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Coexpression cluster:C2840

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Full id: C2840_retinoblastoma_embryonic_carcinoid_medulloblastoma_argyrophil_merkel_neuroblastoma



Phase1 CAGE Peaks

Hg19::chr6:119399805..119399860,-p1@FAM184A
Hg19::chr6:119399865..119399887,-p4@FAM184A
Hg19::chr6:119399895..119399915,-p3@FAM184A
Hg19::chr6:119399919..119399944,-p2@FAM184A


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
neural cell2.19e-0825
Uber Anatomy
Ontology termp-valuen
nervous system1.71e-4289
central nervous system1.46e-3981
adult organism1.01e-36114
neural tube2.28e-3556
neural rod2.28e-3556
future spinal cord2.28e-3556
neural keel2.28e-3556
regional part of nervous system1.03e-3353
regional part of brain1.03e-3353
brain9.38e-3268
future brain9.38e-3268
neurectoderm1.70e-2986
neural plate2.16e-2982
presumptive neural plate2.16e-2982
regional part of forebrain2.60e-2841
forebrain2.60e-2841
anterior neural tube2.60e-2841
future forebrain2.60e-2841
organ system subdivision9.85e-26223
pre-chordal neural plate1.83e-2461
ectoderm-derived structure5.37e-24171
ectoderm5.37e-24171
presumptive ectoderm5.37e-24171
brain grey matter2.03e-2334
gray matter2.03e-2334
telencephalon4.20e-2334
cerebral hemisphere4.08e-2232
regional part of telencephalon6.69e-2232
ecto-epithelium2.96e-21104
cerebral cortex1.81e-1725
pallium1.81e-1725
regional part of cerebral cortex1.87e-1622
structure with developmental contribution from neural crest1.47e-15132
neocortex4.07e-1520
anatomical cluster1.45e-11373
posterior neural tube2.90e-0815
chordal neural plate2.90e-0815
neural nucleus2.13e-079
nucleus of brain2.13e-079
basal ganglion2.39e-079
nuclear complex of neuraxis2.39e-079
aggregate regional part of brain2.39e-079
collection of basal ganglia2.39e-079
cerebral subcortex2.39e-079
segmental subdivision of nervous system2.66e-0713
multi-tissue structure5.72e-07342
tube8.15e-07192
segmental subdivision of hindbrain9.70e-0712
hindbrain9.70e-0712
presumptive hindbrain9.70e-0712


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
BHLHE40#8553444.87181354697742.46312701995675e-071.28687605221242e-05
CCNT2#90546.336201576962630.0006203100587215640.00513389034177205
CHD2#1106410.34402283411698.73193255208051e-050.00129336874742127
CTCF#1066445.360256373075030.001211145381643620.00819453307291256
CTCFL#140690419.74647435897446.5732084880439e-060.000193434579116037
E2F1#186944.907389214879320.001724022357361790.0106768958124115
E2F6#187645.017155731697390.00157802193473060.00998891040919625
HDAC2#3066413.41562023662633.0859005065161e-050.000628242423002017
HMGN3#932448.178547723350590.0002234570284440470.00248563516814015
MAX#414946.452555509007120.0005767613195645490.00486247783774636
SMC3#9126415.04493284493281.95092670935632e-050.000439406587445471
TAF1#687243.343046285745290.008005664898701650.0323206786638642
TBP#690843.706770687096390.005296377814784350.0244940177389303
ZBTB33#10009431.66472502998129.93721537730495e-074.20686192456567e-05
ZNF263#1012736.166381227758010.006539814347975980.0279922815855846



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.