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Coexpression cluster:C1949: Difference between revisions

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{{Coexpression_clusters
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90502793,-0.098202469762216,0.221611588102807,0.146917605400546,-0.241662864220876|full_id=C1949_mature_liver_Hepatocyte_seminal_ductus_pineal_immature|gostat_on_coexpression_clusters=GO:0046439!L-cysteine metabolic process!0.00103026021429412!1036$GO:0019530!taurine metabolic process!0.00103026021429412!1036$GO:0017172!cysteine dioxygenase activity!0.00103026021429412!1036$GO:0042412!taurine biosynthetic process!0.00103026021429412!1036$GO:0006534!cysteine metabolic process!0.00494488509694741!1036$GO:0000097!sulfur amino acid biosynthetic process!0.013732961356353!1036$GO:0000096!sulfur amino acid metabolic process!0.0170658475389813!1036$GO:0042398!amino acid derivative biosynthetic process!0.0205918601248543!1036$GO:0044272!sulfur compound biosynthetic process!0.0205918601248543!1036$GO:0009069!serine family amino acid metabolic process!0.0226477100970827!1036$GO:0051213!dioxygenase activity!0.023150489273369!1036$GO:0016702!oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen!0.023150489273369!1036$GO:0016701!oxidoreductase activity, acting on single donors with incorporation of molecular oxygen!0.023150489273369!1036$GO:0008652!amino acid biosynthetic process!0.023150489273369!1036$GO:0006790!sulfur metabolic process!0.023150489273369!1036$GO:0006575!amino acid derivative metabolic process!0.023150489273369!1036$GO:0009309!amine biosynthetic process!0.0287971847411023!1036$GO:0044271!nitrogen compound biosynthetic 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|full_id=C1949_mature_liver_Hepatocyte_seminal_ductus_pineal_immature
|id=C1949
}}

Latest revision as of 11:55, 17 September 2013


Full id: C1949_mature_liver_Hepatocyte_seminal_ductus_pineal_immature



Phase1 CAGE Peaks

Hg19::chr5:115152347..115152363,-p1@CDO1
Hg19::chr9:130860731..130860742,+p6@SLC25A25
Hg19::chr9:130860748..130860774,+p5@SLC25A25
Hg19::chr9:130860779..130860800,+p3@SLC25A25
Hg19::chr9:130860810..130860828,+p2@SLC25A25


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:0046439L-cysteine metabolic process0.00103026021429412
GO:0019530taurine metabolic process0.00103026021429412
GO:0017172cysteine dioxygenase activity0.00103026021429412
GO:0042412taurine biosynthetic process0.00103026021429412
GO:0006534cysteine metabolic process0.00494488509694741
GO:0000097sulfur amino acid biosynthetic process0.013732961356353
GO:0000096sulfur amino acid metabolic process0.0170658475389813
GO:0042398amino acid derivative biosynthetic process0.0205918601248543
GO:0044272sulfur compound biosynthetic process0.0205918601248543
GO:0009069serine family amino acid metabolic process0.0226477100970827
GO:0051213dioxygenase activity0.023150489273369
GO:0016702oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen0.023150489273369
GO:0016701oxidoreductase activity, acting on single donors with incorporation of molecular oxygen0.023150489273369
GO:0008652amino acid biosynthetic process0.023150489273369
GO:0006790sulfur metabolic process0.023150489273369
GO:0006575amino acid derivative metabolic process0.023150489273369
GO:0009309amine biosynthetic process0.0287971847411023
GO:0044271nitrogen compound biosynthetic process0.0335828456911871



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><br>

Uber Anatomy
Ontology termp-valuen
anatomical cluster1.09e-16373
multi-tissue structure1.65e-13342
multi-cellular organism1.92e-13656
organ8.94e-12503
adult organism1.09e-11114
anatomical conduit1.11e-11240
anatomical system2.06e-11624
anatomical group4.21e-11625
epithelium1.40e-10306
cell layer2.40e-10309
tube1.21e-08192
developing anatomical structure1.80e-08581
organ system subdivision1.92e-08223
embryo2.05e-08592
germ layer4.01e-08560
germ layer / neural crest4.01e-08560
embryonic tissue4.01e-08560
presumptive structure4.01e-08560
germ layer / neural crest derived structure4.01e-08560
epiblast (generic)4.01e-08560
embryonic structure4.71e-08564
organ part1.01e-07218
immaterial anatomical entity3.05e-07117
primordium8.40e-07160
digestive system8.60e-07145
digestive tract8.60e-07145
primitive gut8.60e-07145
organism subdivision9.60e-07264


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)
MA0003.10.481059
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.10.161847
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.195817
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.0853006
MA0056.10
MA0057.10.189508
MA0058.10.523638
MA0059.10.522232
MA0060.15.26847
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.00220137
MA0074.10.730989
MA0076.11.33654
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.11.3271
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.10.175503
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.277033
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.938075
MA0145.10.143698
MA0146.10.0359558
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.20.0118463
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.136971
MA0065.20.449243
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.10.409315
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.469165
MA0163.10.168633
MA0164.10.810347
MA0080.20.456437
MA0018.24.41372
MA0099.20.699641
MA0079.20.00732454
MA0102.21.66336
MA0258.10.345771
MA0259.10.395396
MA0442.10



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
BRCA1#672416.1473845145792.89130901545765e-050.000605262421858852
CEBPB#105146.376918100659850.001113944176677320.0076584303777238
E2F4#1874410.13444825222760.0001818201509632970.00220368048583681
EP300#203356.77394172622327.00901578206049e-050.0011097856265352
FOSL2#2355413.54416048364945.7953819349229e-050.000965179228036059
GTF2F1#2962410.19172870140610.000177833889427640.0021596271602248
HEY1#2346254.040111043105710.0009288852205177990.00674818054713818
HNF4A#3172418.5058322903631.68463364181741e-050.000387877982622947
HNF4G#3174423.00273802115747.10515202727268e-060.000204874371224829
HSF1#32974131.4325333333336.79362350565572e-095.3267210608647e-07
IRF3#3661437.58556176919171.00727027008258e-064.25215439519621e-05
JUN#3725410.01026335386910.0001908531347801070.00230620277025333
JUND#372745.595731153496820.001849593301755460.0109382601835809
MAX#414945.16204440720570.002526309009485180.0140037782836167
MXI1#460147.969257303007440.0004668546380070170.00429622271026653
MYC#460944.177825497287520.005691969036823440.0256909786177797
NFYA#4800414.74046455986444.14733626928016e-050.000752508083091297
NFYB#4801413.40783460282926.03169250119439e-050.000991881488162873
RFX5#599349.638328661756080.000221480125815720.00249823553948244
SIN3A#2594244.327107781452110.004977052855762880.0232499182897088
SP1#666744.558705102512720.00407573565781680.019491975289254
STAT3#677448.415571997723390.0003771527211598630.0037446005366684
TAF1#687253.343046285745290.002394600090870310.0135535247610234
TBP#690853.706770687096390.001428755106721120.00920131680279011
TFAP2C#702248.647382887888180.0003390518878174050.00344927334032359
ZNF263#1012758.221841637010682.6606316672286e-050.000572345439121912



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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