Coexpression cluster:C397: Difference between revisions
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{{Coexpression_clusters | {{Coexpression_clusters | ||
|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.361440044784962,0.115335561311332,0.445699088960055,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.110593802369687,0,0.0310094911974069,0.0560798888033103,0,0,0.0519372574301261,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1.25967990925295,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.034807832411276,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0212213629697974,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 | |||
|full_id=C397_mesenchymal_Myoblast_rhabdomyosarcoma_Hepatic_Melanocyte_astrocytoma_Skeletal | |full_id=C397_mesenchymal_Myoblast_rhabdomyosarcoma_Hepatic_Melanocyte_astrocytoma_Skeletal | ||
|gostat_on_coexpression_clusters=GO:0042488!positive regulation of odontogenesis of dentine-containing teeth!0.0049452490286118!4804$GO:0048635!negative regulation of muscle development!0.0049452490286118!4804$GO:0005030!neurotrophin receptor activity!0.0049452490286118!4804$GO:0042482!positive regulation of odontogenesis!0.0049452490286118!4804$GO:0007517!muscle development!0.00510368093955047!4804;4617$GO:0042481!regulation of odontogenesis!0.00565146362241504!4804$GO:0048406!nerve growth factor binding!0.00565146362241504!4804$GO:0042487!regulation of odontogenesis of dentine-containing teeth!0.00659308309224691!4804$GO:0048634!regulation of muscle development!0.00659308309224691!4804$GO:0021675!nerve development!0.00719213669429478!4804$GO:0016048!detection of temperature stimulus!0.00719213669429478!4804$GO:0043121!neurotrophin binding!0.0082406260734007!4804$GO:0009887!organ morphogenesis!0.0084756982616971!4804;4617$GO:0043588!skin development!0.0084756982616971!4804$GO:0030054!cell junction!0.010513208766455!285489;5913$GO:0048704!embryonic skeletal morphogenesis!0.0109850757914487!4617$GO:0044459!plasma membrane part!0.0109850757914487!4804;285489;5913$GO:0005035!death receptor activity!0.0109850757914487!4804$GO:0048706!embryonic skeletal development!0.01285083614425!4617$GO:0001952!regulation of cell-matrix adhesion!0.01285083614425!4617$GO:0048705!skeletal morphogenesis!0.01412055080712!4617$GO:0001756!somitogenesis!0.016172306480016!4617$GO:0042475!odontogenesis of dentine-containing teeth!0.016327839596185!4804$GO:0005158!insulin receptor binding!0.0189383805889956!285489$GO:0042476!odontogenesis!0.0197582979184786!4804$GO:0035282!segmentation!0.0197582979184786!4617$GO:0003705!RNA polymerase II transcription factor activity, enhancer binding!0.0197582979184786!4617$GO:0009266!response to temperature stimulus!0.0204621440366349!4804$GO:0005886!plasma membrane!0.0278112583159776!4804;285489;5913$GO:0032501!multicellular organismal process!0.0278112583159776!4804;4617;5913$GO:0009582!detection of abiotic stimulus!0.0278112583159776!4804$GO:0030198!extracellular matrix organization and biogenesis!0.0278112583159776!4617$GO:0009653!anatomical structure morphogenesis!0.0278112583159776!4804;4617$GO:0009581!detection of external stimulus!0.0290268206664025!4804$GO:0009952!anterior/posterior pattern formation!0.0298661743075181!4617$GO:0048513!organ development!0.0298661743075181!4804;4617$GO:0007411!axon guidance!0.0298661743075181!4804$GO:0030155!regulation of cell adhesion!0.0338838289822843!4617$GO:0007519!skeletal muscle development!0.0338838289822843!4617$GO:0051093!negative regulation of developmental process!0.0379508218150131!4804$GO:0051606!detection of stimulus!0.0384626346065112!4804$GO:0043062!extracellular structure organization and biogenesis!0.0389706572423428!4617$GO:0003002!regionalization!0.0389706572423428!4617$GO:0014706!striated muscle development!0.0389706572423428!4617$GO:0019838!growth factor binding!0.0389706572423428!4804$GO:0048598!embryonic morphogenesis!0.0389876890311985!4617$GO:0009792!embryonic development ending in birth or egg hatching!0.0389876890311985!4617$GO:0043009!chordate embryonic development!0.0389876890311985!4617$GO:0007160!cell-matrix adhesion!0.0397702834627644!4617$GO:0032403!protein complex binding!0.0397702834627644!285489$GO:0031589!cell-substrate adhesion!0.0397702834627644!4617$GO:0048731!system development!0.0405695329663668!4804;4617$GO:0007409!axonogenesis!0.0423359748223512!4804$GO:0048667!neuron morphogenesis during differentiation!0.0429322859394706!4804$GO:0048812!neurite morphogenesis!0.0429322859394706!4804$GO:0007389!pattern specification process!0.0434856550912361!4617$GO:0000904!cellular morphogenesis during differentiation!0.0434856550912361!4804$GO:0031175!neurite development!0.0436226376512858!4804$GO:0008544!epidermis development!0.0436226376512858!4804$GO:0048869!cellular developmental process!0.0436226376512858!4804;4617$GO:0030154!cell differentiation!0.0436226376512858!4804;4617$GO:0007398!ectoderm development!0.0462836611723014!4804$GO:0045211!postsynaptic membrane!0.0464787764579897!5913$GO:0048666!neuron development!0.0472774191380379!4804$GO:0044456!synapse part!0.0483627566764478!5913$GO:0048856!anatomical structure development!0.0483627566764478!4804;4617$GO:0009628!response to abiotic stimulus!0.0483627566764478!4804 | |gostat_on_coexpression_clusters=GO:0042488!positive regulation of odontogenesis of dentine-containing teeth!0.0049452490286118!4804$GO:0048635!negative regulation of muscle development!0.0049452490286118!4804$GO:0005030!neurotrophin receptor activity!0.0049452490286118!4804$GO:0042482!positive regulation of odontogenesis!0.0049452490286118!4804$GO:0007517!muscle development!0.00510368093955047!4804;4617$GO:0042481!regulation of odontogenesis!0.00565146362241504!4804$GO:0048406!nerve growth factor binding!0.00565146362241504!4804$GO:0042487!regulation of odontogenesis of dentine-containing teeth!0.00659308309224691!4804$GO:0048634!regulation of muscle development!0.00659308309224691!4804$GO:0021675!nerve development!0.00719213669429478!4804$GO:0016048!detection of temperature stimulus!0.00719213669429478!4804$GO:0043121!neurotrophin binding!0.0082406260734007!4804$GO:0009887!organ morphogenesis!0.0084756982616971!4804;4617$GO:0043588!skin development!0.0084756982616971!4804$GO:0030054!cell junction!0.010513208766455!285489;5913$GO:0048704!embryonic skeletal morphogenesis!0.0109850757914487!4617$GO:0044459!plasma membrane part!0.0109850757914487!4804;285489;5913$GO:0005035!death receptor activity!0.0109850757914487!4804$GO:0048706!embryonic skeletal development!0.01285083614425!4617$GO:0001952!regulation of cell-matrix adhesion!0.01285083614425!4617$GO:0048705!skeletal morphogenesis!0.01412055080712!4617$GO:0001756!somitogenesis!0.016172306480016!4617$GO:0042475!odontogenesis of dentine-containing teeth!0.016327839596185!4804$GO:0005158!insulin receptor binding!0.0189383805889956!285489$GO:0042476!odontogenesis!0.0197582979184786!4804$GO:0035282!segmentation!0.0197582979184786!4617$GO:0003705!RNA polymerase II transcription factor activity, enhancer binding!0.0197582979184786!4617$GO:0009266!response to temperature stimulus!0.0204621440366349!4804$GO:0005886!plasma membrane!0.0278112583159776!4804;285489;5913$GO:0032501!multicellular organismal process!0.0278112583159776!4804;4617;5913$GO:0009582!detection of abiotic stimulus!0.0278112583159776!4804$GO:0030198!extracellular matrix organization and biogenesis!0.0278112583159776!4617$GO:0009653!anatomical structure morphogenesis!0.0278112583159776!4804;4617$GO:0009581!detection of external stimulus!0.0290268206664025!4804$GO:0009952!anterior/posterior pattern formation!0.0298661743075181!4617$GO:0048513!organ development!0.0298661743075181!4804;4617$GO:0007411!axon guidance!0.0298661743075181!4804$GO:0030155!regulation of cell adhesion!0.0338838289822843!4617$GO:0007519!skeletal muscle development!0.0338838289822843!4617$GO:0051093!negative regulation of developmental process!0.0379508218150131!4804$GO:0051606!detection of stimulus!0.0384626346065112!4804$GO:0043062!extracellular structure organization and biogenesis!0.0389706572423428!4617$GO:0003002!regionalization!0.0389706572423428!4617$GO:0014706!striated muscle development!0.0389706572423428!4617$GO:0019838!growth factor binding!0.0389706572423428!4804$GO:0048598!embryonic morphogenesis!0.0389876890311985!4617$GO:0009792!embryonic development ending in birth or egg hatching!0.0389876890311985!4617$GO:0043009!chordate embryonic development!0.0389876890311985!4617$GO:0007160!cell-matrix adhesion!0.0397702834627644!4617$GO:0032403!protein complex binding!0.0397702834627644!285489$GO:0031589!cell-substrate adhesion!0.0397702834627644!4617$GO:0048731!system development!0.0405695329663668!4804;4617$GO:0007409!axonogenesis!0.0423359748223512!4804$GO:0048667!neuron morphogenesis during differentiation!0.0429322859394706!4804$GO:0048812!neurite morphogenesis!0.0429322859394706!4804$GO:0007389!pattern specification process!0.0434856550912361!4617$GO:0000904!cellular morphogenesis during differentiation!0.0434856550912361!4804$GO:0031175!neurite development!0.0436226376512858!4804$GO:0008544!epidermis development!0.0436226376512858!4804$GO:0048869!cellular developmental process!0.0436226376512858!4804;4617$GO:0030154!cell differentiation!0.0436226376512858!4804;4617$GO:0007398!ectoderm development!0.0462836611723014!4804$GO:0045211!postsynaptic membrane!0.0464787764579897!5913$GO:0048666!neuron development!0.0472774191380379!4804$GO:0044456!synapse part!0.0483627566764478!5913$GO:0048856!anatomical structure development!0.0483627566764478!4804;4617$GO:0009628!response to abiotic stimulus!0.0483627566764478!4804 |
Revision as of 16:59, 12 September 2012
Full id: C397_mesenchymal_Myoblast_rhabdomyosarcoma_Hepatic_Melanocyte_astrocytoma_Skeletal
Phase1 CAGE Peaks
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 ID | GO name | FDR corrected p-value |
---|---|---|
GO:0042488 | positive regulation of odontogenesis of dentine-containing teeth | 0.0049452490286118 |
GO:0048635 | negative regulation of muscle development | 0.0049452490286118 |
GO:0005030 | neurotrophin receptor activity | 0.0049452490286118 |
GO:0042482 | positive regulation of odontogenesis | 0.0049452490286118 |
GO:0007517 | muscle development | 0.00510368093955047 |
GO:0042481 | regulation of odontogenesis | 0.00565146362241504 |
GO:0048406 | nerve growth factor binding | 0.00565146362241504 |
GO:0042487 | regulation of odontogenesis of dentine-containing teeth | 0.00659308309224691 |
GO:0048634 | regulation of muscle development | 0.00659308309224691 |
GO:0021675 | nerve development | 0.00719213669429478 |
GO:0016048 | detection of temperature stimulus | 0.00719213669429478 |
GO:0043121 | neurotrophin binding | 0.0082406260734007 |
GO:0009887 | organ morphogenesis | 0.0084756982616971 |
GO:0043588 | skin development | 0.0084756982616971 |
GO:0030054 | cell junction | 0.010513208766455 |
GO:0048704 | embryonic skeletal morphogenesis | 0.0109850757914487 |
GO:0044459 | plasma membrane part | 0.0109850757914487 |
GO:0005035 | death receptor activity | 0.0109850757914487 |
GO:0048706 | embryonic skeletal development | 0.01285083614425 |
GO:0001952 | regulation of cell-matrix adhesion | 0.01285083614425 |
GO:0048705 | skeletal morphogenesis | 0.01412055080712 |
GO:0001756 | somitogenesis | 0.016172306480016 |
GO:0042475 | odontogenesis of dentine-containing teeth | 0.016327839596185 |
GO:0005158 | insulin receptor binding | 0.0189383805889956 |
GO:0042476 | odontogenesis | 0.0197582979184786 |
GO:0035282 | segmentation | 0.0197582979184786 |
GO:0003705 | RNA polymerase II transcription factor activity, enhancer binding | 0.0197582979184786 |
GO:0009266 | response to temperature stimulus | 0.0204621440366349 |
GO:0005886 | plasma membrane | 0.0278112583159776 |
GO:0032501 | multicellular organismal process | 0.0278112583159776 |
GO:0009582 | detection of abiotic stimulus | 0.0278112583159776 |
GO:0030198 | extracellular matrix organization and biogenesis | 0.0278112583159776 |
GO:0009653 | anatomical structure morphogenesis | 0.0278112583159776 |
GO:0009581 | detection of external stimulus | 0.0290268206664025 |
GO:0009952 | anterior/posterior pattern formation | 0.0298661743075181 |
GO:0048513 | organ development | 0.0298661743075181 |
GO:0007411 | axon guidance | 0.0298661743075181 |
GO:0030155 | regulation of cell adhesion | 0.0338838289822843 |
GO:0007519 | skeletal muscle development | 0.0338838289822843 |
GO:0051093 | negative regulation of developmental process | 0.0379508218150131 |
GO:0051606 | detection of stimulus | 0.0384626346065112 |
GO:0043062 | extracellular structure organization and biogenesis | 0.0389706572423428 |
GO:0003002 | regionalization | 0.0389706572423428 |
GO:0014706 | striated muscle development | 0.0389706572423428 |
GO:0019838 | growth factor binding | 0.0389706572423428 |
GO:0048598 | embryonic morphogenesis | 0.0389876890311985 |
GO:0009792 | embryonic development ending in birth or egg hatching | 0.0389876890311985 |
GO:0043009 | chordate embryonic development | 0.0389876890311985 |
GO:0007160 | cell-matrix adhesion | 0.0397702834627644 |
GO:0032403 | protein complex binding | 0.0397702834627644 |
GO:0031589 | cell-substrate adhesion | 0.0397702834627644 |
GO:0048731 | system development | 0.0405695329663668 |
GO:0007409 | axonogenesis | 0.0423359748223512 |
GO:0048667 | neuron morphogenesis during differentiation | 0.0429322859394706 |
GO:0048812 | neurite morphogenesis | 0.0429322859394706 |
GO:0007389 | pattern specification process | 0.0434856550912361 |
GO:0000904 | cellular morphogenesis during differentiation | 0.0434856550912361 |
GO:0031175 | neurite development | 0.0436226376512858 |
GO:0008544 | epidermis development | 0.0436226376512858 |
GO:0048869 | cellular developmental process | 0.0436226376512858 |
GO:0030154 | cell differentiation | 0.0436226376512858 |
GO:0007398 | ectoderm development | 0.0462836611723014 |
GO:0045211 | postsynaptic membrane | 0.0464787764579897 |
GO:0048666 | neuron development | 0.0472774191380379 |
GO:0044456 | synapse part | 0.0483627566764478 |
GO:0048856 | anatomical structure development | 0.0483627566764478 |
GO:0009628 | response to abiotic stimulus | 0.0483627566764478 |
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>
Ontology term | p-value | n |
---|---|---|
cell of skeletal muscle | 3.42e-07 | 9 |
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
No analysis results for this cluster
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.