Coexpression cluster:C157: Difference between revisions
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{{Coexpression_clusters | {{Coexpression_clusters|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0948020209911413,0.0540496261796572,0.0477396614475454,0.0428357178336246,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0225177670469836,0,0.366164657984232,0.315733122547147,0.34136204258699,1.10664143010665,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0|full_id=C157_testicular_H9_testis_iPS_teratocarcinoma_colon_trachea|gostat_on_coexpression_clusters=GO:0006355!regulation of transcription, DNA-dependent!0.0181646542156121!27287;57167;54457;20;283150;2494;1993;676;8433$GO:0016070!RNA metabolic process!0.0181646542156121!27287;57167;54457;11030;20;283150;2494;1993;8433;676$GO:0006351!transcription, DNA-dependent!0.0181646542156121!27287;57167;54457;20;283150;2494;1993;676;8433$GO:0032774!RNA biosynthetic process!0.0181646542156121!27287;57167;54457;20;283150;2494;1993;676;8433$GO:0003723!RNA binding!0.0181646542156121!1993;11030;55510;340168;166863$GO:0051177!meiotic sister chromatid cohesion!0.0181646542156121!50511$GO:0035093!spermatogenesis, exchange of chromosomal proteins!0.0181646542156121!50511$GO:0032377!regulation of intracellular lipid transport!0.0181646542156121!20$GO:0032380!regulation of intracellular sterol transport!0.0181646542156121!20$GO:0007066!female meiosis sister chromatid cohesion!0.0181646542156121!50511$GO:0000705!achiasmate meiosis I!0.0181646542156121!50511$GO:0032383!regulation of intracellular cholesterol transport!0.0181646542156121!20$GO:0045449!regulation of transcription!0.0181646542156121!27287;57167;54457;20;283150;2494;1993;676;8433$GO:0003676!nucleic acid binding!0.0181646542156121!27287;56164;57167;11030;55510;340168;50511;283150;84629;2494;1993;166863$GO:0019219!regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process!0.0181646542156121!27287;57167;54457;20;283150;2494;1993;676;8433$GO:0006350!transcription!0.0181646542156121!27287;57167;54457;20;283150;2494;1993;676;8433$GO:0003702!RNA polymerase II transcription factor activity!0.0181646542156121!2494;8433;54457$GO:0010468!regulation of gene expression!0.0181646542156121!27287;57167;54457;20;283150;2494;1993;676;8433$GO:0031323!regulation of cellular metabolic process!0.0181646542156121!27287;57167;54457;20;283150;2494;1993;676;8433$GO:0005889!hydrogen:potassium-exchanging ATPase complex!0.0181646542156121!479$GO:0000802!transverse filament!0.0181646542156121!50511$GO:0042132!fructose-bisphosphatase activity!0.0181646542156121!2203$GO:0032374!regulation of cholesterol transport!0.0181646542156121!20$GO:0032371!regulation of sterol transport!0.0181646542156121!20$GO:0045132!meiotic chromosome segregation!0.0181646542156121!50511$GO:0032368!regulation of lipid transport!0.0181646542156121!20$GO:0006139!nucleobase, nucleoside, nucleotide and nucleic acid metabolic process!0.0192157860280854!27287;57167;54457;11030;20;50511;283150;2494;1993;8433;676$GO:0019222!regulation of metabolic process!0.0214597361942113!27287;57167;54457;20;283150;2494;1993;676;8433$GO:0008900!hydrogen:potassium-exchanging ATPase activity!0.0214597361942113!479$GO:0043486!histone exchange!0.0214597361942113!50511$GO:0007141!male meiosis I!0.0214597361942113!50511$GO:0035092!sperm chromatin condensation!0.0214597361942113!50511$GO:0007143!female meiosis!0.0214597361942113!50511$GO:0007289!spermatid nuclear differentiation!0.024839339906988!50511$GO:0032365!intracellular lipid transport!0.024839339906988!20$GO:0032366!intracellular sterol transport!0.024839339906988!20$GO:0032367!intracellular cholesterol transport!0.024839339906988!20$GO:0000800!lateral element!0.024839339906988!50511$GO:0010467!gene expression!0.0294286409682944!27287;57167;54457;11030;20;283150;2494;1993;8433;676$GO:0043044!ATP-dependent chromatin remodeling!0.034508356674653!50511$GO:0007130!synaptonemal complex assembly!0.034508356674653!50511$GO:0050794!regulation of cellular process!0.0366681540950559!27287;57167;54457;20;50511;283150;2494;1993;676;8433$GO:0065007!biological regulation!0.0366681540950559!27287;57167;54457;20;50511;283150;2494;1993;8433;676;2814$GO:0007129!synapsis!0.0366681540950559!50511$GO:0007140!male meiosis!0.0366681540950559!50511$GO:0004331!fructose-2,6-bisphosphate 2-phosphatase activity!0.0401090432575329!2203$GO:0003730!mRNA 3'-UTR binding!0.0401090432575329!1993$GO:0019203!carbohydrate phosphatase activity!0.0419063281638503!2203$GO:0007062!sister chromatid cohesion!0.0419063281638503!50511$GO:0043190!ATP-binding cassette (ABC) transporter complex!0.0419063281638503!20$GO:0042623!ATPase activity, coupled!0.0419063281638503!55510;479;20$GO:0043283!biopolymer metabolic 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Latest revision as of 10:45, 17 September 2013
Full id: C157_testicular_H9_testis_iPS_teratocarcinoma_colon_trachea
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:0006355 | regulation of transcription, DNA-dependent | 0.0181646542156121 |
GO:0016070 | RNA metabolic process | 0.0181646542156121 |
GO:0006351 | transcription, DNA-dependent | 0.0181646542156121 |
GO:0032774 | RNA biosynthetic process | 0.0181646542156121 |
GO:0003723 | RNA binding | 0.0181646542156121 |
GO:0051177 | meiotic sister chromatid cohesion | 0.0181646542156121 |
GO:0035093 | spermatogenesis, exchange of chromosomal proteins | 0.0181646542156121 |
GO:0032377 | regulation of intracellular lipid transport | 0.0181646542156121 |
GO:0032380 | regulation of intracellular sterol transport | 0.0181646542156121 |
GO:0007066 | female meiosis sister chromatid cohesion | 0.0181646542156121 |
GO:0000705 | achiasmate meiosis I | 0.0181646542156121 |
GO:0032383 | regulation of intracellular cholesterol transport | 0.0181646542156121 |
GO:0045449 | regulation of transcription | 0.0181646542156121 |
GO:0003676 | nucleic acid binding | 0.0181646542156121 |
GO:0019219 | regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 0.0181646542156121 |
GO:0006350 | transcription | 0.0181646542156121 |
GO:0003702 | RNA polymerase II transcription factor activity | 0.0181646542156121 |
GO:0010468 | regulation of gene expression | 0.0181646542156121 |
GO:0031323 | regulation of cellular metabolic process | 0.0181646542156121 |
GO:0005889 | hydrogen:potassium-exchanging ATPase complex | 0.0181646542156121 |
GO:0000802 | transverse filament | 0.0181646542156121 |
GO:0042132 | fructose-bisphosphatase activity | 0.0181646542156121 |
GO:0032374 | regulation of cholesterol transport | 0.0181646542156121 |
GO:0032371 | regulation of sterol transport | 0.0181646542156121 |
GO:0045132 | meiotic chromosome segregation | 0.0181646542156121 |
GO:0032368 | regulation of lipid transport | 0.0181646542156121 |
GO:0006139 | nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 0.0192157860280854 |
GO:0019222 | regulation of metabolic process | 0.0214597361942113 |
GO:0008900 | hydrogen:potassium-exchanging ATPase activity | 0.0214597361942113 |
GO:0043486 | histone exchange | 0.0214597361942113 |
GO:0007141 | male meiosis I | 0.0214597361942113 |
GO:0035092 | sperm chromatin condensation | 0.0214597361942113 |
GO:0007143 | female meiosis | 0.0214597361942113 |
GO:0007289 | spermatid nuclear differentiation | 0.024839339906988 |
GO:0032365 | intracellular lipid transport | 0.024839339906988 |
GO:0032366 | intracellular sterol transport | 0.024839339906988 |
GO:0032367 | intracellular cholesterol transport | 0.024839339906988 |
GO:0000800 | lateral element | 0.024839339906988 |
GO:0010467 | gene expression | 0.0294286409682944 |
GO:0043044 | ATP-dependent chromatin remodeling | 0.034508356674653 |
GO:0007130 | synaptonemal complex assembly | 0.034508356674653 |
GO:0050794 | regulation of cellular process | 0.0366681540950559 |
GO:0065007 | biological regulation | 0.0366681540950559 |
GO:0007129 | synapsis | 0.0366681540950559 |
GO:0007140 | male meiosis | 0.0366681540950559 |
GO:0004331 | fructose-2,6-bisphosphate 2-phosphatase activity | 0.0401090432575329 |
GO:0003730 | mRNA 3'-UTR binding | 0.0401090432575329 |
GO:0019203 | carbohydrate phosphatase activity | 0.0419063281638503 |
GO:0007062 | sister chromatid cohesion | 0.0419063281638503 |
GO:0043190 | ATP-binding cassette (ABC) transporter complex | 0.0419063281638503 |
GO:0042623 | ATPase activity, coupled | 0.0419063281638503 |
GO:0043283 | biopolymer metabolic process | 0.0462109027419868 |
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 |
---|---|---|
embryonic stem cell | 9.04e-70 | 5 |
germ line cell | 6.12e-51 | 7 |
germ cell | 6.12e-51 | 7 |
melanocyte | 1.05e-09 | 10 |
melanoblast | 1.05e-09 | 10 |
pigment cell | 3.44e-07 | 14 |
Ontology term | p-value | n |
---|---|---|
testis | 1.16e-44 | 8 |
male reproductive organ | 1.17e-32 | 11 |
gonad | 2.28e-17 | 21 |
indifferent external genitalia | 2.28e-17 | 21 |
indifferent gonad | 2.28e-17 | 21 |
gonad primordium | 2.28e-17 | 21 |
external genitalia | 1.33e-16 | 22 |
male organism | 1.33e-16 | 22 |
male reproductive system | 1.33e-16 | 22 |
body cavity | 3.83e-08 | 46 |
reproductive organ | 8.12e-08 | 48 |
body cavity or lining | 1.16e-07 | 49 |
body cavity precursor | 5.55e-07 | 54 |
Ontology term | p-value | n |
---|---|---|
germ cell and embryonal cancer | 2.76e-25 | 22 |
germ cell cancer | 2.76e-25 | 22 |
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 | 2.44207e-06 |
MA0004.1 | 3.81855 |
MA0006.1 | 0.313654 |
MA0007.1 | 1.26858 |
MA0009.1 | 1.46781 |
MA0014.1 | 3.75611e-06 |
MA0017.1 | 0.215716 |
MA0019.1 | 0.441564 |
MA0024.1 | 0.0462041 |
MA0025.1 | 0.438389 |
MA0027.1 | 1.40191 |
MA0028.1 | 0.372818 |
MA0029.1 | 0.192642 |
MA0030.1 | 0.408624 |
MA0031.1 | 2.22843 |
MA0038.1 | 1.07874 |
MA0040.1 | 0.438057 |
MA0041.1 | 0.307772 |
MA0042.1 | 0.133457 |
MA0043.1 | 0.0815038 |
MA0046.1 | 0.0771926 |
MA0048.1 | 0.328986 |
MA0050.1 | 0.0649983 |
MA0051.1 | 0.0820645 |
MA0052.1 | 0.0548 |
MA0055.1 | 0.119153 |
MA0056.1 | 0 |
MA0057.1 | 0.362424 |
MA0058.1 | 1.25199 |
MA0059.1 | 2.15182 |
MA0060.1 | 10.7025 |
MA0061.1 | 0.0649524 |
MA0063.1 | 0 |
MA0066.1 | 0.0854411 |
MA0067.1 | 0.252035 |
MA0068.1 | 0.530747 |
MA0069.1 | 0.262233 |
MA0070.1 | 0.911684 |
MA0071.1 | 0.0595777 |
MA0072.1 | 0.245907 |
MA0073.1 | 0.00382594 |
MA0074.1 | 0.179569 |
MA0076.1 | 0.209585 |
MA0077.1 | 0.877682 |
MA0078.1 | 0.571981 |
MA0081.1 | 0.0207521 |
MA0083.1 | 3.35487 |
MA0084.1 | 0.387643 |
MA0087.1 | 0.892292 |
MA0088.1 | 0.0191968 |
MA0089.1 | 0 |
MA0090.1 | 0.143648 |
MA0091.1 | 0.851011 |
MA0092.1 | 0.667619 |
MA0093.1 | 3.08474 |
MA0095.1 | 0 |
MA0098.1 | 0 |
MA0100.1 | 0.0956758 |
MA0101.1 | 0.144248 |
MA0103.1 | 0.71227 |
MA0105.1 | 0.0550814 |
MA0106.1 | 0.0419553 |
MA0107.1 | 0.190173 |
MA0108.2 | 3.33991 |
MA0109.1 | 0 |
MA0111.1 | 0.594096 |
MA0113.1 | 0.472955 |
MA0114.1 | 0.618299 |
MA0115.1 | 0.203203 |
MA0116.1 | 0.131506 |
MA0117.1 | 0.320096 |
MA0119.1 | 0.080436 |
MA0122.1 | 0.35056 |
MA0124.1 | 0.528203 |
MA0125.1 | 1.334 |
MA0130.1 | 0 |
MA0131.1 | 0.0747247 |
MA0132.1 | 0 |
MA0133.1 | 0 |
MA0135.1 | 0.311792 |
MA0136.1 | 0.196205 |
MA0139.1 | 0.0757319 |
MA0140.1 | 1.49967 |
MA0141.1 | 0.566498 |
MA0142.1 | 2.02943 |
MA0143.1 | 0.726943 |
MA0144.1 | 1.43835 |
MA0145.1 | 0.356233 |
MA0146.1 | 0.0486491 |
MA0147.1 | 1.53407 |
MA0148.1 | 0.497685 |
MA0149.1 | 0.00257642 |
MA0062.2 | 0.0335185 |
MA0035.2 | 1.16493 |
MA0039.2 | 2.85847 |
MA0138.2 | 0.575378 |
MA0002.2 | 0.00360269 |
MA0137.2 | 1.16062 |
MA0104.2 | 1.05167 |
MA0047.2 | 0.629544 |
MA0112.2 | 0.00962691 |
MA0065.2 | 1.64938 |
MA0150.1 | 0.0307473 |
MA0151.1 | 0 |
MA0152.1 | 1.20692 |
MA0153.1 | 0.124754 |
MA0154.1 | 0.189023 |
MA0155.1 | 0.371878 |
MA0156.1 | 0.108855 |
MA0157.1 | 2.34677 |
MA0158.1 | 0 |
MA0159.1 | 0.709603 |
MA0160.1 | 0.360797 |
MA0161.1 | 0 |
MA0162.1 | 0.0306223 |
MA0163.1 | 0.0190953 |
MA0164.1 | 0.505053 |
MA0080.2 | 0.0411053 |
MA0018.2 | 0.0424766 |
MA0099.2 | 0.0621168 |
MA0079.2 | 0.123362 |
MA0102.2 | 0.416822 |
MA0258.1 | 0.116534 |
MA0259.1 | 3.16223 |
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