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Coexpression cluster:C4818: Difference between revisions

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{{Coexpression_clusters
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|full_id=C4818_Eosinophils_Neutrophils_CD19_CD14_Dendritic_CD8_Natural
|id=C4818
}}

Latest revision as of 14:20, 17 September 2013


Full id: C4818_Eosinophils_Neutrophils_CD19_CD14_Dendritic_CD8_Natural



Phase1 CAGE Peaks

Hg19::chr9:33167255..33167266,-p6@B4GALT1
Hg19::chr9:33167293..33167307,-p5@B4GALT1
Hg19::chr9:33167308..33167378,-p2@B4GALT1


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

No GOStat results

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
leukocyte1.13e-18136
myeloid leukocyte8.87e-1772
nongranular leukocyte1.74e-15115
classical monocyte1.25e-1342
CD14-positive, CD16-negative classical monocyte1.25e-1342
hematopoietic lineage restricted progenitor cell1.43e-13120
defensive cell2.45e-1348
phagocyte2.45e-1348
granulocyte monocyte progenitor cell4.24e-1267
monopoietic cell4.70e-1259
monocyte4.70e-1259
monoblast4.70e-1259
promonocyte4.70e-1259
myeloid lineage restricted progenitor cell2.18e-1166
macrophage dendritic cell progenitor2.75e-1161
animal cell1.87e-10679
eukaryotic cell1.87e-10679
somatic cell9.11e-10588
epithelial cell6.64e-09253
native cell1.23e-07722
hematopoietic stem cell1.35e-07168
angioblastic mesenchymal cell1.35e-07168
stuff accumulating cell4.85e-0787
hematopoietic cell5.33e-07177
hematopoietic oligopotent progenitor cell6.64e-07161
hematopoietic multipotent progenitor cell6.64e-07161
Uber Anatomy
Ontology termp-valuen
lateral plate mesoderm2.72e-16203
hemolymphoid system2.11e-12108
hematopoietic system1.98e-1198
blood island1.98e-1198
immune system2.11e-1093
bone marrow2.90e-1076
mesoderm5.03e-09315
mesoderm-derived structure5.03e-09315
presumptive mesoderm5.03e-09315
bone element2.95e-0882
skeletal element3.61e-0890
epithelial tube4.14e-07117


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)
MA0003.16.06693
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.14.7105
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
MA0057.10.886807
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.11.15625
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.12.75836
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0834661
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
MA0092.11.84783
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.14.18141
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
MA0145.10.752137
MA0146.11.70974
MA0147.11.38767
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.210.6428
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.731309
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.11.51687
MA0155.11.31345
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.15.21222
MA0163.11.84145
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.212.3219
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#90536.336201576962630.003930750035764890.0191413066156222
CTCF#1066435.360256373075030.0064925092527670.0281754829988255
E2F1#186934.907389214879320.008460985347239390.0328216338699378
E2F6#187635.017155731697390.00791769806886330.0324764931511277
EGR1#195834.988179094810140.008056488137383440.0322887127126977
ELF1#199734.258097958807540.01295179875054610.0465379794160973
HMGN3#932438.178547723350590.001827766942164210.0109361301445253
IRF1#365937.63716375356390.002244692747297240.0128852075318774
MAX#414936.452555509007120.003721913834265510.0187602779409679
MYC#460935.22228187160940.007020843755740150.0296454233446166
NRF1#4899312.21027944771090.0005492172401020010.00473929598769007
PAX5#507936.669565531177830.003370290999677260.017378780572494
RAD21#5885310.35503389545630.0009004912073565420.00669560025666452
SIN3A#2594235.408884726815140.006318961977991520.0278587559635044
SP1#666735.69838137814090.005403962701712170.024815743771891
SPI1#668838.204323508522730.001810593189410520.0109487894220859
TFAP2A#7020316.5186343730450.0002218033880766340.00249837403444085
TFAP2C#7022310.80922860986020.0007916746575753130.00619663565633726
YY1#752834.911170749853860.008441455341808260.0331559666958673
ZBTB7A#5134137.35190930787590.002516255860282270.0141098118546051
ZNF263#1012738.221841637010680.001799043925565870.0110257818521316



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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