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Coexpression cluster:C2428: Difference between revisions

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{{Coexpression_clusters
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hormone receptor activity!0.00364664345425225!8013;4929$GO:0004879!ligand-dependent nuclear receptor activity!0.00364664345425225!8013;4929$GO:0042053!regulation of dopamine metabolic process!0.0106843266182394!4929$GO:0042069!regulation of catecholamine metabolic process!0.0106843266182394!4929$GO:0004887!thyroid hormone receptor activity!0.0195838960000424!8013$GO:0042417!dopamine metabolic process!0.0195838960000424!4929$GO:0016070!RNA metabolic process!0.0284680595302614!1655;8013;4929$GO:0043565!sequence-specific DNA binding!0.0284680595302614!8013;4929$GO:0006584!catecholamine metabolic process!0.0284680595302614!4929$GO:0018958!phenol metabolic process!0.0284680595302614!4929$GO:0003724!RNA helicase activity!0.0284680595302614!1655$GO:0042133!neurotransmitter metabolic process!0.0284680595302614!4929$GO:0010467!gene expression!0.038496700016013!1655;8013;4929$GO:0006139!nucleobase, nucleoside, nucleotide and nucleic acid metabolic process!0.0428660141712666!1655;8013;4929$GO:0003700!transcription factor activity!0.0428660141712666!8013;4929$GO:0005634!nucleus!0.0428660141712666!1655;8013;4929$GO:0006576!biogenic amine metabolic process!0.0437664922796501!4929$GO:0003676!nucleic acid binding!0.0437664922796501!1655;8013;4929$GO:0001505!regulation of neurotransmitter levels!0.0437664922796501!4929$GO:0065007!biological regulation!0.0456741439377732!1655;8013;4929$GO:0006575!amino acid derivative metabolic 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|full_id=C2428_Mast_CD14_Eosinophils_immature_CD19_CD4_CD8
|id=C2428
}}

Latest revision as of 12:05, 17 September 2013


Full id: C2428_Mast_CD14_Eosinophils_immature_CD19_CD4_CD8



Phase1 CAGE Peaks

Hg19::chr17:62502942..62502965,-p6@DDX5
Hg19::chr2:157189180..157189290,-p1@NR4A2
Hg19::chr2:157189298..157189305,-p23@NR4A2
Hg19::chr9:102584128..102584144,+p3@NR4A3


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:0003707steroid hormone receptor activity0.00364664345425225
GO:0004879ligand-dependent nuclear receptor activity0.00364664345425225
GO:0042053regulation of dopamine metabolic process0.0106843266182394
GO:0042069regulation of catecholamine metabolic process0.0106843266182394
GO:0004887thyroid hormone receptor activity0.0195838960000424
GO:0042417dopamine metabolic process0.0195838960000424
GO:0016070RNA metabolic process0.0284680595302614
GO:0043565sequence-specific DNA binding0.0284680595302614
GO:0006584catecholamine metabolic process0.0284680595302614
GO:0018958phenol metabolic process0.0284680595302614
GO:0003724RNA helicase activity0.0284680595302614
GO:0042133neurotransmitter metabolic process0.0284680595302614
GO:0010467gene expression0.038496700016013
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0428660141712666
GO:0003700transcription factor activity0.0428660141712666
GO:0005634nucleus0.0428660141712666
GO:0006576biogenic amine metabolic process0.0437664922796501
GO:0003676nucleic acid binding0.0437664922796501
GO:0001505regulation of neurotransmitter levels0.0437664922796501
GO:0065007biological regulation0.0456741439377732
GO:0006575amino acid derivative metabolic process0.0456741439377732



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
myeloid leukocyte5.32e-2572
classical monocyte1.13e-2442
CD14-positive, CD16-negative classical monocyte1.13e-2442
leukocyte2.92e-24136
defensive cell1.55e-2248
phagocyte1.55e-2248
granulocyte monocyte progenitor cell6.83e-2267
macrophage dendritic cell progenitor1.46e-1961
myeloid lineage restricted progenitor cell8.04e-1966
hematopoietic stem cell2.36e-18168
angioblastic mesenchymal cell2.36e-18168
monopoietic cell2.41e-1859
monocyte2.41e-1859
monoblast2.41e-1859
promonocyte2.41e-1859
hematopoietic lineage restricted progenitor cell1.12e-17120
nongranular leukocyte9.99e-17115
myeloid cell1.86e-16108
common myeloid progenitor1.86e-16108
hematopoietic oligopotent progenitor cell3.47e-16161
hematopoietic multipotent progenitor cell3.47e-16161
hematopoietic cell8.28e-16177
stuff accumulating cell5.49e-0887
Uber Anatomy
Ontology termp-valuen
bone marrow1.54e-1776
bone element3.44e-1782
hematopoietic system1.14e-1598
blood island1.14e-1598
skeletal element9.33e-1490
skeletal system6.82e-13100
immune system1.55e-1293
hemolymphoid system1.10e-11108
adult organism8.80e-11114


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)
MA0003.10.720743
MA0004.10.71247
MA0006.11.31813
MA0007.10.6918
MA0009.11.20602
MA0014.10.896009
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.12.49947
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.709734
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.396851
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.11.80156
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.866596
MA0074.11.91637
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.11.54523
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.11.15856
MA0117.12.78257
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.12.17614
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.11.09982
MA0145.11.08195
MA0146.10.221129
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.931615
MA0035.20.778873
MA0039.20.0247757
MA0138.20.928035
MA0002.20.379056
MA0137.21.37305
MA0104.20.392359
MA0047.20.856092
MA0112.21.65877
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.640035
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.23.34398
MA0099.20.7872
MA0079.20.327251
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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#672315.13817298241780.0004682184421431190.00430119323414418
CCNT2#90546.336201576962630.0006203100587215640.00512049970145601
CTBP2#1488231.35850016966410.001492676882047230.00954003309981829
E2F1#186944.907389214879320.001724022357361790.010647851625104
E2F4#187439.501045236463330.001850751034728270.0109271630570403
E2F6#187645.017155731697390.00157802193473060.0099665597993063
ELF1#199744.258097958807540.003041525565781240.0160845556010242
ELK4#2005312.1767612438510.0008912632577620610.00663738187231973
ETS1#211337.296570691651750.00400857377511390.0192041943348221
FOXA1#3169411.08141974938556.62943068949433e-050.00107029078958123
GABPB1#255335.300762877136630.01012678824234270.0378577383842944
HEY1#2346244.040111043105710.00375304636917980.0185959014019722
IRF1#365947.63716375356390.0002938853996185490.00307392060598514
MAX#414934.839416631755340.01315737137836840.0466190361441652
MYC#460945.22228187160940.001344309395272740.00887417539554322
NFYA#4800313.81918552487290.0006132411806734510.00508707670121959
NFYB#4801312.56984494015230.000811456397697350.0061886734861336
RFX5#599339.035933120396320.002144561191324070.0123846185380533
SETDB1#9869220.16001308900520.00356908685407640.0180842160854301
SIN3A#2594245.408884726815140.001168172384885160.00795946997031712
SP1#666745.69838137814090.0009482606065333980.00683851605342781
TAF1#687243.343046285745290.008005664898701650.0322061413795887
TBP#690843.706770687096390.005296377814784350.024408631303427
TCF7L2#6934410.77017656313737.42969445082454e-050.00115400038481509
USF1#739146.361499277207960.0006105011399140830.00507846503795197
YY1#752844.911170749853860.00171871838055440.0106814179676716



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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