Coexpression cluster:C737: Difference between revisions
From FANTOM5_SSTAR
No edit summary |
No edit summary |
||
Line 3: | Line 3: | ||
|gostat_on_coexpression_clusters=GO:0045211!postsynaptic membrane!6.79938374953971e-05!1144;1140;5913$GO:0044456!synapse part!6.79938374953971e-05!1144;1140;5913$GO:0005892!nicotinic acetylcholine-gated receptor-channel complex!6.79938374953971e-05!1144;1140$GO:0015464!acetylcholine receptor activity!0.000110207136155915!1144;1140$GO:0042166!acetylcholine binding!0.000110207136155915!1144;1140$GO:0004889!nicotinic acetylcholine-activated cation-selective channel activity!0.000110207136155915!1144;1140$GO:0042391!regulation of membrane potential!0.000173536456370901!1144;1140$GO:0043176!amine binding!0.000308677077309302!1144;1140$GO:0030054!cell junction!0.000329255168161089!1144;1140;5913$GO:0005231!excitatory extracellular ligand-gated ion channel activity!0.000666112422770907!1144;1140$GO:0043235!receptor complex!0.00141713184631989!1144;1140$GO:0005230!extracellular ligand-gated ion channel activity!0.00184280447188266!1144;1140$GO:0030594!neurotransmitter receptor activity!0.00193503853896072!1144;1140$GO:0042165!neurotransmitter binding!0.00193503853896072!1144;1140$GO:0015276!ligand-gated ion channel activity!0.00194818366524397!1144;1140$GO:0022834!ligand-gated channel activity!0.00194818366524397!1144;1140$GO:0003012!muscle system process!0.00194818366524397!1144;1140$GO:0006936!muscle contraction!0.00194818366524397!1144;1140$GO:0048625!myoblast cell fate commitment!0.00328069494872328!4654$GO:0007518!myoblast cell fate determination!0.00328069494872328!4654$GO:0055082!cellular chemical homeostasis!0.00328069494872328!1144;1140$GO:0006873!cellular ion homeostasis!0.00328069494872328!1144;1140$GO:0050801!ion homeostasis!0.00397762027942711!1144;1140$GO:0007268!synaptic transmission!0.00439703107944435!1140;5913$GO:0032501!multicellular organismal process!0.00439703107944435!1144;4654;1140;5913$GO:0048878!chemical homeostasis!0.00449427535592236!1144;1140$GO:0003008!system process!0.00484422787117751!1144;1140;5913$GO:0019226!transmission of nerve impulse!0.00497613463498123!1140;5913$GO:0019725!cellular homeostasis!0.00618997073618544!1144;1140$GO:0005515!protein binding!0.00658133782506141!1144;4654;1140;493829;5913$GO:0005261!cation channel activity!0.00724649481992225!1144;1140$GO:0007271!synaptic transmission, cholinergic!0.00832867358554158!1140$GO:0042592!homeostatic process!0.00886226726540242!1144;1140$GO:0046873!metal ion transmembrane transporter activity!0.00923617233921631!1144;1140$GO:0022836!gated channel activity!0.00923617233921631!1144;1140$GO:0044459!plasma membrane part!0.0114977939322784!1144;1140;5913$GO:0007267!cell-cell signaling!0.0139263162510835!1140;5913$GO:0005216!ion channel activity!0.0142062424824373!1144;1140$GO:0022838!substrate specific channel activity!0.0142062424824373!1144;1140$GO:0045445!myoblast differentiation!0.0142062424824373!4654$GO:0003705!RNA polymerase II transcription factor activity, enhancer binding!0.0142062424824373!4654$GO:0022803!passive transmembrane transporter activity!0.0142062424824373!1144;1140$GO:0015267!channel activity!0.0142062424824373!1144;1140$GO:0001709!cell fate determination!0.0146236309168168!4654$GO:0043234!protein complex!0.0179716781370358!1144;4654;1140$GO:0048741!skeletal muscle fiber development!0.0196191815942839!4654$GO:0048747!muscle fiber development!0.0196191815942839!4654$GO:0008324!cation transmembrane transporter activity!0.0196191815942839!1144;1140$GO:0042692!muscle cell differentiation!0.0208083176960963!4654$GO:0065008!regulation of biological quality!0.0224398321940344!1144;1140$GO:0007519!skeletal muscle development!0.0290832469142844!4654$GO:0045165!cell fate commitment!0.0302197586792451!4654$GO:0005886!plasma membrane!0.0338623366681617!1144;1140;5913$GO:0032991!macromolecular complex!0.0348690262537573!1144;4654;1140$GO:0014706!striated muscle development!0.0348690262537573!4654$GO:0050877!neurological system process!0.0348690262537573!1140;5913$GO:0015075!ion transmembrane transporter activity!0.0368473140920722!1144;1140$GO:0005887!integral to plasma membrane!0.0368473140920722!1144;1140$GO:0031226!intrinsic to plasma membrane!0.0370642587046981!1144;1140$GO:0006811!ion transport!0.037387762057121!1144;1140$GO:0022891!substrate-specific transmembrane transporter activity!0.0453015648225363!1144;1140 | |gostat_on_coexpression_clusters=GO:0045211!postsynaptic membrane!6.79938374953971e-05!1144;1140;5913$GO:0044456!synapse part!6.79938374953971e-05!1144;1140;5913$GO:0005892!nicotinic acetylcholine-gated receptor-channel complex!6.79938374953971e-05!1144;1140$GO:0015464!acetylcholine receptor activity!0.000110207136155915!1144;1140$GO:0042166!acetylcholine binding!0.000110207136155915!1144;1140$GO:0004889!nicotinic acetylcholine-activated cation-selective channel activity!0.000110207136155915!1144;1140$GO:0042391!regulation of membrane potential!0.000173536456370901!1144;1140$GO:0043176!amine binding!0.000308677077309302!1144;1140$GO:0030054!cell junction!0.000329255168161089!1144;1140;5913$GO:0005231!excitatory extracellular ligand-gated ion channel activity!0.000666112422770907!1144;1140$GO:0043235!receptor complex!0.00141713184631989!1144;1140$GO:0005230!extracellular ligand-gated ion channel activity!0.00184280447188266!1144;1140$GO:0030594!neurotransmitter receptor activity!0.00193503853896072!1144;1140$GO:0042165!neurotransmitter binding!0.00193503853896072!1144;1140$GO:0015276!ligand-gated ion channel activity!0.00194818366524397!1144;1140$GO:0022834!ligand-gated channel activity!0.00194818366524397!1144;1140$GO:0003012!muscle system process!0.00194818366524397!1144;1140$GO:0006936!muscle contraction!0.00194818366524397!1144;1140$GO:0048625!myoblast cell fate commitment!0.00328069494872328!4654$GO:0007518!myoblast cell fate determination!0.00328069494872328!4654$GO:0055082!cellular chemical homeostasis!0.00328069494872328!1144;1140$GO:0006873!cellular ion homeostasis!0.00328069494872328!1144;1140$GO:0050801!ion homeostasis!0.00397762027942711!1144;1140$GO:0007268!synaptic transmission!0.00439703107944435!1140;5913$GO:0032501!multicellular organismal process!0.00439703107944435!1144;4654;1140;5913$GO:0048878!chemical homeostasis!0.00449427535592236!1144;1140$GO:0003008!system process!0.00484422787117751!1144;1140;5913$GO:0019226!transmission of nerve impulse!0.00497613463498123!1140;5913$GO:0019725!cellular homeostasis!0.00618997073618544!1144;1140$GO:0005515!protein binding!0.00658133782506141!1144;4654;1140;493829;5913$GO:0005261!cation channel activity!0.00724649481992225!1144;1140$GO:0007271!synaptic transmission, cholinergic!0.00832867358554158!1140$GO:0042592!homeostatic process!0.00886226726540242!1144;1140$GO:0046873!metal ion transmembrane transporter activity!0.00923617233921631!1144;1140$GO:0022836!gated channel activity!0.00923617233921631!1144;1140$GO:0044459!plasma membrane part!0.0114977939322784!1144;1140;5913$GO:0007267!cell-cell signaling!0.0139263162510835!1140;5913$GO:0005216!ion channel activity!0.0142062424824373!1144;1140$GO:0022838!substrate specific channel activity!0.0142062424824373!1144;1140$GO:0045445!myoblast differentiation!0.0142062424824373!4654$GO:0003705!RNA polymerase II transcription factor activity, enhancer binding!0.0142062424824373!4654$GO:0022803!passive transmembrane transporter activity!0.0142062424824373!1144;1140$GO:0015267!channel activity!0.0142062424824373!1144;1140$GO:0001709!cell fate determination!0.0146236309168168!4654$GO:0043234!protein complex!0.0179716781370358!1144;4654;1140$GO:0048741!skeletal muscle fiber development!0.0196191815942839!4654$GO:0048747!muscle fiber development!0.0196191815942839!4654$GO:0008324!cation transmembrane transporter activity!0.0196191815942839!1144;1140$GO:0042692!muscle cell differentiation!0.0208083176960963!4654$GO:0065008!regulation of biological quality!0.0224398321940344!1144;1140$GO:0007519!skeletal muscle development!0.0290832469142844!4654$GO:0045165!cell fate commitment!0.0302197586792451!4654$GO:0005886!plasma membrane!0.0338623366681617!1144;1140;5913$GO:0032991!macromolecular complex!0.0348690262537573!1144;4654;1140$GO:0014706!striated muscle development!0.0348690262537573!4654$GO:0050877!neurological system process!0.0348690262537573!1140;5913$GO:0015075!ion transmembrane transporter activity!0.0368473140920722!1144;1140$GO:0005887!integral to plasma membrane!0.0368473140920722!1144;1140$GO:0031226!intrinsic to plasma membrane!0.0370642587046981!1144;1140$GO:0006811!ion transport!0.037387762057121!1144;1140$GO:0022891!substrate-specific transmembrane transporter activity!0.0453015648225363!1144;1140 | ||
|id=C737 | |id=C737 | ||
|ontology_enrichment_celltype=CL:0000066!3.92e-11!254;CL:0002321!9.58e-10!248;CL:0000220!1.79e-09!246;CL:0000188!3.01e-07!9;CL:0002159!8.59e-07!13 | |||
|ontology_enrichment_disease= | |||
|ontology_enrichment_uberon=UBERON:0000483!3.22e-21!309;UBERON:0000119!9.95e-21!312;UBERON:0000481!6.91e-18!347;UBERON:0000475!1.42e-14!365;UBERON:0000922!2.62e-13!612;UBERON:0000468!3.40e-12!659;UBERON:0002050!2.08e-11!605;UBERON:0005423!2.08e-11!605;UBERON:0000923!2.86e-11!604;UBERON:0005291!2.86e-11!604;UBERON:0006598!2.86e-11!604;UBERON:0002532!2.86e-11!604;UBERON:0003104!2.89e-10!238;UBERON:0009142!2.89e-10!238;UBERON:0000467!4.18e-10!625;UBERON:0000480!6.39e-10!626;UBERON:0000490!4.61e-09!138;UBERON:0001048!5.19e-09!168;UBERON:0005177!2.30e-08!107;UBERON:0002100!4.31e-08!216;UBERON:0000020!7.43e-08!23;UBERON:0004111!9.42e-08!241;UBERON:0003103!1.31e-07!69;UBERON:0004121!1.64e-07!169;UBERON:0000466!1.84e-07!126;UBERON:0000924!2.42e-07!173;UBERON:0006601!2.42e-07!173;UBERON:0000025!3.06e-07!194;UBERON:0001032!3.97e-07!24;UBERON:0004456!3.97e-07!24;UBERON:0000970!5.74e-07!20;UBERON:0005256!7.15e-07!143 | |||
}} | }} |
Revision as of 14:57, 21 May 2012
Full id: C737_rhabdomyosarcoma_skeletal_mesenchymal_Skeletal_Pericytes_tongue_diaphragm
Phase1 CAGE Peaks
Hg19::chr11:17741084..17741094,+ | p3@MYOD1 |
Hg19::chr11:47470650..47470653,- | p5@RAPSN |
Hg19::chr11:47470657..47470674,- | p2@RAPSN |
Hg19::chr11:47470682..47470693,- | p1@RAPSN |
Hg19::chr11:47470703..47470715,- | p3@RAPSN |
Hg19::chr12:81102260..81102302,+ | p@chr12:81102260..81102302 + |
Hg19::chr16:31225409..31225428,+ | p3@TRIM72 |
Hg19::chr16:31225432..31225453,+ | p2@TRIM72 |
Hg19::chr17:7348374..7348435,+ | p1@CHRNB1 |
Hg19::chr19:49223185..49223197,- | p6@MAMSTR |
Hg19::chr2:233390890..233390903,+ | p3@CHRND |
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:0045211 | postsynaptic membrane | 6.79938374953971e-05 |
GO:0044456 | synapse part | 6.79938374953971e-05 |
GO:0005892 | nicotinic acetylcholine-gated receptor-channel complex | 6.79938374953971e-05 |
GO:0015464 | acetylcholine receptor activity | 0.000110207136155915 |
GO:0042166 | acetylcholine binding | 0.000110207136155915 |
GO:0004889 | nicotinic acetylcholine-activated cation-selective channel activity | 0.000110207136155915 |
GO:0042391 | regulation of membrane potential | 0.000173536456370901 |
GO:0043176 | amine binding | 0.000308677077309302 |
GO:0030054 | cell junction | 0.000329255168161089 |
GO:0005231 | excitatory extracellular ligand-gated ion channel activity | 0.000666112422770907 |
GO:0043235 | receptor complex | 0.00141713184631989 |
GO:0005230 | extracellular ligand-gated ion channel activity | 0.00184280447188266 |
GO:0030594 | neurotransmitter receptor activity | 0.00193503853896072 |
GO:0042165 | neurotransmitter binding | 0.00193503853896072 |
GO:0015276 | ligand-gated ion channel activity | 0.00194818366524397 |
GO:0022834 | ligand-gated channel activity | 0.00194818366524397 |
GO:0003012 | muscle system process | 0.00194818366524397 |
GO:0006936 | muscle contraction | 0.00194818366524397 |
GO:0048625 | myoblast cell fate commitment | 0.00328069494872328 |
GO:0007518 | myoblast cell fate determination | 0.00328069494872328 |
GO:0055082 | cellular chemical homeostasis | 0.00328069494872328 |
GO:0006873 | cellular ion homeostasis | 0.00328069494872328 |
GO:0050801 | ion homeostasis | 0.00397762027942711 |
GO:0007268 | synaptic transmission | 0.00439703107944435 |
GO:0032501 | multicellular organismal process | 0.00439703107944435 |
GO:0048878 | chemical homeostasis | 0.00449427535592236 |
GO:0003008 | system process | 0.00484422787117751 |
GO:0019226 | transmission of nerve impulse | 0.00497613463498123 |
GO:0019725 | cellular homeostasis | 0.00618997073618544 |
GO:0005515 | protein binding | 0.00658133782506141 |
GO:0005261 | cation channel activity | 0.00724649481992225 |
GO:0007271 | synaptic transmission, cholinergic | 0.00832867358554158 |
GO:0042592 | homeostatic process | 0.00886226726540242 |
GO:0046873 | metal ion transmembrane transporter activity | 0.00923617233921631 |
GO:0022836 | gated channel activity | 0.00923617233921631 |
GO:0044459 | plasma membrane part | 0.0114977939322784 |
GO:0007267 | cell-cell signaling | 0.0139263162510835 |
GO:0005216 | ion channel activity | 0.0142062424824373 |
GO:0022838 | substrate specific channel activity | 0.0142062424824373 |
GO:0045445 | myoblast differentiation | 0.0142062424824373 |
GO:0003705 | RNA polymerase II transcription factor activity, enhancer binding | 0.0142062424824373 |
GO:0022803 | passive transmembrane transporter activity | 0.0142062424824373 |
GO:0015267 | channel activity | 0.0142062424824373 |
GO:0001709 | cell fate determination | 0.0146236309168168 |
GO:0043234 | protein complex | 0.0179716781370358 |
GO:0048741 | skeletal muscle fiber development | 0.0196191815942839 |
GO:0048747 | muscle fiber development | 0.0196191815942839 |
GO:0008324 | cation transmembrane transporter activity | 0.0196191815942839 |
GO:0042692 | muscle cell differentiation | 0.0208083176960963 |
GO:0065008 | regulation of biological quality | 0.0224398321940344 |
GO:0007519 | skeletal muscle development | 0.0290832469142844 |
GO:0045165 | cell fate commitment | 0.0302197586792451 |
GO:0005886 | plasma membrane | 0.0338623366681617 |
GO:0032991 | macromolecular complex | 0.0348690262537573 |
GO:0014706 | striated muscle development | 0.0348690262537573 |
GO:0050877 | neurological system process | 0.0348690262537573 |
GO:0015075 | ion transmembrane transporter activity | 0.0368473140920722 |
GO:0005887 | integral to plasma membrane | 0.0368473140920722 |
GO:0031226 | intrinsic to plasma membrane | 0.0370642587046981 |
GO:0006811 | ion transport | 0.037387762057121 |
GO:0022891 | substrate-specific transmembrane transporter activity | 0.0453015648225363 |
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 |
---|---|---|
epithelial cell | 3.92e-11 | 254 |
embryonic cell | 9.58e-10 | 248 |
cell of skeletal muscle | 3.01e-07 | 9 |
general ecto-epithelial cell | 8.59e-07 | 13 |
Ontology term | p-value | n |
---|---|---|
epithelium | 3.22e-21 | 309 |
cell layer | 9.95e-21 | 312 |
multi-tissue structure | 6.91e-18 | 347 |
organism subdivision | 1.42e-14 | 365 |
embryo | 2.62e-13 | 612 |
multi-cellular organism | 3.40e-12 | 659 |
embryonic structure | 2.08e-11 | 605 |
developing anatomical structure | 2.08e-11 | 605 |
germ layer | 2.86e-11 | 604 |
embryonic tissue | 2.86e-11 | 604 |
presumptive structure | 2.86e-11 | 604 |
epiblast (generic) | 2.86e-11 | 604 |
mesenchyme | 2.89e-10 | 238 |
entire embryonic mesenchyme | 2.89e-10 | 238 |
anatomical system | 4.18e-10 | 625 |
anatomical group | 6.39e-10 | 626 |
unilaminar epithelium | 4.61e-09 | 138 |
primordium | 5.19e-09 | 168 |
trunk region element | 2.30e-08 | 107 |
trunk | 4.31e-08 | 216 |
sense organ | 7.43e-08 | 23 |
anatomical conduit | 9.42e-08 | 241 |
compound organ | 1.31e-07 | 69 |
ectoderm-derived structure | 1.64e-07 | 169 |
immaterial anatomical entity | 1.84e-07 | 126 |
ectoderm | 2.42e-07 | 173 |
presumptive ectoderm | 2.42e-07 | 173 |
tube | 3.06e-07 | 194 |
sensory system | 3.97e-07 | 24 |
entire sense organ system | 3.97e-07 | 24 |
eye | 5.74e-07 | 20 |
trunk mesenchyme | 7.15e-07 | 143 |
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.