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Difference between revisions of "Coexpression cluster:C3063"

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|tf_chipseq_enrich=ATF3#467;2:14.9754496840058:0.00576829454079388:0.0259435387600005!BCLAF1#9774;2:14.4350984067479:0.00620114743554613:0.0273728502544802!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0185693860859339!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0268550279454747!SIX5#147912;2:11.391143570306:0.00987382008142903:0.0370579615296067!SMARCB1#6598;2:12.1684771874383:0.00867500222192174:0.0329697437065242!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.0108794972733931!TFAP2A#7020;2:11.0124229153633:0.0105499065521556:0.0389914958737555
 
|tf_chipseq_enrich=ATF3#467;2:14.9754496840058:0.00576829454079388:0.0259435387600005!BCLAF1#9774;2:14.4350984067479:0.00620114743554613:0.0273728502544802!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0185693860859339!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0268550279454747!SIX5#147912;2:11.391143570306:0.00987382008142903:0.0370579615296067!SMARCB1#6598;2:12.1684771874383:0.00867500222192174:0.0329697437065242!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.0108794972733931!TFAP2A#7020;2:11.0124229153633:0.0105499065521556:0.0389914958737555
 
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 +
|tfbs_overrepresentation_for_novel_motifs=0.699513,0.869629,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.63186,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.242883,0.845342,0.635379,0.743951,2.30584,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,1.46099,0.137917,0.596053,0.855276,0.567465,1.18324,0.598234,0.777097,0.259059,0.63803,0.151453,1.72524,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,4.3166,1.45054,0.430728,0.414196,0.396746,1.12884,1.20029,0.73687,1.16162,1.14559,0.960908,0.498519,1.39759,0.169933,0.303648,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,1.14422,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,1.90788,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,1.63757,0.830777,1.58942,0.594137,0.188952,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,1.8537,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,5.59159,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.265282
 
}}
 
}}

Revision as of 06:54, 26 November 2012


Full id: C3063_immature_Neutrophils_Eosinophils_CD14_Monocytederived_Whole_CD14CD16



Phase1 CAGE Peaks

  Short description
Hg19::chr10:97457405..97457451,+ p@chr10:97457405..97457451
+
Hg19::chr11:85956323..85956338,+ p7@EED
Hg19::chr11:85956340..85956357,+ p9@EED


Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
data


No GOStat results

Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset

cell_data
uberon_data


Cell Type
Ontology termp-valuen
leukocyte2.34e-55136
hematopoietic stem cell4.33e-52168
angioblastic mesenchymal cell4.33e-52168
hematopoietic cell1.49e-49177
hematopoietic oligopotent progenitor cell1.38e-48161
hematopoietic multipotent progenitor cell1.38e-48161
nongranular leukocyte4.39e-44115
myeloid leukocyte1.24e-4272
myeloid cell8.98e-42108
common myeloid progenitor8.98e-42108
macrophage dendritic cell progenitor1.88e-4161
hematopoietic lineage restricted progenitor cell5.28e-41120
monopoietic cell4.49e-3959
monocyte4.49e-3959
monoblast4.49e-3959
promonocyte4.49e-3959
defensive cell4.15e-3848
phagocyte4.15e-3848
granulocyte monocyte progenitor cell2.73e-3767
classical monocyte3.75e-3742
CD14-positive, CD16-negative classical monocyte3.75e-3742
myeloid lineage restricted progenitor cell1.02e-3566
stuff accumulating cell6.63e-1787
dendritic cell4.61e-1310
intermediate monocyte3.73e-119
CD14-positive, CD16-positive monocyte3.73e-119
conventional dendritic cell6.87e-118
mesenchymal cell2.86e-10354
connective tissue cell1.67e-09361
motile cell3.05e-09386
granulocyte5.20e-088
immature conventional dendritic cell6.02e-085
common dendritic progenitor6.02e-085
nucleate cell1.07e-0755
lymphocyte1.54e-0753
common lymphoid progenitor1.54e-0753
lymphoid lineage restricted progenitor cell5.07e-0752
Langerhans cell5.69e-075
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.17e-3898
blood island2.17e-3898
hemolymphoid system1.04e-33108
bone marrow1.82e-3076
bone element8.32e-2982
immune system1.34e-2793
skeletal element1.79e-2590
skeletal system5.40e-22100
lateral plate mesoderm2.09e-09203
connective tissue3.64e-09371
blood6.81e-0715
haemolymphatic fluid6.81e-0715
organism substance6.81e-0715


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
ATF3#467214.97544968400580.005768294540793880.0259435387600005
BCLAF1#9774214.43509840674790.006201147435546130.0273728502544802
MAX#414936.452555509007120.003721913834265510.0185693860859339
NFKB1#479035.488063424193840.006049381815655430.0268550279454747
SIX5#147912211.3911435703060.009873820081429030.0370579615296067
SMARCB1#6598212.16847718743830.008675002221921740.0329697437065242
SPI1#668838.204323508522730.001810593189410520.0108794972733931
TFAP2A#7020211.01242291536330.01054990655215560.0389914958737555



Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.