Coexpression cluster:C1858: Difference between revisions
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Latest revision as of 11:53, 17 September 2013
Full id: C1858_Hepatocyte_parotid_salivary_submaxillary_liver_small_cerebellum
Phase1 CAGE Peaks
| Hg19::chr1:41454160..41454176,+ | p6@CTPS |
| Hg19::chr1:41454185..41454224,+ | p5@CTPS |
| Hg19::chr1:41454251..41454260,+ | p21@CTPS |
| Hg19::chr6:46620445..46620463,- | p1@CYP39A1 |
| Hg19::chr6:46620465..46620476,- | p3@CYP39A1 |
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:0033782 | 24-hydroxycholesterol 7alpha-hydroxylase activity | 0.00300247262451431 |
| GO:0008387 | steroid 7-alpha-hydroxylase activity | 0.00300247262451431 |
| GO:0008396 | oxysterol 7-alpha-hydroxylase activity | 0.00360286108933212 |
| GO:0003883 | CTP synthase activity | 0.00360286108933212 |
| GO:0030573 | bile acid catabolic process | 0.00360286108933212 |
| GO:0006699 | bile acid biosynthetic process | 0.00500345816532559 |
| GO:0006707 | cholesterol catabolic process | 0.00500345816532559 |
| GO:0016127 | sterol catabolic process | 0.00500345816532559 |
| GO:0019752 | carboxylic acid metabolic process | 0.00500345816532559 |
| GO:0006082 | organic acid metabolic process | 0.00500345816532559 |
| GO:0046395 | carboxylic acid catabolic process | 0.00500345816532559 |
| GO:0016054 | organic acid catabolic process | 0.00500345816532559 |
| GO:0008206 | bile acid metabolic process | 0.00643254415861032 |
| GO:0008395 | steroid hydroxylase activity | 0.00643254415861032 |
| GO:0006706 | steroid catabolic process | 0.00680400192983605 |
| GO:0006541 | glutamine metabolic process | 0.00937941257394925 |
| GO:0016709 | oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NADH or NADPH as one donor, and incorporation of one atom of oxygen | 0.0102888888512249 |
| GO:0046036 | CTP metabolic process | 0.0102888888512249 |
| GO:0009209 | pyrimidine ribonucleoside triphosphate biosynthetic process | 0.0102888888512249 |
| GO:0009208 | pyrimidine ribonucleoside triphosphate metabolic process | 0.0102888888512249 |
| GO:0006241 | CTP biosynthetic process | 0.0102888888512249 |
| GO:0009220 | pyrimidine ribonucleotide biosynthetic process | 0.0106981654968376 |
| GO:0009218 | pyrimidine ribonucleotide metabolic process | 0.0106981654968376 |
| GO:0044242 | cellular lipid catabolic process | 0.0120012289244444 |
| GO:0009147 | pyrimidine nucleoside triphosphate metabolic process | 0.0120012289244444 |
| GO:0006221 | pyrimidine nucleotide biosynthetic process | 0.0122314812898656 |
| GO:0044249 | cellular biosynthetic process | 0.0122882589398147 |
| GO:0042493 | response to drug | 0.0134987973254267 |
| GO:0006220 | pyrimidine nucleotide metabolic process | 0.0142733285258762 |
| GO:0008203 | cholesterol metabolic process | 0.0150851187339486 |
| GO:0009064 | glutamine family amino acid metabolic process | 0.0150851187339486 |
| GO:0016053 | organic acid biosynthetic process | 0.0150851187339486 |
| GO:0046394 | carboxylic acid biosynthetic process | 0.0150851187339486 |
| GO:0009058 | biosynthetic process | 0.0152499402383358 |
| GO:0006694 | steroid biosynthetic process | 0.0152499402383358 |
| GO:0016125 | sterol metabolic process | 0.015396771212381 |
| GO:0007586 | digestion | 0.015396771212381 |
| GO:0009201 | ribonucleoside triphosphate biosynthetic process | 0.0190872381079814 |
| GO:0009142 | nucleoside triphosphate biosynthetic process | 0.0193648990451604 |
| GO:0009199 | ribonucleoside triphosphate metabolic process | 0.0197781111761532 |
| GO:0016042 | lipid catabolic process | 0.0209721444520474 |
| GO:0009141 | nucleoside triphosphate metabolic process | 0.0209721444520474 |
| GO:0009260 | ribonucleotide biosynthetic process | 0.0218746911107329 |
| GO:0005792 | microsome | 0.0220070949015963 |
| GO:0042598 | vesicular fraction | 0.0220070949015963 |
| GO:0009259 | ribonucleotide metabolic process | 0.0220070949015963 |
| GO:0016705 | oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen | 0.0225557870057453 |
| GO:0008202 | steroid metabolic process | 0.0278068183692588 |
| GO:0004497 | monooxygenase activity | 0.028456624280113 |
| GO:0009165 | nucleotide biosynthetic process | 0.0305107289082287 |
| GO:0032787 | monocarboxylic acid metabolic process | 0.0328298187167133 |
| GO:0020037 | heme binding | 0.0328298187167133 |
| GO:0046906 | tetrapyrrole binding | 0.0328298187167133 |
| GO:0008610 | lipid biosynthetic process | 0.0368495454127848 |
| GO:0009117 | nucleotide metabolic process | 0.0369362602454575 |
| GO:0055086 | nucleobase, nucleoside and nucleotide metabolic process | 0.0388719701314618 |
| GO:0016879 | ligase activity, forming carbon-nitrogen bonds | 0.0388719701314618 |
| GO:0006066 | alcohol metabolic process | 0.0457713421174718 |
| GO:0005789 | endoplasmic reticulum membrane | 0.0463011143602194 |
| GO:0042175 | nuclear envelope-endoplasmic reticulum network | 0.0463365297057089 |
| GO:0006520 | amino acid metabolic process | 0.0463365297057089 |
| GO:0005506 | iron ion binding | 0.0483575825870521 |
| GO:0044432 | endoplasmic reticulum part | 0.0491860097835861 |
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>
| Ontology term | p-value | n |
|---|---|---|
| metabolising cell | 1.15e-12 | 12 |
| endopolyploid cell | 1.15e-12 | 12 |
| parenchymal cell | 1.15e-12 | 12 |
| polyploid cell | 1.15e-12 | 12 |
| hepatocyte | 1.15e-12 | 12 |
| Ontology term | p-value | n |
|---|---|---|
| vascular disease | 2.66e-07 | 1 |
| ischemia | 2.66e-07 | 1 |
| extrinsic cardiomyopathy | 2.66e-07 | 1 |
| myocardial ischemia | 2.66e-07 | 1 |
| myocardial infarction | 2.66e-07 | 1 |
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 | 0.136928 |
| MA0004.1 | 0.626788 |
| MA0006.1 | 0.452993 |
| MA0007.1 | 0.606704 |
| MA0009.1 | 1.11255 |
| MA0014.1 | 0.161847 |
| MA0017.1 | 1.24112 |
| MA0019.1 | 0.784036 |
| MA0024.1 | 1.00439 |
| MA0025.1 | 4.50736 |
| MA0027.1 | 2.73598 |
| MA0028.1 | 0.470679 |
| MA0029.1 | 1.02437 |
| MA0030.1 | 1.01252 |
| MA0031.1 | 0.945567 |
| MA0038.1 | 0.736268 |
| MA0040.1 | 1.03042 |
| MA0041.1 | 0.64667 |
| MA0042.1 | 0.612397 |
| MA0043.1 | 2.51533 |
| MA0046.1 | 1.10134 |
| MA0048.1 | 0.195817 |
| MA0050.1 | 0.613347 |
| MA0051.1 | 0.731787 |
| MA0052.1 | 1.03442 |
| MA0055.1 | 0.0853006 |
| MA0056.1 | 0 |
| MA0057.1 | 0.189508 |
| MA0058.1 | 0.523638 |
| MA0059.1 | 0.522232 |
| MA0060.1 | 0.860776 |
| MA0061.1 | 0.791444 |
| MA0063.1 | 0 |
| MA0066.1 | 0.736721 |
| MA0067.1 | 1.43651 |
| MA0068.1 | 0.247962 |
| MA0069.1 | 1.09737 |
| MA0070.1 | 1.08584 |
| MA0071.1 | 2.79236 |
| MA0072.1 | 1.0812 |
| MA0073.1 | 0.00220137 |
| MA0074.1 | 0.730989 |
| MA0076.1 | 0.540943 |
| MA0077.1 | 1.07324 |
| MA0078.1 | 0.836493 |
| MA0081.1 | 0.522409 |
| MA0083.1 | 1.12028 |
| MA0084.1 | 1.62584 |
| MA0087.1 | 1.07867 |
| MA0088.1 | 0.132006 |
| MA0089.1 | 0 |
| MA0090.1 | 1.36977 |
| MA0091.1 | 0.629594 |
| MA0092.1 | 0.588959 |
| MA0093.1 | 0.456342 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.750974 |
| MA0101.1 | 0.459973 |
| MA0103.1 | 0.442769 |
| MA0105.1 | 0.175503 |
| MA0106.1 | 1.83541 |
| MA0107.1 | 0.378225 |
| MA0108.2 | 0.94238 |
| MA0109.1 | 0 |
| MA0111.1 | 1.40074 |
| MA0113.1 | 1.8711 |
| MA0114.1 | 0.372523 |
| MA0115.1 | 1.35895 |
| MA0116.1 | 0.382106 |
| MA0117.1 | 1.1512 |
| MA0119.1 | 0.504689 |
| MA0122.1 | 1.17777 |
| MA0124.1 | 1.31673 |
| MA0125.1 | 1.23103 |
| MA0130.1 | 0 |
| MA0131.1 | 0.855546 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 1.14377 |
| MA0136.1 | 0.743749 |
| MA0139.1 | 0.277033 |
| MA0140.1 | 0.692258 |
| MA0141.1 | 0.520334 |
| MA0142.1 | 0.912455 |
| MA0143.1 | 1.87149 |
| MA0144.1 | 0.356507 |
| MA0145.1 | 0.143698 |
| MA0146.1 | 0.333008 |
| MA0147.1 | 0.386018 |
| MA0148.1 | 0.653474 |
| MA0149.1 | 0.681935 |
| MA0062.2 | 0.284987 |
| MA0035.2 | 1.65235 |
| MA0039.2 | 0.0575907 |
| MA0138.2 | 0.837782 |
| MA0002.2 | 0.30855 |
| MA0137.2 | 0.47779 |
| MA0104.2 | 0.320919 |
| MA0047.2 | 0.767096 |
| MA0112.2 | 0.136971 |
| MA0065.2 | 0.146576 |
| MA0150.1 | 0.550239 |
| MA0151.1 | 0 |
| MA0152.1 | 0.69926 |
| MA0153.1 | 2.71958 |
| MA0154.1 | 0.172764 |
| MA0155.1 | 0.409315 |
| MA0156.1 | 0.480289 |
| MA0157.1 | 0.883854 |
| MA0158.1 | 0 |
| MA0159.1 | 0.386729 |
| MA0160.1 | 1.60707 |
| MA0161.1 | 0 |
| MA0162.1 | 0.21472 |
| MA0163.1 | 0.0439995 |
| MA0164.1 | 0.810347 |
| MA0080.2 | 0.456437 |
| MA0018.2 | 0.781393 |
| MA0099.2 | 0.699641 |
| MA0079.2 | 0.0442129 |
| MA0102.2 | 1.66336 |
| MA0258.1 | 0.914277 |
| MA0259.1 | 0.395396 |
| 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
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
This analysis result is provided for C0 - C305 clusters.
