Personal tools

Coexpression cluster:C3624: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 1: Line 1:
{{Coexpression_clusters
{{Coexpression_clusters
|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0504265701716883,0,0,0,0,0,0,0,0,0,0,0.0625128387853364,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0522561809686404,0,0,0,0,0,0,0.0869750240711818,0.0702852779578603,0.29717881608204,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.326613392989952,0,0.240549908522397,0.117672595682223,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.141926672950355,0.104741781954859,0,0,0,0.129877303503011,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0384566032530418,0,0,0.387979180422312,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0267366343438753,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1.11999414118857,0.718986660337222,1.10602920683383,1.23236871682584,0.619776479753698,0,0.0682206429897042,0.360876445088051,0,0.536371294290476,0.87633142724612,0.356863288375568,0.425232851526188,0.861444384422629,0,0,0,0,0,0.0425916600387234,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0390744040629657,0,0,0,0,0,0,0,0,0,0,0,0,0.120729266806363,0,0.173209711509263,0,0,0,0.0642431373077164,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0571597974145305,0,0,0,0,0,0,0.609387400443344,0,0,0,0,0,0,0,0,0,0,0,0.25073299221532,0.252158575354569,0,0,0.098385373642144,0.0921546695012139,0,0,0,0,0,1.06746967086845,1.54888240140395,1.38646796450999,0.219625436886832,0,0,0.0902054036215435,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0505977919678937,0,0,0,0.0914082188667263,0,0.374684632448109,0.643346588432868,0.41133978391229,0,0.115967372264001,0,0.114159389744683,0.210085428295266,0.221323945469862,0.220626815433903,0.211618608948668,0,0,0,0.27133006685894,0.317628064827667,0,0.183036259945092,0,0,0,0,0,0,0.279649371901492,0.29209949161158,0.641290478052651,0,0,0.120782895346206,0,0.079112335990984,0,0,0,0.0584468268118252,0.572122644434782,0,0.148514003485278,0.151802208584906,0.347130606249413,0.198079800894878,0.204234048342335,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.357850505621477,0,0,0.0554560868715733,0.215640892359575,0,0,0,0,0,0,0.758028972021104,1.01439101602445,0.184123832474098,0.0716196360387782,0.332739570830293,0,0,0.304721863811544,0,0,0,0.53078909704316,0,0,0.280236065205986,0,0,0.335166255233928,0.34046263952091,0,0.231677263595219,0,0,0,0,0,0,0,0,0,0,0,0.435779895015581,0,0,0,0.196841684047034,0.443241831651599,0.226099710133404,0,0.210827183867438,0,0,0.677994826614645,0,0.304155888786008,0,0,0,0,0,0,0,0,0,0,0.0641946247847473,0,0.0626808480570541,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.292942235460855,0,0.182411394908525,0,0.0904423417827262,0.0950774961121382,0.186749169737715,0,0,0,0,0.0677931267972615,0.0990731426707233,0,0,0,0,0,0,0,0,0.266054859416761,0,0,0,0,0,0,0,0,0.0444710875952832,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.14382354480865,0,0,0.377726496072456,0,0.934193286856616,0,0.0608566712043477,0.205506209066435,0,0,0.993157643568699,0,0.0550246232064646,0,0,0,0.320966228024776,0,0,0,0,0,0,0,0,0,0,0,0.510947107798475,0,0.314655943152757,0,0,0,0,0,0,0,0.154989455230581,0,0.74299328929719,0,0,0,0,0,0,0,0,0.266413775268255,0,0.644662104209832,1.06111034985017,0,0,0.893617738720494,0,0,0,0,0,0,0,0.126728110199234,0,0,0,0,0,0,0,0.143831671895056,0,0.26606967772796,0,0,0,0,0.0713494635703484,0.131264050546165,0,0,0,0,0.323128486157933,0.0285677922263843,0,0,0,0,0,0.0977197726149849,0,1.06605274036235,0,0,0.261751406228038,0,0,0,0,0,0,0,0,0,0.0461562834654493,0,0,0,0,0,0,0,0.195850654665458,0,0,0.635838725700622,0,0,0.258587567436989,0,0,0
|full_id=C3624_cerebellum_serous_papillary_Renal_signet_teratocarcinoma_osteosarcoma
|full_id=C3624_cerebellum_serous_papillary_Renal_signet_teratocarcinoma_osteosarcoma
|id=C3624
|id=C3624

Revision as of 16:34, 12 September 2012


Full id: C3624_cerebellum_serous_papillary_Renal_signet_teratocarcinoma_osteosarcoma



Phase1 CAGE Peaks

Hg19::chr17:35293932..35293947,-p2@ENST00000529264
Hg19::chr17:35293950..35293973,-p1@ENST00000528383
p1@ENST00000529264
p1@ENST00000532387
Hg19::chr17:35294075..35294102,+p7@LHX1


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

No GOStat results

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
epithelial cell1.54e-12254
kidney cell3.66e-1218
kidney epithelial cell3.66e-1218
kidney tubule cell1.35e-1112
nephron tubule epithelial cell1.35e-1112
epithelial cell of nephron6.12e-1116
kidney cortical cell7.87e-0813
renal cortical epithelial cell7.87e-0813
mesothelial cell2.73e-0719
neural cell5.26e-0725
Uber Anatomy
Ontology termp-valuen
cavitated compound organ3.49e-2232
kidney1.61e-1827
kidney mesenchyme1.61e-1827
kidney rudiment1.61e-1827
kidney field1.61e-1827
central nervous system1.85e-1382
regional part of nervous system4.31e-1394
nervous system4.31e-1394
body cavity precursor7.79e-1363
compound organ7.99e-1369
urinary system structure8.54e-1344
mesonephros9.05e-1318
pronephros9.05e-1318
nephrogenic cord9.05e-1318
pronephric mesoderm9.05e-1318
rostral part of nephrogenic cord9.05e-1318
presumptive pronephric mesoderm9.05e-1318
posterior neural tube1.45e-1215
chordal neural plate1.45e-1215
renal system2.69e-1245
excretory tube8.57e-1217
mesonephric epithelium8.57e-1217
mesonephric tubule8.57e-1217
nephric duct8.57e-1217
kidney epithelium8.57e-1217
renal duct8.57e-1217
mesonephric duct8.57e-1217
pronephric duct8.57e-1217
trunk region element1.11e-11107
renal tubule1.35e-1112
nephron tubule1.35e-1112
nephron tubule epithelium1.35e-1112
anatomical cavity2.35e-1170
intraembryonic coelom3.03e-1121
urogenital ridge6.03e-1120
nephron epithelium6.12e-1116
nephron6.12e-1116
uriniferous tubule6.12e-1116
metanephric mesenchyme6.12e-1116
nephrogenic mesenchyme6.12e-1116
segmental subdivision of hindbrain4.00e-1012
hindbrain4.00e-1012
presumptive hindbrain4.00e-1012
anatomical space5.63e-10104
duct1.18e-0926
brain1.81e-0969
future brain1.81e-0969
head3.33e-09123
segmental subdivision of nervous system4.48e-0913
ectoderm-derived structure5.23e-09169
ectoderm8.58e-09173
presumptive ectoderm8.58e-09173
abdomen element1.17e-0855
abdominal segment element1.17e-0855
organism subdivision2.34e-08365
neural plate2.50e-0886
presumptive neural plate2.50e-0886
neural tube2.97e-0857
neural rod2.97e-0857
future spinal cord2.97e-0857
neural keel2.97e-0857
intermediate mesoderm3.99e-0837
anterior region of body4.02e-08129
craniocervical region4.02e-08129
neurectoderm5.88e-0890
cortex of kidney7.87e-0813
renal parenchyma7.87e-0813
regional part of metencephalon1.83e-079
metencephalon1.83e-079
future metencephalon1.83e-079
cortex4.53e-0716
immaterial anatomical entity5.17e-07126
abdominal segment of trunk5.54e-0761
abdomen5.54e-0761
Disease
Ontology termp-valuen
carcinoma9.61e-13106
cell type cancer7.19e-12143
cancer6.91e-11235
disease of cellular proliferation3.59e-10239


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
E2F6#187635.017155731697390.00791769806886330.0321669766450389
NFYB#4801316.75979325353650.0002123649923296180.00245535120490568



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C3624&oldid=2138434"