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Coexpression cluster:C713: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0043204!perikaryon!0.0027375485694101!11346$GO:0043197!dendritic spine!0.0027375485694101!11346$GO:0043025!cell soma!0.00857765218415165!11346$GO:0030425!dendrite!0.00857765218415165!11346$GO:0044463!cell projection part!0.00857765218415165!11346$GO:0043005!neuron projection!0.0106460222143726!11346$GO:0005923!tight junction!0.0106460222143726!11346$GO:0043296!apical junction complex!0.0106460222143726!11346$GO:0016327!apicolateral plasma membrane!0.0106460222143726!11346$GO:0045211!postsynaptic membrane!0.0131554417363319!11346$GO:0044456!synapse part!0.0131554417363319!11346$GO:0005911!intercellular junction!0.0131554417363319!11346$GO:0015629!actin cytoskeleton!0.0204012548148896!11346$GO:0042995!cell projection!0.0204012548148896!11346$GO:0030054!cell junction!0.0249801306958672!11346$GO:0003779!actin binding!0.0249801306958672!11346$GO:0008092!cytoskeletal protein binding!0.0323674860265547!11346
|gostat_on_coexpression_clusters=GO:0043204!perikaryon!0.0027375485694101!11346$GO:0043197!dendritic spine!0.0027375485694101!11346$GO:0043025!cell soma!0.00857765218415165!11346$GO:0030425!dendrite!0.00857765218415165!11346$GO:0044463!cell projection part!0.00857765218415165!11346$GO:0043005!neuron projection!0.0106460222143726!11346$GO:0005923!tight junction!0.0106460222143726!11346$GO:0043296!apical junction complex!0.0106460222143726!11346$GO:0016327!apicolateral plasma membrane!0.0106460222143726!11346$GO:0045211!postsynaptic membrane!0.0131554417363319!11346$GO:0044456!synapse part!0.0131554417363319!11346$GO:0005911!intercellular junction!0.0131554417363319!11346$GO:0015629!actin cytoskeleton!0.0204012548148896!11346$GO:0042995!cell projection!0.0204012548148896!11346$GO:0030054!cell junction!0.0249801306958672!11346$GO:0003779!actin binding!0.0249801306958672!11346$GO:0008092!cytoskeletal protein binding!0.0323674860265547!11346
|id=C713
|id=C713
|ontology_enrichment_celltype=CL:0000222!4.45e-11!119;CL:0002139!6.97e-09!24;CL:0000213!1.44e-08!57;CL:0000215!1.44e-08!57;CL:0000115!4.22e-08!35;CL:0000220!2.11e-07!246;CL:0000359!2.53e-07!32;CL:0002078!3.60e-07!44;CL:0002321!4.63e-07!248;CL:0000071!9.98e-07!18;CL:0002546!9.98e-07!18
|ontology_enrichment_celltype=CL:0000115!3.32e-10!36;CL:0002139!9.11e-10!24;CL:0000213!1.07e-09!58;CL:0000215!1.07e-09!58;CL:0002078!1.10e-08!45;CL:0000222!6.37e-08!121;CL:0000071!3.59e-07!18;CL:0002546!3.59e-07!18
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004111!8.20e-36!241;UBERON:0000477!9.67e-35!286;UBERON:0007023!2.16e-30!115;UBERON:0000025!3.83e-30!194;UBERON:0000483!9.84e-27!309;UBERON:0000119!1.84e-26!312;UBERON:0000481!1.64e-21!347;UBERON:0004872!2.50e-20!84;UBERON:0000055!5.94e-19!69;UBERON:0002049!3.19e-18!79;UBERON:0007798!3.19e-18!79;UBERON:0003914!4.17e-18!118;UBERON:0000475!7.61e-18!365;UBERON:0001981!2.13e-17!60;UBERON:0007500!2.13e-17!60;UBERON:0004537!2.13e-17!60;UBERON:0006965!2.13e-17!60;UBERON:0001009!3.29e-17!113;UBERON:0003075!2.50e-16!86;UBERON:0007284!2.50e-16!86;UBERON:0004535!9.13e-16!110;UBERON:0002346!1.29e-15!90;UBERON:0001049!6.38e-15!57;UBERON:0005068!6.38e-15!57;UBERON:0006241!6.38e-15!57;UBERON:0007135!6.38e-15!57;UBERON:0003080!8.79e-14!42;UBERON:0002780!1.73e-13!41;UBERON:0001890!1.73e-13!41;UBERON:0006240!1.73e-13!41;UBERON:0002616!2.82e-13!59;UBERON:0000467!5.05e-13!625;UBERON:0000955!5.18e-13!69;UBERON:0006238!5.18e-13!69;UBERON:0000480!6.39e-13!626;UBERON:0000468!1.06e-12!659;UBERON:0001869!1.10e-12!32;UBERON:0000033!1.10e-12!123;UBERON:0001893!1.48e-12!34;UBERON:0001637!2.16e-12!42;UBERON:0003509!2.16e-12!42;UBERON:0004572!2.16e-12!42;UBERON:0002020!2.68e-12!34;UBERON:0003528!2.68e-12!34;UBERON:0003056!3.57e-12!61;UBERON:0000153!4.45e-12!129;UBERON:0007811!4.45e-12!129;UBERON:0005743!4.54e-12!86;UBERON:0002791!4.57e-12!33;UBERON:0001017!8.34e-12!82;UBERON:0000490!5.05e-11!138;UBERON:0007100!6.70e-11!27;UBERON:0002619!7.43e-11!22;UBERON:0000073!1.75e-10!94;UBERON:0001016!1.75e-10!94;UBERON:0003103!2.59e-10!69;UBERON:0001950!1.10e-09!20;UBERON:0000956!1.17e-09!25;UBERON:0000203!1.17e-09!25;UBERON:0002050!2.06e-09!605;UBERON:0005423!2.06e-09!605;UBERON:0000923!2.33e-09!604;UBERON:0005291!2.33e-09!604;UBERON:0006598!2.33e-09!604;UBERON:0002532!2.33e-09!604;UBERON:0000948!3.56e-09!24;UBERON:0005498!3.56e-09!24;UBERON:0004140!3.56e-09!24;UBERON:0009881!3.56e-09!24;UBERON:0004141!3.56e-09!24;UBERON:0003084!3.56e-09!24;UBERON:0007005!3.56e-09!24;UBERON:0004139!3.56e-09!24;UBERON:0004291!3.56e-09!24;UBERON:0000922!4.11e-09!612;UBERON:0004573!8.95e-09!33;UBERON:0004571!8.95e-09!33;UBERON:0004121!4.98e-08!169;UBERON:0000924!7.62e-08!173;UBERON:0006601!7.62e-08!173;UBERON:0000064!2.74e-07!219;UBERON:0001986!9.98e-07!18;UBERON:0004638!9.98e-07!18;UBERON:0004852!9.98e-07!18
|ontology_enrichment_uberon=UBERON:0007023!3.96e-30!114;UBERON:0004111!2.84e-29!240;UBERON:0000477!3.52e-26!373;UBERON:0000025!9.27e-25!192;UBERON:0000483!1.59e-17!306;UBERON:0004872!3.76e-17!83;UBERON:0000119!3.85e-17!309;UBERON:0000055!1.33e-16!68;UBERON:0002049!1.65e-16!78;UBERON:0007798!1.65e-16!78;UBERON:0007500!3.37e-15!59;UBERON:0001981!3.37e-15!59;UBERON:0004537!3.37e-15!59;UBERON:0006965!3.37e-15!59;UBERON:0001009!4.48e-15!112;UBERON:0010314!2.18e-14!132;UBERON:0003914!2.51e-14!117;UBERON:0000481!2.54e-14!342;UBERON:0004535!1.29e-13!109;UBERON:0002780!2.09e-13!41;UBERON:0001890!2.09e-13!41;UBERON:0003080!2.09e-13!41;UBERON:0006240!2.09e-13!41;UBERON:0001893!4.49e-13!34;UBERON:0001869!4.50e-13!32;UBERON:0001049!5.39e-13!56;UBERON:0005068!5.39e-13!56;UBERON:0006241!5.39e-13!56;UBERON:0007135!5.39e-13!56;UBERON:0003528!7.44e-13!34;UBERON:0002020!7.44e-13!34;UBERON:0000073!9.28e-13!53;UBERON:0002616!9.28e-13!53;UBERON:0002791!1.15e-12!32;UBERON:0003075!3.41e-12!82;UBERON:0007284!3.41e-12!82;UBERON:0000955!9.86e-12!68;UBERON:0006238!9.86e-12!68;UBERON:0002346!3.48e-11!86;UBERON:0002619!7.60e-11!22;UBERON:0007100!1.66e-10!27;UBERON:0001637!5.45e-10!42;UBERON:0003509!5.45e-10!42;UBERON:0004572!5.45e-10!42;UBERON:0000956!9.50e-10!25;UBERON:0000203!9.50e-10!25;UBERON:0001017!1.02e-09!81;UBERON:0001950!1.65e-09!20;UBERON:0010371!1.74e-09!104;UBERON:0003056!2.57e-09!61;UBERON:0000467!5.90e-09!624;UBERON:0000480!8.14e-09!625;UBERON:0003103!9.09e-09!68;UBERON:0000948!1.20e-08!24;UBERON:0005498!1.20e-08!24;UBERON:0004140!1.20e-08!24;UBERON:0009881!1.20e-08!24;UBERON:0004141!1.20e-08!24;UBERON:0003084!1.20e-08!24;UBERON:0007005!1.20e-08!24;UBERON:0004139!1.20e-08!24;UBERON:0004291!1.20e-08!24;UBERON:0000468!5.94e-08!656;UBERON:0011216!2.01e-07!223;UBERON:0002050!2.22e-07!564;UBERON:0001016!2.22e-07!89;UBERON:0000923!2.68e-07!560;UBERON:0010316!2.68e-07!560;UBERON:0005291!2.68e-07!560;UBERON:0006598!2.68e-07!560;UBERON:0010317!2.68e-07!560;UBERON:0002532!2.68e-07!560;UBERON:0004638!3.59e-07!18;UBERON:0001986!3.59e-07!18;UBERON:0004852!3.59e-07!18
|tf_chipseq_enrich=ZNF263#10127;8:5.48122775800712:1.50025403478449e-05:0.000355456059752399
|tf_chipseq_enrich=ZNF263#10127;8:5.48122775800712:1.50025403478449e-05:0.000355456059752399
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}}
}}

Revision as of 16:37, 19 October 2012


Full id: C713_skeletal_heart_Renal_aorta_Fibroblast_Smooth_mature



Phase1 CAGE Peaks

Hg19::chr5:150004188..150004308,+p1@SYNPO
Hg19::chr5:150027636..150027663,+p2@AB384087
Hg19::chr5:150027742..150027754,+p3@AB384087
Hg19::chr5:150027815..150027828,+p1@AB384087
Hg19::chr5:150027838..150027865,+p6@SYNPO
Hg19::chr5:150027893..150027907,+p15@SYNPO
Hg19::chr5:150027978..150028011,+p13@SYNPO
Hg19::chr5:150028043..150028054,+p23@SYNPO
Hg19::chr5:150028060..150028075,+p22@SYNPO
Hg19::chr5:150028080..150028174,-p@chr5:150028080..150028174
-
Hg19::chr5:150028254..150028266,+p16@SYNPO
Hg19::chr5:150029105..150029117,+p@chr5:150029105..150029117
+


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:0043204perikaryon0.0027375485694101
GO:0043197dendritic spine0.0027375485694101
GO:0043025cell soma0.00857765218415165
GO:0030425dendrite0.00857765218415165
GO:0044463cell projection part0.00857765218415165
GO:0043005neuron projection0.0106460222143726
GO:0005923tight junction0.0106460222143726
GO:0043296apical junction complex0.0106460222143726
GO:0016327apicolateral plasma membrane0.0106460222143726
GO:0045211postsynaptic membrane0.0131554417363319
GO:0044456synapse part0.0131554417363319
GO:0005911intercellular junction0.0131554417363319
GO:0015629actin cytoskeleton0.0204012548148896
GO:0042995cell projection0.0204012548148896
GO:0030054cell junction0.0249801306958672
GO:0003779actin binding0.0249801306958672
GO:0008092cytoskeletal protein binding0.0323674860265547



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>

Uber Anatomy
Ontology termp-valuen
adult organism3.96e-30114
anatomical conduit2.84e-29240
anatomical cluster3.52e-26373
tube9.27e-25192
epithelium1.59e-17306
splanchnic layer of lateral plate mesoderm3.76e-1783
cell layer3.85e-17309
vessel1.33e-1668
vasculature1.65e-1678
vascular system1.65e-1678
epithelial tube open at both ends3.37e-1559
blood vessel3.37e-1559
blood vasculature3.37e-1559
vascular cord3.37e-1559
circulatory system4.48e-15112
structure with developmental contribution from neural crest2.18e-14132
epithelial tube2.51e-14117
multi-tissue structure2.54e-14342
cardiovascular system1.29e-13109
regional part of forebrain2.09e-1341
forebrain2.09e-1341
anterior neural tube2.09e-1341
future forebrain2.09e-1341
telencephalon4.49e-1334
cerebral hemisphere4.50e-1332
neural tube5.39e-1356
neural rod5.39e-1356
future spinal cord5.39e-1356
neural keel5.39e-1356
brain grey matter7.44e-1334
gray matter7.44e-1334
regional part of nervous system9.28e-1353
regional part of brain9.28e-1353
regional part of telencephalon1.15e-1232
neural plate3.41e-1282
presumptive neural plate3.41e-1282
brain9.86e-1268
future brain9.86e-1268
neurectoderm3.48e-1186
regional part of cerebral cortex7.60e-1122
primary circulatory organ1.66e-1027
artery5.45e-1042
arterial blood vessel5.45e-1042
arterial system5.45e-1042
cerebral cortex9.50e-1025
pallium9.50e-1025
central nervous system1.02e-0981
neocortex1.65e-0920
ecto-epithelium1.74e-09104
pre-chordal neural plate2.57e-0961
anatomical system5.90e-09624
anatomical group8.14e-09625
compound organ9.09e-0968
heart1.20e-0824
primitive heart tube1.20e-0824
primary heart field1.20e-0824
anterior lateral plate mesoderm1.20e-0824
heart tube1.20e-0824
heart primordium1.20e-0824
cardiac mesoderm1.20e-0824
cardiogenic plate1.20e-0824
heart rudiment1.20e-0824
multi-cellular organism5.94e-08656
organ system subdivision2.01e-07223
embryonic structure2.22e-07564
nervous system2.22e-0789
germ layer2.68e-07560
germ layer / neural crest2.68e-07560
embryonic tissue2.68e-07560
presumptive structure2.68e-07560
germ layer / neural crest derived structure2.68e-07560
epiblast (generic)2.68e-07560
blood vessel endothelium3.59e-0718
endothelium3.59e-0718
cardiovascular system endothelium3.59e-0718


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
ZNF263#1012785.481227758007121.50025403478449e-050.000355456059752399



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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