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Coexpression cluster:C1131: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;6:4.59450546263574:0.000247839207568764:0.00267452769159683!THAP1#55145;5:22.4065318591795:6.54085242188212e-07:2.9649309292055e-05!YY1#7528;5:3.50797910703847:0.00507257067280898:0.0236105806443309
|tf_chipseq_enrich=CTCF#10664;6:4.59450546263574:0.000247839207568764:0.00267452769159683!THAP1#55145;5:22.4065318591795:6.54085242188212e-07:2.9649309292055e-05!YY1#7528;5:3.50797910703847:0.00507257067280898:0.0236105806443309
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|tfbs_overrepresentation_for_novel_motifs=1.79738,0.75236,0.384703,0.529489,0.343148,0.52784,0.604235,0.226729,0.224331,3.41696,0.497563,0.647852,0.541517,0.592674,0.341795,0.365029,0.827563,0.28906,0.19568,0.0986842,0.384762,0.0646572,0.520063,0.338096,0.430372,0.670692,0.957451,0.517892,2.47668,0.150685,0.475674,0.864517,0.257226,0.186138,0.309012,0.71891,0.305874,0.529001,0.282922,1.7673,0.307642,0.459366,0.0729319,0.340293,0.265117,0.415364,0.60533,0.486696,0.0670664,0.915545,0.684981,0.617179,0.117127,0.941629,1.09491,0.595623,0.350547,0.562713,0.150585,0.561701,0.905643,0.60771,0.638689,0.799729,0.625758,0.76514,1.18348,1.55228,0.854088,1.38987,1.13397,0.232216,4.65558,1.0929,0.531388,1.54605,0.156354,0.782748,0.850825,1.0864,0.200147,0.798651,0.625403,0.229431,1.04131,6.88016,0.097572,6.0778,0.711163,1.65172,1.27705,1.01423,0.881388,0.26423,0.343884,0.277058,1.07593,0.924148,1.70279,0.132387,1.41651,0.875714,0.918549,0.831244,0.753567,0.493026,0.815341,0.589207,0.43012,0.873303,0.395884,0.915771,0.379203,0.507004,1.22894,0.304323,2.44333,0.474472,0.762789,0.26701,1.0846,0.708722,0.525076,0.636741,1.33983,0.783512,1.45665,0.886402,1.12733,0.27799,1.01492,0.47854,1.14174,0.633392,1.28996,1.37933,0.469685,0.518459,1.24743,2.10682,1.70417,1.21002,0.59959,0.920609,0.755332,0.554217,0.738579,1.94751,0.456039,0.26104,0.106334,6.8703,1.0153,1.16378,0.607223,1.42052,0.694887,0.329354,0.430431,0.401655,1.2088,0.996724,0.850033,0.404861,0.7715,0.624608,0.695791,0.602897,0.00626991
}}
}}

Revision as of 14:42, 26 November 2012


Full id: C1131_skeletal_salivary_lung_adipose_mature_vagina_aorta



Phase1 CAGE Peaks

Hg19::chr11:113930291..113930339,+p2@ZBTB16
Hg19::chr11:113930355..113930366,+p5@ZBTB16
Hg19::chr11:113930401..113930422,+p3@ZBTB16
Hg19::chr11:113930425..113930471,+p1@ZBTB16
Hg19::chr11:113930477..113930488,+p4@ZBTB16
Hg19::chr11:113986083..113986087,+p@chr11:113986083..113986087
+
Hg19::chr11:114037970..114037982,+p@chr11:114037970..114037982
+


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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
adult organism1.38e-57114
neural tube4.90e-2756
neural rod4.90e-2756
future spinal cord4.90e-2756
neural keel4.90e-2756
regional part of nervous system3.15e-2553
regional part of brain3.15e-2553
neurectoderm5.68e-2386
neural plate5.73e-2282
presumptive neural plate5.73e-2282
brain5.08e-2168
future brain5.08e-2168
regional part of forebrain3.09e-2041
forebrain3.09e-2041
anterior neural tube3.09e-2041
future forebrain3.09e-2041
central nervous system1.26e-1981
nervous system6.23e-1789
structure with developmental contribution from neural crest7.92e-17132
brain grey matter2.57e-1634
gray matter2.57e-1634
telencephalon2.73e-1634
regional part of telencephalon3.28e-1532
cerebral hemisphere5.55e-1532
ecto-epithelium6.93e-15104
organ system subdivision8.56e-15223
pre-chordal neural plate9.54e-1561
regional part of cerebral cortex2.35e-1422
ectoderm-derived structure2.62e-13171
ectoderm2.62e-13171
presumptive ectoderm2.62e-13171
neocortex6.71e-1320
cerebral cortex1.53e-1125
pallium1.53e-1125
multi-tissue structure8.70e-11342
anatomical cluster6.64e-09373
posterior neural tube5.83e-0815
chordal neural plate5.83e-0815
anatomical conduit1.53e-07240
segmental subdivision of nervous system4.67e-0713


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
CTCF#1066464.594505462635740.0002478392075687640.00267452769159683
THAP1#55145522.40653185917956.54085242188212e-072.9649309292055e-05
YY1#752853.507979107038470.005072570672808980.0236105806443309



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.