Coexpression cluster:C770: Difference between revisions
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Latest revision as of 11:30, 17 September 2013
Full id: C770_Mesenchymal_chorionic_tubular_ovary_Smooth_mesenchymal_granulosa
Phase1 CAGE Peaks
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 ID | GO name | FDR corrected p-value |
---|---|---|
GO:0018993 | somatic sex determination | 0.000718238549393618 |
GO:0019101 | female somatic sex determination | 0.000718238549393618 |
GO:0002074 | extraocular skeletal muscle development | 0.000718238549393618 |
GO:0030237 | female sex determination | 0.000718238549393618 |
GO:0042703 | menstruation | 0.000718238549393618 |
GO:0060014 | granulosa cell differentiation | 0.00119706424898936 |
GO:0048048 | embryonic eye morphogenesis | 0.00205211014112462 |
GO:0048562 | embryonic organ morphogenesis | 0.00448899093371011 |
GO:0006309 | DNA fragmentation during apoptosis | 0.00495926617438451 |
GO:0001541 | ovarian follicle development | 0.00495926617438451 |
GO:0048568 | embryonic organ development | 0.00495926617438451 |
GO:0007530 | sex determination | 0.00495926617438451 |
GO:0043028 | caspase regulator activity | 0.00495926617438451 |
GO:0006921 | cell structure disassembly during apoptosis | 0.00495926617438451 |
GO:0030262 | apoptotic nuclear changes | 0.00495926617438451 |
GO:0022601 | menstrual cycle phase | 0.00495926617438451 |
GO:0022602 | menstrual cycle process | 0.00495926617438451 |
GO:0048592 | eye morphogenesis | 0.00495926617438451 |
GO:0008585 | female gonad development | 0.00495926617438451 |
GO:0046545 | development of primary female sexual characteristics | 0.00495926617438451 |
GO:0046660 | female sex differentiation | 0.00495926617438451 |
GO:0042698 | menstrual cycle | 0.00523715608932846 |
GO:0043010 | camera-type eye development | 0.00523715608932846 |
GO:0006308 | DNA catabolic process | 0.00523715608932846 |
GO:0006997 | nuclear organization and biogenesis | 0.0054586129753915 |
GO:0001654 | eye development | 0.00622473409474469 |
GO:0022411 | cellular component disassembly | 0.00622473409474469 |
GO:0043280 | positive regulation of caspase activity | 0.00622473409474469 |
GO:0008406 | gonad development | 0.00622473409474469 |
GO:0048608 | reproductive structure development | 0.00622473409474469 |
GO:0045137 | development of primary sexual characteristics | 0.0064430222813251 |
GO:0043281 | regulation of caspase activity | 0.0064430222813251 |
GO:0048609 | reproductive process in a multicellular organism | 0.0064430222813251 |
GO:0032504 | multicellular organism reproduction | 0.0064430222813251 |
GO:0007519 | skeletal muscle development | 0.00687456897276748 |
GO:0051345 | positive regulation of hydrolase activity | 0.00758140691026597 |
GO:0007548 | sex differentiation | 0.00779551596293073 |
GO:0007423 | sensory organ development | 0.00779551596293073 |
GO:0003006 | reproductive developmental process | 0.00779551596293073 |
GO:0014706 | striated muscle development | 0.00779551596293073 |
GO:0008632 | apoptotic program | 0.00779551596293073 |
GO:0048598 | embryonic morphogenesis | 0.00795192679685792 |
GO:0045944 | positive regulation of transcription from RNA polymerase II promoter | 0.0116087393448503 |
GO:0007517 | muscle development | 0.0140382989199662 |
GO:0006917 | induction of apoptosis | 0.0166287838066131 |
GO:0012502 | induction of programmed cell death | 0.0166287838066131 |
GO:0045893 | positive regulation of transcription, DNA-dependent | 0.0170390634590188 |
GO:0009790 | embryonic development | 0.0175818811570313 |
GO:0043085 | positive regulation of catalytic activity | 0.018167210367015 |
GO:0043065 | positive regulation of apoptosis | 0.018167210367015 |
GO:0043068 | positive regulation of programmed cell death | 0.018167210367015 |
GO:0045941 | positive regulation of transcription | 0.0192681303154634 |
GO:0045935 | positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 0.0195821642240336 |
GO:0022414 | reproductive process | 0.0200453849694401 |
GO:0051336 | regulation of hydrolase activity | 0.0200453849694401 |
GO:0009887 | organ morphogenesis | 0.0229962342569009 |
GO:0031325 | positive regulation of cellular metabolic process | 0.0229962342569009 |
GO:0009893 | positive regulation of metabolic process | 0.0242095924838711 |
GO:0006357 | regulation of transcription from RNA polymerase II promoter | 0.0257470259655509 |
GO:0043285 | biopolymer catabolic process | 0.0271733584520586 |
GO:0042981 | regulation of apoptosis | 0.0333633390686068 |
GO:0043067 | regulation of programmed cell death | 0.0333633390686068 |
GO:0050790 | regulation of catalytic activity | 0.0344868509827888 |
GO:0009057 | macromolecule catabolic process | 0.0350702416696102 |
GO:0006366 | transcription from RNA polymerase II promoter | 0.0353594362778397 |
GO:0065009 | regulation of a molecular function | 0.0365104595941756 |
GO:0044248 | cellular catabolic process | 0.043362312422346 |
GO:0006915 | apoptosis | 0.0447360010765168 |
GO:0012501 | programmed cell death | 0.0447360010765168 |
GO:0043565 | sequence-specific DNA binding | 0.0447360010765168 |
GO:0016265 | death | 0.0452889307534309 |
GO:0008219 | cell death | 0.0452889307534309 |
GO:0048522 | positive regulation of cellular process | 0.0469314778165419 |
GO:0009056 | catabolic process | 0.0472193316594588 |
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>
Ontology term | p-value | n |
---|---|---|
female reproductive organ | 1.51e-10 | 37 |
female reproductive system | 1.51e-10 | 37 |
embryonic uterus | 2.46e-09 | 22 |
female organism | 2.47e-09 | 41 |
reproductive organ | 2.60e-09 | 48 |
reproductive structure | 1.07e-08 | 59 |
reproductive system | 1.07e-08 | 59 |
uterus | 2.65e-07 | 21 |
internal female genitalia | 6.09e-07 | 22 |
Ontology term | p-value | n |
---|---|---|
cell type benign neoplasm | 3.81e-07 | 3 |
leiomyoma | 3.81e-07 | 3 |
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) |
---|---|
MA0003.1 | 1.92888 |
MA0004.1 | 0.349539 |
MA0006.1 | 0.605586 |
MA0007.1 | 2.41122 |
MA0009.1 | 0.79061 |
MA0014.1 | 1.37711 |
MA0017.1 | 0.24363 |
MA0019.1 | 0.486183 |
MA0024.1 | 1.64584 |
MA0025.1 | 0.921763 |
MA0027.1 | 2.39404 |
MA0028.1 | 0.224112 |
MA0029.1 | 0.707146 |
MA0030.1 | 0.696006 |
MA0031.1 | 0.633489 |
MA0038.1 | 0.443833 |
MA0040.1 | 0.712837 |
MA0041.1 | 0.366339 |
MA0042.1 | 0.337481 |
MA0043.1 | 0.790919 |
MA0046.1 | 0.779945 |
MA0048.1 | 0.0494179 |
MA0050.1 | 0.338274 |
MA0051.1 | 0.439895 |
MA0052.1 | 0.716602 |
MA0055.1 | 0.00989454 |
MA0056.1 | 0 |
MA0057.1 | 3.20993 |
MA0058.1 | 0.265212 |
MA0059.1 | 0.2641 |
MA0060.1 | 0.119532 |
MA0061.1 | 0.100525 |
MA0063.1 | 0 |
MA0066.1 | 0.444231 |
MA0067.1 | 1.1037 |
MA0068.1 | 0.0758327 |
MA0069.1 | 0.776171 |
MA0070.1 | 0.765217 |
MA0071.1 | 0.40788 |
MA0072.1 | 0.760818 |
MA0073.1 | 0.304769 |
MA0074.1 | 0.439193 |
MA0076.1 | 0.278993 |
MA0077.1 | 0.753278 |
MA0078.1 | 0.533387 |
MA0081.1 | 1.34305 |
MA0083.1 | 0.79797 |
MA0084.1 | 1.28962 |
MA0087.1 | 0.758426 |
MA0088.1 | 0.0234479 |
MA0089.1 | 0 |
MA0090.1 | 0.792817 |
MA0091.1 | 0.351901 |
MA0092.1 | 0.318032 |
MA0093.1 | 0.213288 |
MA0095.1 | 0 |
MA0098.1 | 0 |
MA0100.1 | 0.456802 |
MA0101.1 | 0.216017 |
MA0103.1 | 0.587485 |
MA0105.1 | 1.91523 |
MA0106.1 | 0.482519 |
MA0107.1 | 0.156959 |
MA0108.2 | 0.630531 |
MA0109.1 | 0 |
MA0111.1 | 2.26737 |
MA0113.1 | 0.498009 |
MA0114.1 | 0.908082 |
MA0115.1 | 1.02805 |
MA0116.1 | 0.159642 |
MA0117.1 | 0.827487 |
MA0119.1 | 0.250314 |
MA0122.1 | 0.852927 |
MA0124.1 | 0.98702 |
MA0125.1 | 0.904129 |
MA0130.1 | 0 |
MA0131.1 | 0.550695 |
MA0132.1 | 0 |
MA0133.1 | 0 |
MA0135.1 | 0.820382 |
MA0136.1 | 0.450422 |
MA0139.1 | 2.79395 |
MA0140.1 | 0.405425 |
MA0141.1 | 0.2626 |
MA0142.1 | 0.602852 |
MA0143.1 | 0.498176 |
MA0144.1 | 0.142196 |
MA0145.1 | 0.515404 |
MA0146.1 | 1.91914 |
MA0147.1 | 0.162359 |
MA0148.1 | 0.372124 |
MA0149.1 | 0.396509 |
MA0062.2 | 0.0969238 |
MA0035.2 | 0.404774 |
MA0039.2 | 3.21617 |
MA0138.2 | 0.534556 |
MA0002.2 | 0.111226 |
MA0137.2 | 0.229531 |
MA0104.2 | 0.118985 |
MA0047.2 | 0.47109 |
MA0112.2 | 0.487949 |
MA0065.2 | 1.6488 |
MA0150.1 | 0.286461 |
MA0151.1 | 0 |
MA0152.1 | 0.411494 |
MA0153.1 | 0.887528 |
MA0154.1 | 1.89039 |
MA0155.1 | 0.0230394 |
MA0156.1 | 0.231442 |
MA0157.1 | 0.576556 |
MA0158.1 | 0 |
MA0159.1 | 7.34279 |
MA0160.1 | 0.386031 |
MA0161.1 | 0 |
MA0162.1 | 0.324348 |
MA0163.1 | 0.122012 |
MA0164.1 | 0.509774 |
MA0080.2 | 0.21336 |
MA0018.2 | 0.483823 |
MA0099.2 | 0.411824 |
MA0079.2 | 12.3862 |
MA0102.2 | 1.32663 |
MA0258.1 | 0.135061 |
MA0259.1 | 0.168926 |
MA0442.1 | 0 |
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 | #promoters | Enrichment | p-value | q-value |
---|---|---|---|---|
CCNT2#905 | 9 | 5.18416492660579 | 2.45776684955985e-06 | 8.6835829499723e-05 |
CEBPB#1051 | 8 | 5.79719827332714 | 7.09770251647579e-06 | 0.000204772638982932 |
E2F1#1869 | 9 | 4.01513663035581 | 2.22155664174121e-05 | 0.000486205268455176 |
E2F6#1876 | 8 | 3.64884053214355 | 0.000229244879929919 | 0.00252847249075941 |
EGR1#1958 | 9 | 4.08123744120829 | 1.93184303045374e-05 | 0.00043586034620341 |
ELF1#1997 | 8 | 3.09679851549639 | 0.000758011352761729 | 0.00595815064883587 |
HEY1#23462 | 8 | 2.93826257680415 | 0.00110599738805138 | 0.00768626971058677 |
HMGN3#9324 | 9 | 6.69153904637776 | 2.65773098024031e-07 | 1.36936736973516e-05 |
NRF1#4899 | 8 | 8.88020323469884 | 2.65835991535536e-07 | 1.36901603155719e-05 |
SMARCB1#6598 | 9 | 14.9340401845833 | 2.20335696545219e-10 | 2.26492517829588e-08 |
SPI1#6688 | 8 | 5.96678073347107 | 5.69573958039735e-06 | 0.000171428629981879 |
TAF1#6872 | 8 | 2.43130638963294 | 0.00420424418913911 | 0.020019471065039 |
TBP#6908 | 9 | 3.03281238035159 | 0.000238825863057691 | 0.00260091077287614 |
USF1#7391 | 8 | 4.62654492887852 | 3.91779279463149e-05 | 0.000731837527595274 |
YY1#7528 | 8 | 3.57176054534826 | 0.000268200586690672 | 0.00286524151732683 |
ZBTB7A#51341 | 8 | 5.34684313300065 | 1.31319566009782e-05 | 0.000320891065851558 |
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.