Personal tools

Coexpression cluster:C180

From FANTOM5_SSTAR

Revision as of 17:40, 8 August 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C180_skeletal_heart_Hepatocyte_acute_occipital_hippocampus_middle



Phase1 CAGE Peaks

Hg19::chr11:114126059..114126109,+p@chr11:114126059..114126109
+
Hg19::chr1:160111262..160111295,+p@chr1:160111262..160111295
+
Hg19::chr1:160113171..160113182,+p@chr1:160113171..160113182
+
Hg19::chr1:569901..569922,+p1@ENST00000416718
Hg19::chr1:569934..569952,-p@chr1:569934..569952
-
Hg19::chr2:88124475..88124516,+p1@MT-ATP8
Hg19::chr3:25508993..25509011,+p@chr3:25508993..25509011
+
Hg19::chr4:8036848..8036871,-p@chr4:8036848..8036871
-
Hg19::chr5:134259184..134259218,-p@chr5:134259184..134259218
-
Hg19::chr5:134259896..134259899,+p2@MTND6P4
Hg19::chr5:134260273..134260314,-p@chr5:134260273..134260314
-
Hg19::chr5:134261636..134261669,-p1@MTND5P11
Hg19::chr5:134262765..134262773,-p@chr5:134262765..134262773
-
Hg19::chr5:134264011..134264014,-p1@MIR4461
Hg19::chr8:100508136..100508173,-p@chr8:100508136..100508173
-
Hg19::chrM:10053..10073,+p1@AB017116
Hg19::chrM:10173..10184,+p11@uc004cov.3
Hg19::chrM:10464..10480,+p1@uc004cov.3
Hg19::chrM:10568..10581,+p5@uc004cov.3
Hg19::chrM:10642..10656,+p8@uc004cov.3
Hg19::chrM:10671..10697,+p3@uc004cov.3
Hg19::chrM:10722..10734,+p7@uc004cov.3
Hg19::chrM:10741..10754,+p4@uc004cov.3
Hg19::chrM:10758..10771,+p6@uc004cov.3
Hg19::chrM:10850..10862,+p9@uc004cov.3
Hg19::chrM:10882..10893,+p12@uc004cov.3
Hg19::chrM:10902..10945,+p2@uc004cov.3
Hg19::chrM:11163..11176,+p1@AK129724
Hg19::chrM:11216..11233,+p2@AK129724
Hg19::chrM:11243..11254,+p3@Y17178
Hg19::chrM:11272..11283,+p2@Y17178
Hg19::chrM:11324..11335,+p4@Y17178
Hg19::chrM:11437..11449,+p1@Y17178
Hg19::chrM:11554..11580,-p@chrM:11554..11580
-
Hg19::chrM:11795..11807,+p1@uc004cow.1
Hg19::chrM:12331..12348,+p1@uc004cox.3
Hg19::chrM:12769..12780,+p2@uc004cox.3
Hg19::chrM:13632..13643,+p@chrM:13632..13643
+
Hg19::chrM:13938..13949,+p@chrM:13938..13949
+
Hg19::chrM:13966..13989,+p@chrM:13966..13989
+
Hg19::chrM:14077..14089,+p@chrM:14077..14089
+
Hg19::chrM:15039..15050,+p3@BC016999
Hg19::chrM:15149..15161,+p4@BC016999
Hg19::chrM:15168..15192,+p2@BC016999
Hg19::chrM:15239..15263,+p1@BC016999
Hg19::chrM:15280..15291,+p5@BC016999
Hg19::chrM:15293..15304,+p3@AF391805
Hg19::chrM:15306..15332,+p2@AF391805
Hg19::chrM:15419..15448,+p1@AF391805
Hg19::chrM:15517..15545,+p1@uc004coz.1
Hg19::chrM:15611..15622,+p3@uc004coz.1
Hg19::chrM:16098..16117,+p2@uc004coz.1
Hg19::chrM:16145..16159,+p4@uc004coz.1
Hg19::chrM:16183..16194,+p9@uc004coz.1
Hg19::chrM:16229..16242,+p10@uc004coz.1
Hg19::chrM:16274..16381,-p@chrM:16274..16381
-
Hg19::chrM:16481..16490,-p@chrM:16481..16490
-
Hg19::chrM:2028..2040,+p6@uc004cos.3
Hg19::chrM:3299..3324,+p2@TPT1
Hg19::chrM:3434..3445,+p1@AF216862
Hg19::chrM:3565..3576,+p1@AK123234
Hg19::chrM:3695..3706,+p2@AK123234
Hg19::chrM:4012..4049,+p1@M25300
Hg19::chrM:4716..4729,+p1@AK026903
Hg19::chrM:4817..4837,+p4@AF275801
Hg19::chrM:4876..4946,+p2@AF275801
Hg19::chrM:4960..4989,+p1@AF275801
Hg19::chrM:5028..5039,+p5@AF275801
Hg19::chrM:5113..5148,+p3@AF275801
Hg19::chrM:526..537,-p4@uc004coq.3
Hg19::chrM:5984..6024,+p7@uc011mfh.1
Hg19::chrM:6190..6248,+p2@uc011mfh.1
Hg19::chrM:6250..6272,+p4@uc011mfh.1
Hg19::chrM:6330..6392,+p1@uc011mfh.1
Hg19::chrM:6437..6448,+p3@AK026547
Hg19::chrM:6463..6517,+p1@AK026547
Hg19::chrM:6523..6548,+p2@AK026547
Hg19::chrM:6608..6637,+p4@AK026547
Hg19::chrM:6910..6936,+p1@BC018860
Hg19::chrM:7109..7147,+p4@uc004cou.3
Hg19::chrM:7213..7257,+p7@uc004cou.3
Hg19::chrM:7604..7655,+p1@uc004cou.3
Hg19::chrM:7678..7687,+p10@uc004cou.3
Hg19::chrM:7689..7700,+p5@uc004cou.3
Hg19::chrM:7772..7783,+p11@uc004cou.3
Hg19::chrM:7787..7811,+p3@uc004cou.3
Hg19::chrM:7840..7897,+p2@uc004cou.3
Hg19::chrM:7993..8026,+p6@uc004cou.3
Hg19::chrM:8423..8463,+p1@uc011mfi.1
Hg19::chrM:8512..8534,-p@chrM:8512..8534
-
Hg19::chrM:8630..8675,+p2@uc011mfi.1
Hg19::chrM:8717..8734,-p4@AF271776
Hg19::chrM:9226..9255,+p1@AL359334
p1@L08441
Hg19::chrM:9538..9549,+p2@BC023992
Hg19::chrX:125606790..125606809,+p1@MTND4P24


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:0045298tubulin complex0.00417991286942188
GO:0005771multivesicular body0.00417991286942188
GO:0005770late endosome0.0271694336512422
GO:0055074calcium ion homeostasis0.0271694336512422
GO:0006874cellular calcium ion homeostasis0.0271694336512422
GO:0006875cellular metal ion homeostasis0.0271694336512422
GO:0055065metal ion homeostasis0.0271694336512422
GO:0006916anti-apoptosis0.0271694336512422
GO:0030005cellular di-, tri-valent inorganic cation homeostasis0.0271694336512422
GO:0055066di-, tri-valent inorganic cation homeostasis0.0271694336512422
GO:0006816calcium ion transport0.0271694336512422
GO:0005768endosome0.0271694336512422
GO:0030003cellular cation homeostasis0.0271694336512422
GO:0055080cation homeostasis0.0271694336512422
GO:0043066negative regulation of apoptosis0.0271694336512422
GO:0043069negative regulation of programmed cell death0.0271694336512422
GO:0055082cellular chemical homeostasis0.0271694336512422
GO:0006873cellular ion homeostasis0.0271694336512422
GO:0015674di-, tri-valent inorganic cation transport0.0271694336512422
GO:0050801ion homeostasis0.027900918403391
GO:0005874microtubule0.0286894019673956
GO:0048878chemical homeostasis0.0286894019673956
GO:0019725cellular homeostasis0.0340753766528957
GO:0042592homeostatic process0.0417991286942188
GO:0015630microtubule cytoskeleton0.0424421922125913
GO:0005615extracellular space0.0424421922125913
GO:0042981regulation of apoptosis0.0429933895140536
GO:0043067regulation of programmed cell death0.0429933895140536
GO:0030001metal ion transport0.04915000994734



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><br>uberon_data<br>disease_data<br>


Uber Anatomy
Ontology termp-valuen
neural tube3.60e-2057
neural rod3.60e-2057
future spinal cord3.60e-2057
neural keel3.60e-2057
adult organism4.46e-20115
central nervous system3.05e-1782
regional part of forebrain7.07e-1741
forebrain7.07e-1741
future forebrain7.07e-1741
anterior neural tube1.01e-1642
regional part of nervous system5.65e-1694
nervous system5.65e-1694
brain1.69e-1569
future brain1.69e-1569
regional part of brain5.80e-1559
gray matter1.97e-1434
brain grey matter1.97e-1434
telencephalon2.26e-1334
regional part of telencephalon3.63e-1333
cerebral hemisphere7.55e-1332
neurectoderm7.83e-1290
regional part of cerebral cortex1.59e-1122
neural plate2.57e-1186
presumptive neural plate2.57e-1186
neocortex2.86e-1020
cerebral cortex2.03e-0925
pallium2.03e-0925
pre-chordal neural plate1.53e-0861
ectoderm2.01e-07173
presumptive ectoderm2.01e-07173
ectoderm-derived structure5.35e-07169
nucleus of brain8.27e-079
neural nucleus8.27e-079
basal ganglion8.99e-079
nuclear complex of neuraxis8.99e-079
aggregate regional part of brain8.99e-079
collection of basal ganglia8.99e-079
cerebral subcortex8.99e-079
Disease
Ontology termp-valuen
disease of cellular proliferation5.13e-17239
cancer3.08e-16235
cell type cancer5.59e-09143
organ system cancer8.40e-09137


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.