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{{Coexpression_clusters
{{Coexpression_clusters
|full_id=C205_mycosis_cord_hairy_xeroderma_CD4_B_b
|full_id=C205_mycosis_cord_hairy_xeroderma_CD4_B_b
|gostat_on_coexpression_clusters=GO:0006955!immune response!0.000349807746282106!4065;27040;7293;55801;6346;4049$GO:0002376!immune system process!0.000426313808965761!4065;27040;7293;55801;6346;4049$GO:0019722!calcium-mediated signaling!0.00630455178790549!27040;4049$GO:0005125!cytokine activity!0.00973443726723401!55801;6346;4049$GO:0051952!regulation of amine transport!0.0168129406759757!4049$GO:0002036!regulation of L-glutamate transport!0.0168129406759757!4049$GO:0051953!negative regulation of amine transport!0.0168129406759757!4049$GO:0051956!negative regulation of amino acid transport!0.0168129406759757!4049$GO:0002037!negative regulation of L-glutamate transport!0.0168129406759757!4049$GO:0051955!regulation of amino acid transport!0.0168129406759757!4049$GO:0005615!extracellular space!0.0168129406759757!55801;6346;4049$GO:0009605!response to external stimulus!0.0247994292453115!4065;6346;4049$GO:0007267!cell-cell signaling!0.0247994292453115!55801;6346;4049$GO:0046325!negative regulation of glucose import!0.0252186099539889!4049$GO:0048535!lymph node development!0.0271409218658873!4049$GO:0050806!positive regulation of synaptic transmission!0.0271409218658873!4049$GO:0001775!cell activation!0.0271409218658873!27040;4049$GO:0051971!positive regulation of transmission of nerve impulse!0.0271409218658873!4049$GO:0043303!mast cell degranulation!0.0271409218658873!27040$GO:0002448!mast cell mediated immunity!0.0271409218658873!27040$GO:0045576!mast cell activation!0.0271409218658873!27040$GO:0043299!leukocyte degranulation!0.0271409218658873!27040$GO:0046323!glucose import!0.0271409218658873!4049$GO:0046324!regulation of glucose import!0.0271409218658873!4049$GO:0031646!positive regulation of neurological process!0.0271409218658873!4049$GO:0005031!tumor necrosis factor receptor activity!0.0271409218658873!7293$GO:0043525!positive regulation of neuron apoptosis!0.0273704643242504!4049$GO:0002444!myeloid leukocyte mediated immunity!0.0273704643242504!27040$GO:0043120!tumor necrosis factor binding!0.0273704643242504!7293$GO:0044421!extracellular region part!0.027743861225859!55801;6346;4049$GO:0005035!death receptor activity!0.027743861225859!7293$GO:0016021!integral to membrane!0.027743861225859!7352;4065;780776;27040;7293;120425;4049$GO:0031224!intrinsic to membrane!0.027743861225859!7352;4065;780776;27040;7293;120425;4049$GO:0051222!positive regulation of protein transport!0.027743861225859!4049$GO:0019932!second-messenger-mediated signaling!0.027743861225859!27040;4049$GO:0051239!regulation of multicellular organismal process!0.0285894817718104!27040;4049$GO:0045840!positive regulation of mitosis!0.0285894817718104!4049$GO:0006954!inflammatory response!0.028644406585695!4065;6346$GO:0015813!L-glutamate transport!0.028644406585695!4049$GO:0015800!acidic amino acid transport!0.028644406585695!4049$GO:0005102!receptor binding!0.030947997828804!55801;6346;4049$GO:0050804!regulation of synaptic transmission!0.033559563047681!4049$GO:0009612!response to mechanical stimulus!0.0340307536623605!4049$GO:0001772!immunological synapse!0.0340307536623605!27040$GO:0051969!regulation of transmission of nerve impulse!0.0352261380904179!4049$GO:0044459!plasma membrane part!0.0354480104691158!4065;27040;7293;120425$GO:0016020!membrane!0.0372626362680686!7352;4065;23180;27040;120425;780776;7293;4049$GO:0005886!plasma membrane!0.0372626362680686!4065;23180;27040;7293;120425$GO:0044425!membrane part!0.0422303467262425!7352;4065;780776;27040;7293;120425;4049$GO:0045787!positive regulation of progression through cell cycle!0.0422303467262425!4049$GO:0031644!regulation of neurological process!0.0422911808133526!4049$GO:0043523!regulation of neuron apoptosis!0.0422911808133526!4049$GO:0009611!response to wounding!0.0439685993139882!4065;6346$GO:0002274!myeloid leukocyte activation!0.0439685993139882!27040$GO:0051223!regulation of protein transport!0.0447607868065524!4049$GO:0007585!respiratory gaseous exchange!0.0453502471319412!7352$GO:0051402!neuron apoptosis!0.0453502471319412!4049$GO:0015758!glucose transport!0.0453502471319412!4049$GO:0051051!negative regulation of transport!0.0453502471319412!4049$GO:0008645!hexose transport!0.0453502471319412!4049$GO:0015749!monosaccharide transport!0.0453502471319412!4049$GO:0003993!acid phosphatase activity!0.0453502471319412!92370
|id=C205
|id=C205
}}
}}

Revision as of 17:36, 18 May 2012


Full id: C205_mycosis_cord_hairy_xeroderma_CD4_B_b



Phase1 CAGE Peaks

Hg19::chr10:110789709..110789714,-p@chr10:110789709..110789714
-
Hg19::chr10:89577732..89577739,-p13@ATAD1
Hg19::chr11:118075251..118075262,-p7@AMICA1
Hg19::chr11:35109970..35109983,+p@chr11:35109970..35109983
+
Hg19::chr11:35110037..35110046,+p@chr11:35110037..35110046
+
Hg19::chr11:73720276..73720286,-p2@UCP3
Hg19::chr12:104319259..104319279,+p@chr12:104319259..104319279
+
Hg19::chr12:29165730..29165749,-p@chr12:29165730..29165749
-
Hg19::chr12:39299722..39299767,-p5@CPNE8
Hg19::chr12:68619488..68619503,-p3@IL26
Hg19::chr12:68619586..68619593,-p1@IL26
Hg19::chr12:81172256..81172287,+p@chr12:81172256..81172287
+
Hg19::chr13:39462565..39462604,-p@chr13:39462565..39462604
-
Hg19::chr13:40880982..40881019,-p@chr13:40880982..40881019
-
Hg19::chr13:40881048..40881070,-p@chr13:40881048..40881070
-
Hg19::chr13:42968329..42968343,+p@chr13:42968329..42968343
+
Hg19::chr13:50802126..50802138,+p@chr13:50802126..50802138
+
Hg19::chr14:22355984..22355994,+p2@TRAV12-2
Hg19::chr14:22356029..22356043,+p1@TRAV12-2
Hg19::chr14:22356073..22356080,+p3@TRAV12-2
Hg19::chr14:22356128..22356162,+p4@TRAV12-2
Hg19::chr14:22356420..22356461,+p1@AB305742
p1@AF532837
p1@AF532838
p1@AF532839
p1@AF532840
p1@AF532841
p1@AF532842
p1@AF532843
p1@AF532844
p1@AF532845
p1@AF532847
p1@AF532848
p1@AF532849
p1@AF532850
p1@AF532851
p1@AF532852
p1@AF532853
p1@AF532854
p1@AF532856
p1@AY135832
p1@AY135833
p1@AY135834
p1@AY135835
p1@AY135836
p1@AY135837
p1@AY135838
p1@AY135839
p1@AY135840
p1@AY135841
p1@AY135842
p1@AY135843
p1@AY135844
p1@AY135846
p1@AY135847
p1@AY135849
p1@AY135850
p1@AY135851
p1@AY135852
p1@AY135853
p1@EU340840
p1@M17652
p1@M17653
p1@M27369
p1@S82064
p1@X04940
p1@X04946
p1@X92766
p1@X92783
p1@X92883
Hg19::chr14:51651959..51651967,-p@chr14:51651959..51651967
-
Hg19::chr14:65803148..65803157,+p@chr14:65803148..65803157
+
Hg19::chr14:65803162..65803174,+p@chr14:65803162..65803174
+
Hg19::chr14:82495120..82495125,-p@chr14:82495120..82495125
-
Hg19::chr15:45174767..45174793,-p@chr15:45174767..45174793
-
Hg19::chr16:10912591..10912602,-p10@FAM18A
Hg19::chr16:11301790..11301804,+p1@AK127887
Hg19::chr16:11301814..11301825,+p2@AK127887
Hg19::chr16:28996572..28996586,+p6@LAT
Hg19::chr17:32687516..32687555,-p@chr17:32687516..32687555
-
Hg19::chr17:32690382..32690387,-p2@CCL1
Hg19::chr17:32690435..32690446,-p3@CCL1
Hg19::chr18:56816533..56816576,+p@chr18:56816533..56816576
+
Hg19::chr19:35476657..35476668,+p@chr19:35476657..35476668
+
Hg19::chr19:35492016..35492027,+p@chr19:35492016..35492027
+
Hg19::chr19:35492031..35492059,+p@chr19:35492031..35492059
+
Hg19::chr19:4229557..4229568,+p1@CU677281
Hg19::chr19:4229572..4229583,+p2@CU677281
Hg19::chr1:1148422..1148468,-p@chr1:1148422..1148468
-
Hg19::chr1:1149506..1149515,-p2@TNFRSF4
Hg19::chr1:1173212..1173215,-p@chr1:1173212..1173215
-
Hg19::chr1:93043060..93043065,-p@chr1:93043060..93043065
-
Hg19::chr1:93043102..93043113,-p@chr1:93043102..93043113
-
Hg19::chr1:93043161..93043170,-p@chr1:93043161..93043170
-
Hg19::chr1:98642709..98642713,-p@chr1:98642709..98642713
-
Hg19::chr20:44692500..44692506,-p@chr20:44692500..44692506
-
Hg19::chr21:36430055..36430067,+p@chr21:36430055..36430067
+
Hg19::chr21:43826483..43826494,-p@chr21:43826483..43826494
-
Hg19::chr21:43826497..43826511,-p@chr21:43826497..43826511
-
Hg19::chr2:160760800..160760805,+p2@AK125488
Hg19::chr2:53979000..53979012,-p@chr2:53979000..53979012
-
Hg19::chr3:140980521..140980532,+p9@ACPL2
Hg19::chr3:16412407..16412418,-p10@RFTN1
Hg19::chr3:186194261..186194278,+p1@ENST00000456535
Hg19::chr3:186194280..186194291,+p2@ENST00000456535
Hg19::chr3:189026010..189026019,+p@chr3:189026010..189026019
+
Hg19::chr4:2934426..2934445,-p8@MFSD10
Hg19::chr5:107253874..107253881,-p@chr5:107253874..107253881
-
Hg19::chr5:107253962..107253972,-p@chr5:107253962..107253972
-
Hg19::chr5:131541116..131541121,-p@chr5:131541116..131541121
-
Hg19::chr6:100604462..100604467,-p@chr6:100604462..100604467
-
Hg19::chr6:128134176..128134183,-p10@THEMIS
Hg19::chr6:31540488..31540521,+p2@LTA
Hg19::chr6:31541252..31541272,+p@chr6:31541252..31541272
+
Hg19::chr6:31541315..31541329,-p1@CU689955
Hg19::chr7:109650548..109650592,+p@chr7:109650548..109650592
+
Hg19::chr7:109650713..109650723,+p@chr7:109650713..109650723
+
Hg19::chr7:142511059..142511075,-p2@TRBV30
Hg19::chr8:124008167..124008169,+p@chr8:124008167..124008169
+
Hg19::chr8:29351739..29351773,+p@chr8:29351739..29351773
+
Hg19::chr8:42037604..42037608,-p@chr8:42037604..42037608
-
Hg19::chr9:87359709..87359717,+p@chr9:87359709..87359717
+
Hg19::chr9:92116537..92116544,-p@chr9:92116537..92116544
-
Hg19::chr9:92116561..92116575,-p@chr9:92116561..92116575
-
Hg19::chr9:93728939..93728974,-p@chr9:93728939..93728974
-
Hg19::chr9:93917134..93917162,-p@chr9:93917134..93917162
-


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:0006955immune response0.000349807746282106
GO:0002376immune system process0.000426313808965761
GO:0019722calcium-mediated signaling0.00630455178790549
GO:0005125cytokine activity0.00973443726723401
GO:0051952regulation of amine transport0.0168129406759757
GO:0002036regulation of L-glutamate transport0.0168129406759757
GO:0051953negative regulation of amine transport0.0168129406759757
GO:0051956negative regulation of amino acid transport0.0168129406759757
GO:0002037negative regulation of L-glutamate transport0.0168129406759757
GO:0051955regulation of amino acid transport0.0168129406759757
GO:0005615extracellular space0.0168129406759757
GO:0009605response to external stimulus0.0247994292453115
GO:0007267cell-cell signaling0.0247994292453115
GO:0046325negative regulation of glucose import0.0252186099539889
GO:0048535lymph node development0.0271409218658873
GO:0050806positive regulation of synaptic transmission0.0271409218658873
GO:0001775cell activation0.0271409218658873
GO:0051971positive regulation of transmission of nerve impulse0.0271409218658873
GO:0043303mast cell degranulation0.0271409218658873
GO:0002448mast cell mediated immunity0.0271409218658873
GO:0045576mast cell activation0.0271409218658873
GO:0043299leukocyte degranulation0.0271409218658873
GO:0046323glucose import0.0271409218658873
GO:0046324regulation of glucose import0.0271409218658873
GO:0031646positive regulation of neurological process0.0271409218658873
GO:0005031tumor necrosis factor receptor activity0.0271409218658873
GO:0043525positive regulation of neuron apoptosis0.0273704643242504
GO:0002444myeloid leukocyte mediated immunity0.0273704643242504
GO:0043120tumor necrosis factor binding0.0273704643242504
GO:0044421extracellular region part0.027743861225859
GO:0005035death receptor activity0.027743861225859
GO:0016021integral to membrane0.027743861225859
GO:0031224intrinsic to membrane0.027743861225859
GO:0051222positive regulation of protein transport0.027743861225859
GO:0019932second-messenger-mediated signaling0.027743861225859
GO:0051239regulation of multicellular organismal process0.0285894817718104
GO:0045840positive regulation of mitosis0.0285894817718104
GO:0006954inflammatory response0.028644406585695
GO:0015813L-glutamate transport0.028644406585695
GO:0015800acidic amino acid transport0.028644406585695
GO:0005102receptor binding0.030947997828804
GO:0050804regulation of synaptic transmission0.033559563047681
GO:0009612response to mechanical stimulus0.0340307536623605
GO:0001772immunological synapse0.0340307536623605
GO:0051969regulation of transmission of nerve impulse0.0352261380904179
GO:0044459plasma membrane part0.0354480104691158
GO:0016020membrane0.0372626362680686
GO:0005886plasma membrane0.0372626362680686
GO:0044425membrane part0.0422303467262425
GO:0045787positive regulation of progression through cell cycle0.0422303467262425
GO:0031644regulation of neurological process0.0422911808133526
GO:0043523regulation of neuron apoptosis0.0422911808133526
GO:0009611response to wounding0.0439685993139882
GO:0002274myeloid leukocyte activation0.0439685993139882
GO:0051223regulation of protein transport0.0447607868065524
GO:0007585respiratory gaseous exchange0.0453502471319412
GO:0051402neuron apoptosis0.0453502471319412
GO:0015758glucose transport0.0453502471319412
GO:0051051negative regulation of transport0.0453502471319412
GO:0008645hexose transport0.0453502471319412
GO:0015749monosaccharide transport0.0453502471319412
GO:0003993acid phosphatase activity0.0453502471319412



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>disease_data<br>

Cell Type
Ontology termp-valuen

Uber Anatomy
Ontology termp-valuen

Disease
Ontology termp-valuen


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

"{{{coexpression_dpi_cluster_scores_median}}}" is not a number.

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