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Coexpression cluster:C3547: Difference between revisions

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{{Coexpression_clusters
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|full_id=C3547_granulocyte_acute_Eosinophils_salivary_hepatoblastoma_cerebellum_tridermal
|id=C3547
}}

Latest revision as of 12:28, 17 September 2013


Full id: C3547_granulocyte_acute_Eosinophils_salivary_hepatoblastoma_cerebellum_tridermal



Phase1 CAGE Peaks

Hg19::chr16:2802623..2802721,+p1@SRRM2
Hg19::chr19:5622779..5622813,-p1@SAFB2
Hg19::chr19:5623083..5623158,+p1@SAFB


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:0003723RNA binding0.00137547276961258



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 cell8.18e-33168
angioblastic mesenchymal cell8.18e-33168
hematopoietic cell5.89e-31177
hematopoietic oligopotent progenitor cell7.21e-31161
hematopoietic multipotent progenitor cell7.21e-31161
leukocyte1.15e-24136
myeloid cell3.62e-23108
common myeloid progenitor3.62e-23108
hematopoietic lineage restricted progenitor cell6.94e-19120
nongranular leukocyte1.99e-17115
classical monocyte2.51e-1542
CD14-positive, CD16-negative classical monocyte2.51e-1542
myeloid leukocyte1.47e-1472
granulocyte monocyte progenitor cell3.90e-1267
myeloid lineage restricted progenitor cell1.74e-1166
defensive cell4.43e-1148
phagocyte4.43e-1148
macrophage dendritic cell progenitor3.68e-1061
monopoietic cell1.40e-0959
monocyte1.40e-0959
monoblast1.40e-0959
promonocyte1.40e-0959
nucleate cell6.26e-0855
lymphocyte1.70e-0753
common lymphoid progenitor1.70e-0753
lymphoid lineage restricted progenitor cell1.96e-0752
Uber Anatomy
Ontology termp-valuen
adult organism2.97e-22114
neural tube1.73e-1456
neural rod1.73e-1456
future spinal cord1.73e-1456
neural keel1.73e-1456
regional part of nervous system8.53e-1453
regional part of brain8.53e-1453
hematopoietic system4.43e-1398
blood island4.43e-1398
nervous system6.58e-1289
regional part of forebrain1.47e-1141
forebrain1.47e-1141
anterior neural tube1.47e-1141
future forebrain1.47e-1141
central nervous system2.00e-1181
brain4.20e-1168
future brain4.20e-1168
hemolymphoid system6.01e-11108
neurectoderm1.31e-1086
neural plate4.73e-1082
presumptive neural plate4.73e-1082
bone element1.31e-0982
brain grey matter1.32e-0934
gray matter1.32e-0934
telencephalon1.38e-0934
bone marrow1.47e-0976
regional part of telencephalon5.11e-0932
cerebral hemisphere1.15e-0832
immune system1.21e-0893
pre-chordal neural plate5.69e-0861
regional part of cerebral cortex1.62e-0722
neocortex6.27e-0720
Disease
Ontology termp-valuen
leukemia1.46e-0739
myeloid leukemia3.43e-0731
hematologic cancer4.07e-0751
immune system cancer4.07e-0751


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)
MA0003.10.401049
MA0004.10.826076
MA0006.12.61424
MA0007.10.804807
MA0009.11.3275
MA0014.11.24048
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
MA0057.10.333427
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
MA0088.10.715722
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
MA0144.10.531867
MA0145.11.37817
MA0146.11.16674
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
MA0104.21.2307
MA0047.20.973066
MA0112.20.264678
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
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.12.05956
MA0163.10.387745
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.09178
MA0102.21.88331
MA0258.10.519674
MA0259.12.40872
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#90536.336201576962630.003930750035764890.0189732219339672
E2F1#186934.907389214879320.008460985347239390.0324718645015373
E2F4#1874312.66806031528440.0004917987006298980.00436537179118528
E2F6#187635.017155731697390.00791769806886330.0321532183145662
ELF1#199734.258097958807540.01295179875054610.0461348195671311
MAX#414936.452555509007120.003721913834265510.0186281189886833
MYC#460935.22228187160940.007020843755740150.0294017362767451
NANOG#79923329.24477848101273.99627955670032e-050.000736877543471443
NFKB1#479035.488063424193840.006049381815655430.0269248407178878
NRF1#4899312.21027944771090.0005492172401020010.00470585768635761
POU2F2#545239.106124057742520.001324165192682130.00881137231975336
SIN3A#2594235.408884726815140.006318961977991520.0276151171654304
TAF7#6879311.43306940492390.0006690181981945830.00541892287895487
THAP1#55145220.91276306856750.002983447413736940.0158641751664005
YY1#752834.911170749853860.008441455341808260.032874082871322
ZNF143#7702313.50087655222790.0004062804962997170.00388567113123133



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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