytoplasmic microtubule organization and biogenesis0.00304662663369834
GO:0051645Golgi localization0.00304662663369834
GO:0015630microtubule cytoskeleton0.0157887649980403
GO:0005801cis-Golgi network0.018273841294435
GO:0044430cytoskeletal part0.0296554642569538
GO:0051640organelle localization0.0334813341011192
GO:0008017microtubule binding0.0425925335828027
GO:0005856cytoskeleton0.043737425088151
GO:0015631tubulin binding0.0452728129930291
GO:0005819spindle0.0474197284120837



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
leukocyte7.09e-36136
hematopoietic stem cell1.31e-33168
angioblastic mesenchymal cell1.31e-33168
hematopoietic oligopotent progenitor cell7.32e-31161
hematopoietic multipotent progenitor cell7.32e-31161
hematopoietic cell8.78e-30177
hematopoietic lineage restricted progenitor cell1.17e-27120
nongranular leukocyte2.38e-25115
myeloid leukocyte8.33e-2472
myeloid cell3.71e-23108
common myeloid progenitor3.71e-23108
granulocyte monocyte progenitor cell1.16e-2167
myeloid lineage restricted progenitor cell4.09e-2066
macrophage dendritic cell progenitor9.47e-1961
monopoietic cell1.42e-1759
monocyte1.42e-1759
monoblast1.42e-1759
promonocyte1.42e-1759
classical monocyte3.72e-1742
CD14-positive, CD16-negative classical monocyte3.72e-1742
defensive cell6.58e-1648
phagocyte6.58e-1648
nucleate cell8.45e-0855
lymphoid lineage restricted progenitor cell1.62e-0752
lymphocyte1.69e-0753
common lymphoid progenitor1.69e-0753
mature alpha-beta T cell4.07e-0718
alpha-beta T cell4.07e-0718
immature T cell4.07e-0718
mature T cell4.07e-0718
immature alpha-beta T cell4.07e-0718
dendritic cell4.69e-0710
Uber Anatomy
Ontology termp-valuen
adult organism1.51e-26114
hematopoietic system1.36e-2098
blood island1.36e-2098
hemolymphoid system1.77e-17108
bone marrow7.48e-1776
bone element1.19e-1682
immune system3.32e-1593
skeletal element5.12e-1390
neural tube1.15e-1256
neural rod1.15e-1256
future spinal cord1.15e-1256
neural keel1.15e-1256
skeletal system5.71e-12100
regional part of nervous system1.05e-1153
regional part of brain1.05e-1153
regional part of forebrain7.50e-1141
forebrain7.50e-1141
anterior neural tube7.50e-1141
future forebrain7.50e-1141
brain2.47e-1068
future brain2.47e-1068
central nervous system9.45e-1081
nervous system1.82e-0989
brain grey matter3.04e-0834
gray matter3.04e-0834
telencephalon7.92e-0834
regional part of telencephalon1.77e-0732
cerebral hemisphere3.71e-0732


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)
MA0003.11.54338
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.13.14798
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
MA0055.11.06172
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
MA0069.11.31207
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
MA0111.10.767139
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
MA0146.11.70974
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.432958
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
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.12.76014
MA0163.10.387745
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.21.90288
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
BRCA1#672213.45615376214920.007119807716084560.0296095885820155
E2F1#186934.907389214879320.008460985347239390.0323600852777799
ELF1#199734.258097958807540.01295179875054610.0460092826431389
GTF2B#2959221.29588662288280.002878180589911410.015573220527912
HMGN3#932438.178547723350590.001827766942164210.0108300324334896
NFKB1#479035.488063424193840.006049381815655430.0268607366797856
PAX5#507936.669565531177830.003370290999677260.0172290661632547
POU2F2#545239.106124057742520.001324165192682130.00879456207049469
SIN3A#2594235.408884726815140.006318961977991520.0275425094954074
XRCC4#751811432.767441860460.0006977913838891460.00561150645584034
ZBTB33#10009221.10981668665410.002928597060603240.0156282125804681



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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