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Coexpression cluster:C3380: Difference between revisions

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|tf_chipseq_enrich=BRCA1#672;2:13.4561537621492:0.00711980771608456:0.0296131261672702!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.032421825304727!EBF1#1879;3:8.906466846569:0.0014152328356098:0.0091333808390442!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0319648810766322!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0460860927978019!FOSL2#2355;2:11.2868004030411:0.010053458697312:0.0376617946443044!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.015380276376548!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0127784512065288!USF1#7391;3:6.36149927720796:0.0038840405729056:0.018981998754969
|tf_chipseq_enrich=BRCA1#672;2:13.4561537621492:0.00711980771608456:0.0296131261672702!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.032421825304727!EBF1#1879;3:8.906466846569:0.0014152328356098:0.0091333808390442!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0319648810766322!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0460860927978019!FOSL2#2355;2:11.2868004030411:0.010053458697312:0.0376617946443044!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.015380276376548!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0127784512065288!USF1#7391;3:6.36149927720796:0.0038840405729056:0.018981998754969
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2548,0.175934,0.157274,0.215705,0.252796,0.205954,0.361435
|tfbs_overrepresentation_for_novel_motifs=0.699513,0.869629,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.63186,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.680949,0.845342,0.635379,0.743951,1.00973,1.05396,0.842925,2.63304,1.00813,0.795576,1.21459,0.534793,0.439574,0.599922,0.137917,1.45286,0.855276,1.39264,0.469078,0.598234,0.777097,0.259059,0.63803,0.901413,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.893117,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,3.32688,1.45054,1.92922,1.87308,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,0.977977,0.303648,0.993996,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,1.54991,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,1.66424,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,3.66389,1.37083,1.21015,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.56135
}}
}}

Revision as of 16:06, 26 November 2012


Full id: C3380_Eosinophils_CD14_Mast_Neutrophils_CD19_CD14CD16_CD34



Phase1 CAGE Peaks

Hg19::chr13:50698820..50698842,+p@chr13:50698820..50698842
+
Hg19::chr6:32163757..32163854,+p@chr6:32163757..32163854
+
Hg19::chr8:12613275..12613329,+p@chr8:12613275..12613329
+


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
leukocyte1.89e-41136
hematopoietic cell2.85e-36177
hematopoietic stem cell1.76e-35168
angioblastic mesenchymal cell1.76e-35168
hematopoietic lineage restricted progenitor cell3.13e-33120
nongranular leukocyte7.69e-33115
hematopoietic oligopotent progenitor cell3.11e-32161
hematopoietic multipotent progenitor cell3.11e-32161
myeloid leukocyte3.68e-2372
classical monocyte6.63e-2042
CD14-positive, CD16-negative classical monocyte6.63e-2042
granulocyte monocyte progenitor cell1.07e-1967
defensive cell6.16e-1848
phagocyte6.16e-1848
myeloid lineage restricted progenitor cell1.07e-1766
macrophage dendritic cell progenitor1.32e-1761
myeloid cell1.97e-17108
common myeloid progenitor1.97e-17108
monopoietic cell1.11e-1659
monocyte1.11e-1659
monoblast1.11e-1659
promonocyte1.11e-1659
lymphocyte2.80e-1453
common lymphoid progenitor2.80e-1453
lymphoid lineage restricted progenitor cell2.90e-1452
nucleate cell1.21e-1355
mature alpha-beta T cell3.19e-0918
alpha-beta T cell3.19e-0918
immature T cell3.19e-0918
mature T cell3.19e-0918
immature alpha-beta T cell3.19e-0918
stuff accumulating cell1.94e-0887
T cell3.58e-0825
pro-T cell3.58e-0825
B cell1.43e-0714
intermediate monocyte2.01e-079
CD14-positive, CD16-positive monocyte2.01e-079
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.59e-2498
blood island1.59e-2498
hemolymphoid system6.13e-20108
bone marrow1.43e-1876
bone element3.98e-1782
immune system1.52e-1493
skeletal element1.84e-1490
lateral plate mesoderm1.26e-12203
skeletal system4.00e-11100
blood3.69e-0715
haemolymphatic fluid3.69e-0715
organism substance3.69e-0715


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
BRCA1#672213.45615376214920.007119807716084560.0296131261672702
E2F1#186934.907389214879320.008460985347239390.032421825304727
EBF1#187938.9064668465690.00141523283560980.0091333808390442
EGR1#195834.988179094810140.008056488137383440.0319648810766322
ELF1#199734.258097958807540.01295179875054610.0460860927978019
FOSL2#2355211.28680040304110.0100534586973120.0376617946443044
GABPB1#255337.067683836182170.002832212825417420.015380276376548
IRF1#365937.63716375356390.002244692747297240.0127784512065288
USF1#739136.361499277207960.00388404057290560.018981998754969



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.