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Coexpression cluster:C2175: Difference between revisions

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|tf_chipseq_enrich=HNF4A#3172;2:11.5661451814768:0.0105758568176249:0.0390625233475714
|tf_chipseq_enrich=HNF4A#3172;2:11.5661451814768:0.0105758568176249:0.0390625233475714
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|tfbs_overrepresentation_for_novel_motifs=0.590005,0.620826,0.581696,0.741427,1.32255,0.739643,0.821651,0.395818,1.01802,0.151681,0.706765,0.867962,0.341754,0.809319,0.532789,0.559384,1.05593,0.471262,0.356737,0.223552,0.581762,0.505745,0.731221,0.528529,0.632849,0.892087,0.316693,0.728867,0.537869,0.806311,0.682839,1.09415,0.433165,0.344471,0.49475,0.0842336,0.491074,0.740899,0.463978,0.971732,0.493145,0.66492,0.539378,0.53106,1.08066,0.61613,0.822818,0.694903,0.515703,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.806003,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,1.03936,0.248021,1.32819,0.336329,0.859396,0.305238,1.00941,1.08,0.62601,0.95118,1.02594,1.96757,0.399165,1.27559,0.109222,0.221873,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,2.0177,0.934671,1.15558,0.939507,1.37313,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,0.12452,0.681522,0.988625,1.1313,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,1.62065,0.729481,1.48509,2.34913,1.94535,3.19017,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,1.23342,0.175846,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,1.08488,0.820225,0.0401987
}}
}}

Revision as of 15:20, 26 November 2012


Full id: C2175_CD14_CD14CD16_splenic_migratory_Peripheral_Basophils_Whole



Phase1 CAGE Peaks

Hg19::chr12:10124110..10124121,+p2@CLEC12A
Hg19::chr4:38080384..38080414,+p@chr4:38080384..38080414
+
Hg19::chr5:54070798..54070804,+p@chr5:54070798..54070804
+
Hg19::chr9:136343729..136343751,-p4@SLC2A6


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:0005355glucose transmembrane transporter activity0.0164759143109795
GO:0015149hexose transmembrane transporter activity0.0164759143109795
GO:0015145monosaccharide transmembrane transporter activity0.0164759143109795
GO:0005351sugar:hydrogen ion symporter activity0.022368731471487
GO:0051119sugar transmembrane transporter activity0.022368731471487
GO:0015144carbohydrate transmembrane transporter activity0.022368731471487
GO:0008643carbohydrate transport0.022368731471487
GO:0015293symporter activity0.0425894721577773



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
monopoietic cell2.35e-8159
monocyte2.35e-8159
monoblast2.35e-8159
promonocyte2.35e-8159
myeloid leukocyte3.49e-7972
macrophage dendritic cell progenitor4.32e-7861
myeloid lineage restricted progenitor cell1.03e-7566
defensive cell1.00e-7448
phagocyte1.00e-7448
granulocyte monocyte progenitor cell2.66e-7467
classical monocyte2.97e-6942
CD14-positive, CD16-negative classical monocyte2.97e-6942
leukocyte7.17e-66136
nongranular leukocyte3.93e-63115
myeloid cell9.13e-57108
common myeloid progenitor9.13e-57108
hematopoietic lineage restricted progenitor cell1.03e-56120
hematopoietic stem cell6.69e-53168
angioblastic mesenchymal cell6.69e-53168
hematopoietic oligopotent progenitor cell4.86e-51161
hematopoietic multipotent progenitor cell4.86e-51161
hematopoietic cell3.08e-50177
stuff accumulating cell2.26e-3587
intermediate monocyte1.49e-169
CD14-positive, CD16-positive monocyte1.49e-169
mesenchymal cell1.24e-14354
connective tissue cell6.82e-14361
motile cell8.03e-12386
multi fate stem cell3.38e-09427
stem cell3.59e-09441
somatic stem cell9.20e-09433
conventional dendritic cell1.57e-078
macrophage4.72e-076
non-classical monocyte8.67e-073
CD14-low, CD16-positive monocyte8.67e-073
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.73e-7198
blood island2.73e-7198
hemolymphoid system6.82e-71108
immune system2.73e-6693
bone marrow2.91e-6376
bone element3.03e-5782
skeletal element1.80e-5090
skeletal system3.76e-45100
lateral plate mesoderm8.74e-29203
musculoskeletal system1.77e-20167
mesoderm1.20e-13315
mesoderm-derived structure1.20e-13315
presumptive mesoderm1.20e-13315
connective tissue2.00e-13371


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
HNF4A#3172211.56614518147680.01057585681762490.0390625233475714



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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