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Coexpression cluster:C1473: Difference between revisions

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|tf_chipseq_enrich=ZBTB7A#51341;4:4.90127287191726:0.00407962811884375:0.019490063634048
|tf_chipseq_enrich=ZBTB7A#51341;4:4.90127287191726:0.00407962811884375:0.019490063634048
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|tfbs_overrepresentation_for_novel_motifs=1.97464,1.35536,0.436508,0.58616,0.393082,0.584466,0.662701,0.269608,0.267027,1.41135,0.553339,0.707204,0.635275,0.650887,0.391663,0.415981,0.889639,0.336106,0.236034,0.402028,0.436569,0.0880431,0.576478,0.387783,0.483957,0.730467,0.202389,0.574247,1.02557,0.547818,0.530785,0.92701,0.816912,1.19786,0.35719,0.909936,2.51365,0.585658,0.329602,0.69481,0.355745,0.513952,0.664116,0.390088,0.992846,1.18176,0.66382,0.542147,0.304272,0.396429,0.745008,0.675919,0.455399,1.00488,1.15929,0.653901,0.400834,0.62023,0.186533,0.619193,0.968558,0.666252,0.737866,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.275507,2.04216,1.15727,1.17153,0.594475,0.192925,0.84426,0.913168,1.20149,0.240887,0.86037,0.684313,0.749276,1.10535,0.406668,0.398737,0.536262,0.771626,1.71797,1.34233,1.07807,0.94406,0.30974,0.393853,0.32338,0.234532,0.987239,0.776336,0.166235,0.330999,0.938327,0.981588,0.893363,0.814675,1.35291,0.877269,0.647343,1.21459,0.982236,0.44815,0.978783,0.430775,0.563054,1.29401,0.352243,1.21803,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,0.324369,1.07876,1.32127,1.20639,0.692462,1.35529,0.999497,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,0.306342,0.424432,4.24288,1.07915,0.717973,0.665754,1.48627,0.755083,0.378604,0.484017,1.15112,1.27379,1.06043,0.912368,0.457485,0.83286,0.683502,0.29379,0.661335,0.0564726
}}
}}

Revision as of 14:55, 26 November 2012


Full id: C1473_CD4_cerebellum_thymus_neuroblastoma_CD8_Peripheral_caudate



Phase1 CAGE Peaks

Hg19::chr1:24829320..24829332,+p6@RCAN3
Hg19::chr1:24829340..24829375,+p4@RCAN3
Hg19::chr5:110560072..110560106,+p1@CAMK4
Hg19::chr5:110560211..110560222,+p6@CAMK4
Hg19::chr5:110574533..110574537,+p@chr5:110574533..110574537
+
Hg19::chr5:110576837..110576844,+p@chr5:110576837..110576844
+


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:0007270nerve-nerve synaptic transmission0.0432581913920992
GO:0004683calmodulin-dependent protein kinase activity0.0432581913920992



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
lymphocyte1.13e-1753
common lymphoid progenitor1.13e-1753
lymphoid lineage restricted progenitor cell2.75e-1752
T cell2.53e-1625
pro-T cell2.53e-1625
nucleate cell1.55e-1555
mature alpha-beta T cell1.24e-1318
alpha-beta T cell1.24e-1318
immature T cell1.24e-1318
mature T cell1.24e-1318
immature alpha-beta T cell1.24e-1318
CD8-positive, alpha-beta T cell6.73e-0911
leukocyte2.19e-07136
nongranular leukocyte4.56e-07115
Uber Anatomy
Ontology termp-valuen
adult organism5.07e-22114
nervous system6.88e-2289
central nervous system1.65e-2181
neural tube3.58e-2056
neural rod3.58e-2056
future spinal cord3.58e-2056
neural keel3.58e-2056
regional part of nervous system7.07e-1953
regional part of brain7.07e-1953
brain1.91e-1768
future brain1.91e-1768
neural plate4.43e-1682
presumptive neural plate4.43e-1682
regional part of forebrain2.26e-1441
forebrain2.26e-1441
anterior neural tube2.26e-1441
future forebrain2.26e-1441
ecto-epithelium2.51e-14104
neurectoderm9.97e-1486
ectoderm-derived structure2.58e-12171
ectoderm2.58e-12171
presumptive ectoderm2.58e-12171
organ system subdivision4.17e-12223
pre-chordal neural plate6.97e-1261
brain grey matter1.37e-1134
gray matter1.37e-1134
telencephalon1.52e-1134
cerebral hemisphere6.73e-1132
regional part of telencephalon1.03e-1032
structure with developmental contribution from neural crest2.86e-09132
blood7.97e-0915
haemolymphatic fluid7.97e-0915
organism substance7.97e-0915
regional part of cerebral cortex4.24e-0822
neocortex4.29e-0820
cerebral cortex5.23e-0825
pallium5.23e-0825
posterior neural tube4.18e-0715
chordal neural plate4.18e-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
ZBTB7A#5134144.901272871917260.004079628118843750.019490063634048



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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