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Coexpression cluster:C4473: Difference between revisions

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{{Coexpression_clusters
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|full_id=C4473_Neutrophils_CD14_Eosinophils_lymphangiectasia_Dendritic_myeloma_Burkitt
|id=C4473
}}

Latest revision as of 12:46, 17 September 2013


Full id: C4473_Neutrophils_CD14_Eosinophils_lymphangiectasia_Dendritic_myeloma_Burkitt



Phase1 CAGE Peaks

Hg19::chr5:142782862..142782881,-p11@NR3C1
Hg19::chr6:90062427..90062459,-p1@UBE2J1
Hg19::chr6:90062488..90062504,-p3@UBE2J1


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:0004883glucocorticoid receptor activity0.0057694572000471



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
leukocyte1.91e-35136
myeloid leukocyte2.00e-3372
nongranular leukocyte1.42e-30115
granulocyte monocyte progenitor cell3.48e-2967
macrophage dendritic cell progenitor9.52e-2961
monopoietic cell3.74e-2859
monocyte3.74e-2859
monoblast3.74e-2859
promonocyte3.74e-2859
hematopoietic lineage restricted progenitor cell9.54e-28120
hematopoietic stem cell3.60e-27168
angioblastic mesenchymal cell3.60e-27168
defensive cell7.50e-2748
phagocyte7.50e-2748
classical monocyte8.76e-2642
CD14-positive, CD16-negative classical monocyte8.76e-2642
hematopoietic cell1.41e-25177
myeloid lineage restricted progenitor cell2.06e-2566
hematopoietic oligopotent progenitor cell4.90e-24161
hematopoietic multipotent progenitor cell4.90e-24161
myeloid cell2.30e-19108
common myeloid progenitor2.30e-19108
mesenchymal cell3.85e-16354
connective tissue cell5.22e-15361
multi fate stem cell6.43e-14427
somatic stem cell3.56e-12433
lymphocyte of B lineage1.12e-1124
pro-B cell1.12e-1124
stem cell2.56e-11441
motile cell9.56e-10386
stuff accumulating cell1.74e-0887
B cell6.54e-0814
intermediate monocyte6.58e-079
CD14-positive, CD16-positive monocyte6.58e-079
granulocyte8.40e-078
Uber Anatomy
Ontology termp-valuen
hemolymphoid system1.15e-30108
hematopoietic system1.46e-3098
blood island1.46e-3098
immune system3.97e-2693
bone marrow6.66e-2676
lateral plate mesoderm7.36e-26203
bone element1.89e-2482
skeletal element6.09e-2190
skeletal system7.59e-19100
connective tissue7.61e-15371
musculoskeletal system9.65e-13167
mesoderm1.83e-12315
mesoderm-derived structure1.83e-12315
presumptive mesoderm1.83e-12315


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)
MA0003.11.0927
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.758317
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
MA0055.10.190716
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
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0185922
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.11.31954
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
MA0139.10.440097
MA0140.10.894983
MA0141.11.6959
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.14.82347
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
MA0104.21.2307
MA0047.20.973066
MA0112.20.731309
MA0065.20.277623
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
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.455568
MA0163.10.122425
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
CCNT2#90536.336201576962630.003930750035764890.0190834698301064
CTCF#1066435.360256373075030.0064925092527670.0280832956657583
CTCFL#140690213.16431623931620.007433367036996010.0306936077166341
E2F1#186934.907389214879320.008460985347239390.0327086485297725
E2F6#187635.017155731697390.00791769806886330.0323849169191671
ELF1#199734.258097958807540.01295179875054610.0464373273956635
GATA1#2623313.56030814380040.0004009615963782630.0038911009258641
GTF2B#2959221.29588662288280.002878180589911410.0155877568258534
THAP1#55145220.91276306856750.002983447413736940.0158763000327765
YY1#752834.911170749853860.008441455341808260.0330813191160643



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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