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Coexpression cluster:C806: Difference between revisions

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|tf_chipseq_enrich=BATF#10538;4:9.74312071692145:0.000488289084255501:0.00436650600826786!BCL11A#53335;3:8.51083653108212:0.00435985480765636:0.020670913213039!BHLHE40#8553;3:13.4615440640932:0.00118010821523276:0.0080073623889484!CCNT2#905;5:3.16810078848132:0.0122715766979429:0.0444794613297863!E2F6#1876;6:3.01029343901843:0.00625579584731478:0.0276047432185951!FOS#2353;8:7.19836424711553:8.49742894810215e-07:3.69160974172563e-05!HMGN3#9324;5:4.0892738616753:0.00403802327158728:0.0193337510870263!MAFK#7975;3:8.13021994134897:0.00495756569707518:0.0231619935509007!MAX#4149;5:3.22627775450356:0.0113549221837195:0.0416294000051069!NFE2#4778;5:38.6021303258145:8.66761903293144e-08:5.14339468284276e-06!NFKB1#4790;6:3.2928380545163:0.0039127525205927:0.0190687802378992!NRF1#4899;4:4.88411177908436:0.0063093473218055:0.0278269393978904!PAX5#5079;5:3.33478276558891:0.00985362449367583:0.0370300704722756!POLR2A#5430;10:2.14745317655807:0.000479337749163792:0.00436418404541167!USF1#7391;6:3.81689956632477:0.00178092866379164:0.0109275840854084!USF2#7392;5:6.4960986925348:0.000489096753205606:0.00437335409315413
|tf_chipseq_enrich=BATF#10538;4:9.74312071692145:0.000488289084255501:0.00436650600826786!BCL11A#53335;3:8.51083653108212:0.00435985480765636:0.020670913213039!BHLHE40#8553;3:13.4615440640932:0.00118010821523276:0.0080073623889484!CCNT2#905;5:3.16810078848132:0.0122715766979429:0.0444794613297863!E2F6#1876;6:3.01029343901843:0.00625579584731478:0.0276047432185951!FOS#2353;8:7.19836424711553:8.49742894810215e-07:3.69160974172563e-05!HMGN3#9324;5:4.0892738616753:0.00403802327158728:0.0193337510870263!MAFK#7975;3:8.13021994134897:0.00495756569707518:0.0231619935509007!MAX#4149;5:3.22627775450356:0.0113549221837195:0.0416294000051069!NFE2#4778;5:38.6021303258145:8.66761903293144e-08:5.14339468284276e-06!NFKB1#4790;6:3.2928380545163:0.0039127525205927:0.0190687802378992!NRF1#4899;4:4.88411177908436:0.0063093473218055:0.0278269393978904!PAX5#5079;5:3.33478276558891:0.00985362449367583:0.0370300704722756!POLR2A#5430;10:2.14745317655807:0.000479337749163792:0.00436418404541167!USF1#7391;6:3.81689956632477:0.00178092866379164:0.0109275840854084!USF2#7392;5:6.4960986925348:0.000489096753205606:0.00437335409315413
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}}
}}

Revision as of 14:29, 26 November 2012


Full id: C806_Melanocyte_CD14_Monocytederived_Macrophage_granulocyte_Mast_Eosinophils



Phase1 CAGE Peaks

Hg19::chr11:68816311..68816323,+p3@TPCN2
Hg19::chr11:68816334..68816353,+p2@TPCN2
Hg19::chr11:68816356..68816464,+p1@TPCN2
Hg19::chr14:93651358..93651412,+p1@C14orf109
Hg19::chr16:1524969..1525015,-p2@CLCN7
Hg19::chr1:2487325..2487330,+p15@TNFRSF14
Hg19::chr1:2487402..2487416,+p5@TNFRSF14
Hg19::chr1:2487548..2487559,+p11@TNFRSF14
Hg19::chr1:2487562..2487573,+p8@TNFRSF14
Hg19::chr4:3387396..3387446,+p4@RGS12


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:0022832voltage-gated channel activity0.0291262085968781
GO:0005244voltage-gated ion channel activity0.0291262085968781
GO:0005031tumor necrosis factor receptor activity0.0291262085968781
GO:0043120tumor necrosis factor binding0.0291262085968781
GO:0005035death receptor activity0.0291262085968781
GO:0022836gated channel activity0.0353237716946849
GO:0005216ion channel activity0.0400503140713481
GO:0022838substrate specific channel activity0.0400503140713481
GO:0022803passive transmembrane transporter activity0.0400503140713481
GO:0015267channel activity0.0400503140713481
GO:0000794condensed nuclear chromosome0.0401184445550083
GO:0008277regulation of G-protein coupled receptor protein signaling pathway0.0401184445550083
GO:0005247voltage-gated chloride channel activity0.0401184445550083
GO:0022844voltage-gated anion channel activity0.0401184445550083
GO:0016021integral to membrane0.0401184445550083
GO:0031224intrinsic to membrane0.0401184445550083
GO:0000793condensed chromosome0.0444359502873847
GO:0043168anion binding0.0458535690852464
GO:0031404chloride ion binding0.0458535690852464



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 leukocyte1.17e-4472
granulocyte monocyte progenitor cell1.06e-4067
macrophage dendritic cell progenitor2.01e-3961
myeloid lineage restricted progenitor cell4.30e-3966
monopoietic cell1.07e-3859
monocyte1.07e-3859
monoblast1.07e-3859
promonocyte1.07e-3859
defensive cell1.80e-3848
phagocyte1.80e-3848
classical monocyte1.15e-3342
CD14-positive, CD16-negative classical monocyte1.15e-3342
leukocyte2.38e-32136
myeloid cell3.39e-31108
common myeloid progenitor3.39e-31108
hematopoietic lineage restricted progenitor cell1.32e-26120
hematopoietic stem cell6.19e-26168
angioblastic mesenchymal cell6.19e-26168
hematopoietic cell7.61e-26177
nongranular leukocyte8.17e-26115
stuff accumulating cell1.43e-2587
hematopoietic oligopotent progenitor cell3.26e-24161
hematopoietic multipotent progenitor cell3.26e-24161
intermediate monocyte7.15e-089
CD14-positive, CD16-positive monocyte7.15e-089
Uber Anatomy
Ontology termp-valuen
hemolymphoid system7.38e-37108
hematopoietic system9.19e-3798
blood island9.19e-3798
immune system1.32e-3593
bone marrow4.81e-3576
bone element3.26e-3282
skeletal element4.35e-2790
skeletal system6.73e-21100
lateral plate mesoderm7.40e-14203
adult organism5.35e-09114


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)

{{{tfbs_overrepresentation_jaspar}}}



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
BATF#1053849.743120716921450.0004882890842555010.00436650600826786
BCL11A#5333538.510836531082120.004359854807656360.020670913213039
BHLHE40#8553313.46154406409320.001180108215232760.0080073623889484
CCNT2#90553.168100788481320.01227157669794290.0444794613297863
E2F6#187663.010293439018430.006255795847314780.0276047432185951
FOS#235387.198364247115538.49742894810215e-073.69160974172563e-05
HMGN3#932454.08927386167530.004038023271587280.0193337510870263
MAFK#797538.130219941348970.004957565697075180.0231619935509007
MAX#414953.226277754503560.01135492218371950.0416294000051069
NFE2#4778538.60213032581458.66761903293144e-085.14339468284276e-06
NFKB1#479063.29283805451630.00391275252059270.0190687802378992
NRF1#489944.884111779084360.00630934732180550.0278269393978904
PAX5#507953.334782765588910.009853624493675830.0370300704722756
POLR2A#5430102.147453176558070.0004793377491637920.00436418404541167
USF1#739163.816899566324770.001780928663791640.0109275840854084
USF2#739256.49609869253480.0004890967532056060.00437335409315413



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.