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{{Coexpression_clusters
{{Coexpression_clusters
|coexpression_dpi_cluster_scores_median=0.188938360773272,0.358810769997231,0.0825627103636605,0,0,0,0,0.354768937993072,0.18252057552538,0,0,0,0,0.174660194252277,0.124307696593413,0.223320720221072,0.204850754147253,0,0.234170358386092,0.0956024239401108,0.259116505425895,0,0,0,0,0,0,0,0,0,0.0625128387853364,0,0,0,0,0,0,0,0.0793782434714987,0.0426472287497177,0,0,0,0.449715908632996,0.244463143941376,0.237481450510321,0.377172732108371,0.260628401312869,0.209357552049835,0.479121164717847,0.358087876963302,0.130190073715096,0.342396423162991,0,0,0.581949496788172,0.397463522205836,0.223799672996739,0.537651782554888,0.21533560773887,0.357682244950033,0.448605113731709,0.39689368781652,0.267746377672919,0.437949505236807,0.195175748476722,0.210270953277894,0.438902254787546,0.408994025090247,0.156663521505759,0.397106262277117,0.136174228629411,0.119408455420648,0,0,0,0.0671238391320836,0.0874130823459109,0,0,0.0787890013723437,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0261280904843202,0,0,0.0587472679543123,0,0,0,0,0,0.143931545137586,0,0,0.12206750241012,0.129773480880396,0.390748920079961,0,0,0,0.0787331152135556,0,0.12941289334046,0,0.152135224370875,0,0.151673147612848,0,0,0,0,0,0.0948420448069823,0.135979123430744,0,0.103084722628515,0.087969206950705,0.0463435368962281,0,0,0.135578961919851,0,0,0,0,0.0749115209770284,0.0540033816753664,0.386353243554989,0.182330314034704,0,0,0,0,0.0548851394659095,0.122845985799448,0.11484936557738,0.197604689528463,0.0914282698219536,0.319466529424201,0.196030148402437,0.445508224364991,0.274121334816387,0.257526118389602,0.231024371917556,0.207489627025517,0.136245738543973,0.296867231791801,0,0.0959594073735869,0.281070056064076,0.499116961684888,0.067567801197968,0.117703674292546,0.148849775633542,0,0.058052678619159,0,0,0.297676740102059,0.084060318828564,0.153468449462275,0.422630963215205,0.209063106658541,0.307616288783483,0.241662864220876,0.265733044952828,0.142936064165064,0.177498277011549,0.07338830676488,0.0650738225586148,0.233000982852579,0.0972108786684727,0.068022726550833,0,0,0,0,0,0,0,0,0,0.409001911408146,0.74057477613172,0.376823087293191,0.37896153349969,0.388058367669498,0,0,0,0,0,0,0,0,0,0,0,0,0,0.681481032425686,0.297284871485779,0.270191966560285,0,0,0,0,0,0,0,0.061240367628562,0.309616283677893,0,0,0,0,0,0,0,0,0.0955936734149088,0.091316660769536,0.2026312372254,0,0,0,0.0372505621677013,0,0,0,0.0366482282265911,0,0.0292357798753831,0,0,0,0,0,0.0425075842205678,0,0,0.0878744294302742,0,0.147020962338212,0,0.660539583551993,0.347958828004523,0,0,0.0994069197460863,0,0.185498059694978,0.0580378687812504,0.319156715876182,0,0.122457109962761,0,0.253326341486756,0,0,0,0,0.176744262785174,0.492528432668985,0,0,0,0.333122453125138,0.562068960554454,0.256129030472657,0,0,0,0,0,0,0,0,0,0.397594876354309,0.99890610258435,0.206375296087236,0.115706333736811,0.398028867207316,0.10423609841563,0.0820564584332857,0.233938840156098,0.0635969392553137,0.0697614199996087,0,0,0.154253470262378,0,0.0734870933250891,0.414686560385328,0.143515142523472,0.226931452698605,0,0.0848314897427103,0.0440407241264263,0,0,0,0.0962521000248044,0.0620032815069762,0.193491975450777,0.0523626705930769,0,0.0647775726819609,0,0.518350568747563,0.552024054744934,0.219327029071247,0.614425410394021,0.540929716833131,0,0,0,0.0472025886002021,0.189286314149658,0.0535103765953433,0,0,0,0,0,0,0.225406165405455,0.0849035433286077,0,0,0,0.138753339255263,0.131353186234183,0.160693426449034,0,0,0,0,0,0.116980464645417,0,0,0,0,0,0.197849381981336,0.228263261385601,0.22763571129755,0.227676666647595,0.256441797392186,0.362699237121318,0.225777710137492,0,0,0,0,0,0.082895917934131,0.460728612413362,0.229691380353826,0.162539149315186,0,0,0.192001960980818,0,0.0687021194498525,0,0,0,0.154709651609437,0.213891194797874,0.251625724314337,0.0718350632709503,0.105352457754613,0.111662364707184,0.079970395058755,0,0.152673061679609,0,0.451052955872166,0.313129023768005,0.0555694062070307,0.232240431040792,0.328396152435088,0.190714085371158,0.221006873012398,0.273441543989027,0.198320387665648,0.219032729756858,0.0802332713627146,0.11721277736131,0.107784894264258,0,0.0407008327132364,0,0.232874726698813,0.152965337431574,0.219738986542308,0.0698566296461665,0.130312767515111,0,0,0,0.108034143853115,0,0,0,0,0,0,0.195802046114694,0.0464009723343685,0,0,0.187529586342753,0,0,0,0,0,0,0,0,0,0.222071545190249,0.153310840807784,0,0.107480362063099,0,0.118383716248073,0,0.0339614479152723,0,0,0,0,0,0,0,0,0,0,0.187777656048789,0,0,0,0.0296885786825552,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.117615805682075,0.0373740412220293,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0380625695285996,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.639624669661735,0.346755838223862,0,0,0,0,0,0,0,0,0,0,0.534002526650922,0,0.0266094859650764,0,0,0,0.1241754307343,0.118573193298914,0,0,0,0,0,0,0,0.204022632363678,0,0,0,0,0,0,0.169691863105055,0,0,0,0,0.31306863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|full_id=C403_small_Neutrophils_temporal_leiomyoma_Hair_colon_pancreas
|full_id=C403_small_Neutrophils_temporal_leiomyoma_Hair_colon_pancreas
|gostat_on_coexpression_clusters=GO:0016284!alanine aminopeptidase activity!0.02320538482672!290$GO:0004179!membrane alanyl aminopeptidase activity!0.02320538482672!290$GO:0005793!ER-Golgi intermediate compartment!0.02320538482672!290$GO:0004177!aminopeptidase activity!0.0268750735900153!290$GO:0008235!metalloexopeptidase activity!0.0268750735900153!290$GO:0001525!angiogenesis!0.0268750735900153!290$GO:0048514!blood vessel morphogenesis!0.0268750735900153!290$GO:0048646!anatomical structure formation!0.0268750735900153!290$GO:0001568!blood vessel development!0.0268750735900153!290$GO:0001944!vasculature development!0.0268750735900153!290$GO:0008238!exopeptidase activity!0.0275226657247145!290$GO:0042277!peptide binding!0.0280623258369638!290$GO:0005625!soluble fraction!0.0291416460614624!290$GO:0009887!organ morphogenesis!0.0406903724635975!290$GO:0008237!metallopeptidase activity!0.0406903724635975!290
|gostat_on_coexpression_clusters=GO:0016284!alanine aminopeptidase activity!0.02320538482672!290$GO:0004179!membrane alanyl aminopeptidase activity!0.02320538482672!290$GO:0005793!ER-Golgi intermediate compartment!0.02320538482672!290$GO:0004177!aminopeptidase activity!0.0268750735900153!290$GO:0008235!metalloexopeptidase activity!0.0268750735900153!290$GO:0001525!angiogenesis!0.0268750735900153!290$GO:0048514!blood vessel morphogenesis!0.0268750735900153!290$GO:0048646!anatomical structure formation!0.0268750735900153!290$GO:0001568!blood vessel development!0.0268750735900153!290$GO:0001944!vasculature development!0.0268750735900153!290$GO:0008238!exopeptidase activity!0.0275226657247145!290$GO:0042277!peptide binding!0.0280623258369638!290$GO:0005625!soluble fraction!0.0291416460614624!290$GO:0009887!organ morphogenesis!0.0406903724635975!290$GO:0008237!metallopeptidase activity!0.0406903724635975!290

Revision as of 17:04, 12 September 2012


Full id: C403_small_Neutrophils_temporal_leiomyoma_Hair_colon_pancreas



Phase1 CAGE Peaks

Hg19::chr15:90333754..90333771,-p@chr15:90333754..90333771
-
Hg19::chr15:90334271..90334330,-p@chr15:90334271..90334330
-
Hg19::chr15:90335468..90335503,-p@chr15:90335468..90335503
-
Hg19::chr15:90335773..90335792,-p@chr15:90335773..90335792
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Hg19::chr15:90336331..90336350,-p20@ANPEP
Hg19::chr15:90340830..90340881,-p@chr15:90340830..90340881
-
Hg19::chr15:90344690..90344735,-p@chr15:90344690..90344735
-
Hg19::chr15:90344759..90344769,-p@chr15:90344759..90344769
-
Hg19::chr15:90346462..90346504,+p@chr15:90346462..90346504
+
Hg19::chr15:90346527..90346545,-p@chr15:90346527..90346545
-
Hg19::chr15:90346711..90346744,-p@chr15:90346711..90346744
-
Hg19::chr15:90346918..90346991,-p@chr15:90346918..90346991
-
Hg19::chr15:90347171..90347214,-p8@ANPEP
Hg19::chr15:90347564..90347578,-p15@ANPEP
Hg19::chr15:90347748..90347765,-p19@ANPEP
Hg19::chr15:90347792..90347817,-p6@ANPEP
Hg19::chr15:90348382..90348416,-p16@ANPEP
Hg19::chr15:90348639..90348671,-p12@ANPEP
Hg19::chr15:90348673..90348697,-p11@ANPEP
Hg19::chr15:90349254..90349268,-p@chr15:90349254..90349268
-
Hg19::chr15:90349462..90349473,-p11@AB462940
Hg19::chr15:90349509..90349523,-p7@AB462940
Hg19::chr15:90349753..90349762,-p9@AB462940
Hg19::chr15:90349765..90349774,-p10@AB462940
Hg19::chr15:90349797..90349814,-p3@AB462940
Hg19::chr15:90349899..90349910,-p14@ANPEP


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:0016284alanine aminopeptidase activity0.02320538482672
GO:0004179membrane alanyl aminopeptidase activity0.02320538482672
GO:0005793ER-Golgi intermediate compartment0.02320538482672
GO:0004177aminopeptidase activity0.0268750735900153
GO:0008235metalloexopeptidase activity0.0268750735900153
GO:0001525angiogenesis0.0268750735900153
GO:0048514blood vessel morphogenesis0.0268750735900153
GO:0048646anatomical structure formation0.0268750735900153
GO:0001568blood vessel development0.0268750735900153
GO:0001944vasculature development0.0268750735900153
GO:0008238exopeptidase activity0.0275226657247145
GO:0042277peptide binding0.0280623258369638
GO:0005625soluble fraction0.0291416460614624
GO:0009887organ morphogenesis0.0406903724635975
GO:0008237metallopeptidase activity0.0406903724635975



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
multi fate stem cell9.53e-32430
somatic stem cell2.57e-30436
stem cell1.04e-28444
somatic cell1.78e-25591
connective tissue cell6.44e-20365
non-terminally differentiated cell1.29e-19180
mesenchymal cell7.17e-18358
fibroblast6.73e-1675
muscle precursor cell1.29e-1557
myoblast1.29e-1557
multi-potent skeletal muscle stem cell1.29e-1557
contractile cell1.16e-1459
muscle cell4.80e-1454
CD14-positive, CD16-negative classical monocyte5.05e-1442
myeloid leukocyte6.03e-1476
motile cell8.10e-13390
monopoietic cell1.73e-1263
monocyte1.73e-1263
monoblast1.73e-1263
promonocyte1.73e-1263
macrophage dendritic cell progenitor1.04e-1165
myeloid lineage restricted progenitor cell1.61e-1170
classical monocyte1.61e-1145
granulocyte monocyte progenitor cell1.87e-1171
smooth muscle cell4.67e-1142
smooth muscle myoblast4.67e-1142
mesodermal cell1.20e-10119
electrically responsive cell1.40e-1060
electrically active cell1.40e-1060
skin fibroblast1.48e-0923
vascular associated smooth muscle cell2.93e-0932
animal cell2.44e-08679
eukaryotic cell2.44e-08679
myeloid cell4.97e-08112
common myeloid progenitor4.97e-08112
Uber Anatomy
Ontology termp-valuen
musculoskeletal system1.30e-25167
mesoderm1.41e-21448
mesoderm-derived structure1.41e-21448
presumptive mesoderm1.41e-21448
lateral plate mesoderm3.07e-20216
connective tissue5.03e-19375
dermomyotome9.52e-1970
somite1.07e-1783
paraxial mesoderm1.07e-1783
presomitic mesoderm1.07e-1783
presumptive segmental plate1.07e-1783
trunk paraxial mesoderm1.07e-1783
presumptive paraxial mesoderm1.07e-1783
trunk mesenchyme5.05e-16143
muscle tissue1.15e-1463
musculature1.15e-1463
musculature of body1.15e-1463
skeletal muscle tissue2.87e-1461
striated muscle tissue2.87e-1461
myotome2.87e-1461
multilaminar epithelium5.60e-1482
tissue6.66e-13787
immune system1.29e-12115
bone marrow4.09e-1280
cardiovascular system1.03e-11110
vasculature1.10e-1179
vascular system1.10e-1179
epithelial tube1.61e-11118
circulatory system3.21e-11113
multi-cellular organism4.56e-11659
anatomical system5.30e-11625
artery6.10e-1142
arterial blood vessel6.10e-1142
arterial system6.10e-1142
anatomical group6.56e-11626
vessel9.70e-1169
blood vessel1.16e-1060
epithelial tube open at both ends1.16e-1060
blood vasculature1.16e-1060
vascular cord1.16e-1060
hemolymphoid system3.06e-10112
bone element3.75e-1086
unilaminar epithelium4.01e-10138
skeletal element4.33e-10101
skeletal system4.33e-10101
trunk6.13e-10216
hematopoietic system7.05e-10102
blood island7.05e-10102
systemic artery1.06e-0933
systemic arterial system1.06e-0933
splanchnic layer of lateral plate mesoderm2.39e-0984
integument7.59e-0945
integumental system7.59e-0945
skin of body3.04e-0740
germ layer6.69e-07604
embryonic tissue6.69e-07604
presumptive structure6.69e-07604
epiblast (generic)6.69e-07604
embryonic structure7.42e-07605
developing anatomical structure7.42e-07605


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
HNF4G#317444.42360346560720.0118468334703830.0431556135616787



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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