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Coexpression cluster:C2495: Difference between revisions

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|tf_chipseq_enrich=BATF#10538;2:12.1789008961518:0.00956675880504781:0.0360181226690839!BCL11A#53335;3:21.2770913277053:0.000170483911460614:0.00208125882279778!BCLAF1#9774;2:10.8263238050609:0.0120220381643258:0.0436552847204207!CEBPB#1051;3:5.97836071936861:0.00715383248472697:0.0297285974404106!CHD2#1106;3:7.75801712558764:0.00335152246453634:0.0172973737237454!JUND#3727;3:5.24599795640327:0.0104343275174842:0.0386930383325711!TFAP2A#7020;3:12.3889757797837:0.00084694130358843:0.00638009974072937!TFAP2C#7022;3:8.10692145739517:0.00294701173986644:0.0157168441556407
|tf_chipseq_enrich=BATF#10538;2:12.1789008961518:0.00956675880504781:0.0360181226690839!BCL11A#53335;3:21.2770913277053:0.000170483911460614:0.00208125882279778!BCLAF1#9774;2:10.8263238050609:0.0120220381643258:0.0436552847204207!CEBPB#1051;3:5.97836071936861:0.00715383248472697:0.0297285974404106!CHD2#1106;3:7.75801712558764:0.00335152246453634:0.0172973737237454!JUND#3727;3:5.24599795640327:0.0104343275174842:0.0386930383325711!TFAP2A#7020;3:12.3889757797837:0.00084694130358843:0.00638009974072937!TFAP2C#7022;3:8.10692145739517:0.00294701173986644:0.0157168441556407
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|tfbs_overrepresentation_for_novel_motifs=0.590005,0.0888524,0.581696,0.741427,0.534346,0.739643,0.821651,0.395818,0.392841,0.151681,0.706765,2.01638,0.905351,0.809319,0.532789,0.559384,1.05593,1.18793,0.356737,0.635753,0.581762,0.975621,0.731221,0.528529,0.632849,0.892087,0.316693,0.728867,0.537869,0.806311,0.682839,1.09415,1.10579,0.344471,1.23824,0.0842336,1.23038,0.740899,0.463978,0.971732,0.493145,0.66492,0.183156,0.53106,0.314427,0.61613,0.822818,0.694903,0.173425,0.538016,0.90714,0.83543,0.699149,1.17354,1.33024,0.812467,0.54284,1.82985,0.297448,0.776148,1.13655,1.92893,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,1.03936,0.248021,1.32819,0.893276,0.321165,0.305238,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,1.03184,1.27559,1.17995,0.6318,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,1.15724,0.934671,1.15558,0.939507,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,0.393155,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.774456,0.676268,1.73115,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,0.66252,0.175846,1.24902,0.997363,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,1.4289
}}
}}

Revision as of 15:32, 26 November 2012


Full id: C2495_Neutrophils_CD14_Eosinophils_immature_Natural_CD8_Peripheral



Phase1 CAGE Peaks

Hg19::chr19:49378898..49378909,+p@chr19:49378898..49378909
+
Hg19::chr1:184942789..184942813,-p@chr1:184942789..184942813
-
Hg19::chr21:46294651..46294656,+p@chr21:46294651..46294656
+
Hg19::chr9:95895999..95896035,-p@chr9:95895999..95896035
-


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
leukocyte3.95e-65136
classical monocyte6.28e-6042
CD14-positive, CD16-negative classical monocyte6.28e-6042
myeloid leukocyte3.71e-5972
hematopoietic stem cell9.36e-52168
angioblastic mesenchymal cell9.36e-52168
defensive cell3.06e-5148
phagocyte3.06e-5148
granulocyte monocyte progenitor cell1.38e-4867
hematopoietic cell2.40e-48177
hematopoietic lineage restricted progenitor cell4.63e-48120
nongranular leukocyte1.77e-46115
macrophage dendritic cell progenitor1.24e-4561
hematopoietic oligopotent progenitor cell7.92e-45161
hematopoietic multipotent progenitor cell7.92e-45161
myeloid lineage restricted progenitor cell7.88e-4466
monopoietic cell1.08e-4159
monocyte1.08e-4159
monoblast1.08e-4159
promonocyte1.08e-4159
myeloid cell1.12e-39108
common myeloid progenitor1.12e-39108
stuff accumulating cell4.32e-2487
mesenchymal cell1.86e-16354
granulocyte2.09e-168
connective tissue cell7.68e-16361
motile cell2.10e-14386
blood cell1.31e-1111
multi fate stem cell4.91e-11427
somatic stem cell1.13e-10433
stem cell3.32e-10441
neutrophil1.77e-093
natural killer cell5.01e-093
pro-NK cell5.01e-093
single nucleate cell8.81e-093
mononuclear cell8.81e-093
basophil1.70e-083
Uber Anatomy
Ontology termp-valuen
bone marrow4.63e-4476
bone element4.53e-4082
hematopoietic system4.90e-4098
blood island4.90e-4098
skeletal element1.42e-3590
hemolymphoid system2.91e-35108
immune system4.37e-3493
skeletal system5.81e-31100
lateral plate mesoderm3.03e-15203
connective tissue5.32e-15371
musculoskeletal system2.11e-14167
mesoderm4.77e-08315
mesoderm-derived structure4.77e-08315
presumptive mesoderm4.77e-08315


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#10538212.17890089615180.009566758805047810.0360181226690839
BCL11A#53335321.27709132770530.0001704839114606140.00208125882279778
BCLAF1#9774210.82632380506090.01202203816432580.0436552847204207
CEBPB#105135.978360719368610.007153832484726970.0297285974404106
CHD2#110637.758017125587640.003351522464536340.0172973737237454
JUND#372735.245997956403270.01043432751748420.0386930383325711
TFAP2A#7020312.38897577978370.000846941303588430.00638009974072937
TFAP2C#702238.106921457395170.002947011739866440.0157168441556407



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.