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Coexpression cluster:C3899: Difference between revisions

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|tf_chipseq_enrich=BCL11A#53335;3:28.3694551036071:4.37778126761649e-05:0.000777966816077247!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0269731199011757!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0173001976661405!POU2F2#5452;3:9.10612405774252:0.00132416519268213:0.00882599327069557!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00629627361865637
|tf_chipseq_enrich=BCL11A#53335;3:28.3694551036071:4.37778126761649e-05:0.000777966816077247!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0269731199011757!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0173001976661405!POU2F2#5452;3:9.10612405774252:0.00132416519268213:0.00882599327069557!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00629627361865637
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|tfbs_overrepresentation_for_novel_motifs=0.699513,0.14394,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.221898,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,1.14835,0.305559,0.69094,1.26332,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,0.843849,0.596053,0.855276,0.567465,0.469078,0.598234,0.777097,0.259059,2.6102,0.151453,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,0.430728,1.06461,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,0.169933,0.303648,2.64731,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,1.94007,1.58942,0.594137,0.188952,0.794219,1.10778,0.547323,1.44203,2.38853,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,0.250511,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.0768232
}}
}}

Revision as of 16:25, 26 November 2012


Full id: C3899_acute_Burkitt_diffuse_myelodysplastic_eye_occipital_brain



Phase1 CAGE Peaks

Hg19::chr1:167298384..167298412,+p3@POU2F1
Hg19::chr1:167298425..167298440,+p8@POU2F1
Hg19::chr1:167298449..167298461,+p9@POU2F1


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>disease_data<br>


Uber Anatomy
Ontology termp-valuen
telencephalon9.08e-3834
cerebral hemisphere1.83e-3732
regional part of forebrain1.43e-3541
forebrain1.43e-3541
anterior neural tube1.43e-3541
future forebrain1.43e-3541
regional part of telencephalon1.87e-3432
brain grey matter4.43e-3234
gray matter4.43e-3234
regional part of nervous system6.59e-3053
regional part of brain6.59e-3053
neural tube7.07e-2856
neural rod7.07e-2856
future spinal cord7.07e-2856
neural keel7.07e-2856
cerebral cortex1.68e-2725
pallium1.68e-2725
brain1.37e-2668
future brain1.37e-2668
central nervous system1.00e-2581
regional part of cerebral cortex1.88e-2522
neocortex4.60e-2520
pre-chordal neural plate1.76e-2361
nervous system3.19e-2289
neural plate4.91e-1882
presumptive neural plate4.91e-1882
neurectoderm8.11e-1786
adult organism1.04e-12114
ecto-epithelium1.58e-12104
corpus striatum2.97e-104
striatum2.97e-104
ventral part of telencephalon2.97e-104
future corpus striatum2.97e-104
structure with developmental contribution from neural crest8.24e-10132
gyrus1.54e-096
basal ganglion5.59e-099
nuclear complex of neuraxis5.59e-099
aggregate regional part of brain5.59e-099
collection of basal ganglia5.59e-099
cerebral subcortex5.59e-099
ectoderm-derived structure7.95e-09171
ectoderm7.95e-09171
presumptive ectoderm7.95e-09171
temporal lobe1.42e-086
organ system subdivision1.99e-08223
telencephalic nucleus2.26e-087
caudate-putamen5.67e-083
dorsal striatum5.67e-083
parietal lobe1.16e-075
occipital lobe1.37e-075
spleen3.05e-073
gastrointestinal system mesentery3.05e-073
stomach region3.05e-073
mesentery3.05e-073
gastrointestinal system serosa3.05e-073
mesentery of stomach3.05e-073
gut mesentery3.05e-073
dorsal mesentery3.05e-073
dorsal mesogastrium3.05e-073
peritoneal cavity3.05e-073
spleen primordium3.05e-073
Disease
Ontology termp-valuen
hematologic cancer6.75e-1451
immune system cancer6.75e-1451
lymphoma2.60e-0810
leukemia9.85e-0839
myeloid leukemia3.35e-0731


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
BCL11A#53335328.36945510360714.37778126761649e-050.000777966816077247
NFKB1#479035.488063424193840.006049381815655430.0269731199011757
PAX5#507936.669565531177830.003370290999677260.0173001976661405
POU2F2#545239.106124057742520.001324165192682130.00882599327069557
TCF12#6938310.63446490218640.0008313523990202070.00629627361865637



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.