Coexpression cluster:C1110: Difference between revisions
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{{Coexpression_clusters | {{Coexpression_clusters|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0504125515893149,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.202227296137227,1.10512082111075,0.151580601421971,0,0,0,0,0,0,0,0,0,0,0.114159389744683,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.301016310671738,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0|full_id=C1110_cord_mycosis_colon_embryonic_argyrophil_xeroderma_CD19|gostat_on_coexpression_clusters=GO:0051952!regulation of amine transport!0.00494510345594605!4049$GO:0002036!regulation of L-glutamate transport!0.00494510345594605!4049$GO:0051953!negative regulation of amine transport!0.00494510345594605!4049$GO:0051956!negative regulation of amino acid transport!0.00494510345594605!4049$GO:0002037!negative regulation of L-glutamate transport!0.00494510345594605!4049$GO:0051955!regulation of amino acid transport!0.00494510345594605!4049$GO:0046325!negative regulation of glucose import!0.00847582299419329!4049$GO:0048535!lymph node development!0.00847582299419329!4049$GO:0050806!positive regulation of synaptic transmission!0.00847582299419329!4049$GO:0042127!regulation of cell proliferation!0.00847582299419329!3651;4049$GO:0051971!positive regulation of transmission of nerve impulse!0.00847582299419329!4049$GO:0046323!glucose import!0.00847582299419329!4049$GO:0046324!regulation of glucose import!0.00847582299419329!4049$GO:0031646!positive regulation of neurological process!0.00847582299419329!4049$GO:0043525!positive regulation of neuron apoptosis!0.00889935214910135!4049$GO:0031016!pancreas development!0.00926988558275227!3651$GO:0051222!positive regulation of protein transport!0.00959677548276263!4049$GO:0045840!positive regulation of mitosis!0.00963982957309548!4049$GO:0015813!L-glutamate transport!0.00963982957309548!4049$GO:0015800!acidic amino acid transport!0.00963982957309548!4049$GO:0050804!regulation of synaptic transmission!0.0108424725521954!4049$GO:0008283!cell proliferation!0.0108424725521954!3651;4049$GO:0009612!response to mechanical stimulus!0.0109603882890473!4049$GO:0051969!regulation of transmission of nerve impulse!0.0111212430341185!4049$GO:0045787!positive regulation of progression through cell cycle!0.0137271002031507!4049$GO:0031644!regulation of neurological process!0.0137271002031507!4049$GO:0043523!regulation of neuron apoptosis!0.0137271002031507!4049$GO:0048522!positive regulation of cellular process!0.0137671221908496!3651;4049$GO:0051223!regulation of protein transport!0.0137671221908496!4049$GO:0051402!neuron apoptosis!0.0137671221908496!4049$GO:0015758!glucose transport!0.0137671221908496!4049$GO:0051051!negative regulation of transport!0.0137671221908496!4049$GO:0008645!hexose transport!0.0137671221908496!4049$GO:0015749!monosaccharide transport!0.0137671221908496!4049$GO:0048518!positive regulation of biological process!0.0137671221908496!3651;4049$GO:0019722!calcium-mediated signaling!0.0144486788814349!4049$GO:0048513!organ development!0.0144486788814349!3651;4049$GO:0051050!positive regulation of transport!0.0144486788814349!4049$GO:0005164!tumor necrosis factor receptor binding!0.0144486788814349!4049$GO:0003704!specific RNA polymerase II transcription factor activity!0.0144486788814349!3651$GO:0032813!tumor necrosis factor receptor superfamily binding!0.014818285051059!4049$GO:0007088!regulation of mitosis!0.0236205980833195!4049$GO:0006865!amino acid transport!0.0241021943152424!4049$GO:0048731!system development!0.0246724218389829!3651;4049$GO:0006959!humoral immune response!0.0246724218389829!4049$GO:0015837!amine transport!0.0270252262450758!4049$GO:0048869!cellular developmental process!0.0287158030664027!3651;4049$GO:0030154!cell differentiation!0.0287158030664027!3651;4049$GO:0046942!carboxylic acid transport!0.0287158030664027!4049$GO:0015849!organic acid transport!0.0287158030664027!4049$GO:0043123!positive regulation of I-kappaB kinase/NF-kappaB cascade!0.0287158030664027!4049$GO:0043122!regulation of I-kappaB kinase/NF-kappaB cascade!0.0303970611682208!4049$GO:0051049!regulation of transport!0.0303970611682208!4049$GO:0008643!carbohydrate transport!0.0303970611682208!4049$GO:0048856!anatomical structure development!0.0306502575807213!3651;4049$GO:0045944!positive regulation of transcription from RNA polymerase II promoter!0.0360316312609124!3651$GO:0007249!I-kappaB kinase/NF-kappaB cascade!0.0360316312609124!4049$GO:0007275!multicellular organismal development!0.037986522699988!3651;4049$GO:0009967!positive regulation of signal transduction!0.0383004752371746!4049$GO:0009628!response to abiotic stimulus!0.0406016596967475!4049$GO:0048534!hemopoietic or lymphoid organ development!0.0418624765584408!4049$GO:0002520!immune system development!0.0433184679915768!4049$GO:0006006!glucose metabolic process!0.0449599678871934!3651$GO:0001775!cell activation!0.0475808260858078!4049$GO:0006917!induction of apoptosis!0.0475808260858078!4049$GO:0012502!induction of programmed cell death!0.0475808260858078!4049$GO:0045893!positive regulation of transcription, DNA-dependent!0.0487658922195956!3651$GO:0008285!negative regulation of cell 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Latest revision as of 11:37, 17 September 2013
Full id: C1110_cord_mycosis_colon_embryonic_argyrophil_xeroderma_CD19
Phase1 CAGE Peaks
| Hg19::chr10:133058641..133058652,- | p6@TCERG1L |
| Hg19::chr13:28494375..28494416,+ | p4@PDX1 |
| Hg19::chr13:28498703..28498710,+ | p@chr13:28498703..28498710 + |
| Hg19::chr6:31540557..31540570,+ | p4@LTA |
| Hg19::chr6:31541218..31541237,+ | p@chr6:31541218..31541237 + |
| Hg19::chr6:31541408..31541421,+ | p@chr6:31541408..31541421 + |
| Hg19::chr7:102944849..102944859,+ | p@chr7:102944849..102944859 + |
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:0051952 | regulation of amine transport | 0.00494510345594605 |
| GO:0002036 | regulation of L-glutamate transport | 0.00494510345594605 |
| GO:0051953 | negative regulation of amine transport | 0.00494510345594605 |
| GO:0051956 | negative regulation of amino acid transport | 0.00494510345594605 |
| GO:0002037 | negative regulation of L-glutamate transport | 0.00494510345594605 |
| GO:0051955 | regulation of amino acid transport | 0.00494510345594605 |
| GO:0046325 | negative regulation of glucose import | 0.00847582299419329 |
| GO:0048535 | lymph node development | 0.00847582299419329 |
| GO:0050806 | positive regulation of synaptic transmission | 0.00847582299419329 |
| GO:0042127 | regulation of cell proliferation | 0.00847582299419329 |
| GO:0051971 | positive regulation of transmission of nerve impulse | 0.00847582299419329 |
| GO:0046323 | glucose import | 0.00847582299419329 |
| GO:0046324 | regulation of glucose import | 0.00847582299419329 |
| GO:0031646 | positive regulation of neurological process | 0.00847582299419329 |
| GO:0043525 | positive regulation of neuron apoptosis | 0.00889935214910135 |
| GO:0031016 | pancreas development | 0.00926988558275227 |
| GO:0051222 | positive regulation of protein transport | 0.00959677548276263 |
| GO:0045840 | positive regulation of mitosis | 0.00963982957309548 |
| GO:0015813 | L-glutamate transport | 0.00963982957309548 |
| GO:0015800 | acidic amino acid transport | 0.00963982957309548 |
| GO:0050804 | regulation of synaptic transmission | 0.0108424725521954 |
| GO:0008283 | cell proliferation | 0.0108424725521954 |
| GO:0009612 | response to mechanical stimulus | 0.0109603882890473 |
| GO:0051969 | regulation of transmission of nerve impulse | 0.0111212430341185 |
| GO:0045787 | positive regulation of progression through cell cycle | 0.0137271002031507 |
| GO:0031644 | regulation of neurological process | 0.0137271002031507 |
| GO:0043523 | regulation of neuron apoptosis | 0.0137271002031507 |
| GO:0048522 | positive regulation of cellular process | 0.0137671221908496 |
| GO:0051223 | regulation of protein transport | 0.0137671221908496 |
| GO:0051402 | neuron apoptosis | 0.0137671221908496 |
| GO:0015758 | glucose transport | 0.0137671221908496 |
| GO:0051051 | negative regulation of transport | 0.0137671221908496 |
| GO:0008645 | hexose transport | 0.0137671221908496 |
| GO:0015749 | monosaccharide transport | 0.0137671221908496 |
| GO:0048518 | positive regulation of biological process | 0.0137671221908496 |
| GO:0019722 | calcium-mediated signaling | 0.0144486788814349 |
| GO:0048513 | organ development | 0.0144486788814349 |
| GO:0051050 | positive regulation of transport | 0.0144486788814349 |
| GO:0005164 | tumor necrosis factor receptor binding | 0.0144486788814349 |
| GO:0003704 | specific RNA polymerase II transcription factor activity | 0.0144486788814349 |
| GO:0032813 | tumor necrosis factor receptor superfamily binding | 0.014818285051059 |
| GO:0007088 | regulation of mitosis | 0.0236205980833195 |
| GO:0006865 | amino acid transport | 0.0241021943152424 |
| GO:0048731 | system development | 0.0246724218389829 |
| GO:0006959 | humoral immune response | 0.0246724218389829 |
| GO:0015837 | amine transport | 0.0270252262450758 |
| GO:0048869 | cellular developmental process | 0.0287158030664027 |
| GO:0030154 | cell differentiation | 0.0287158030664027 |
| GO:0046942 | carboxylic acid transport | 0.0287158030664027 |
| GO:0015849 | organic acid transport | 0.0287158030664027 |
| GO:0043123 | positive regulation of I-kappaB kinase/NF-kappaB cascade | 0.0287158030664027 |
| GO:0043122 | regulation of I-kappaB kinase/NF-kappaB cascade | 0.0303970611682208 |
| GO:0051049 | regulation of transport | 0.0303970611682208 |
| GO:0008643 | carbohydrate transport | 0.0303970611682208 |
| GO:0048856 | anatomical structure development | 0.0306502575807213 |
| GO:0045944 | positive regulation of transcription from RNA polymerase II promoter | 0.0360316312609124 |
| GO:0007249 | I-kappaB kinase/NF-kappaB cascade | 0.0360316312609124 |
| GO:0007275 | multicellular organismal development | 0.037986522699988 |
| GO:0009967 | positive regulation of signal transduction | 0.0383004752371746 |
| GO:0009628 | response to abiotic stimulus | 0.0406016596967475 |
| GO:0048534 | hemopoietic or lymphoid organ development | 0.0418624765584408 |
| GO:0002520 | immune system development | 0.0433184679915768 |
| GO:0006006 | glucose metabolic process | 0.0449599678871934 |
| GO:0001775 | cell activation | 0.0475808260858078 |
| GO:0006917 | induction of apoptosis | 0.0475808260858078 |
| GO:0012502 | induction of programmed cell death | 0.0475808260858078 |
| GO:0045893 | positive regulation of transcription, DNA-dependent | 0.0487658922195956 |
| GO:0008285 | negative regulation of cell proliferation | 0.0487658922195956 |
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 |
|---|---|---|
| circulating cell | 5.37e-50 | 6 |
| Ontology term | p-value | n |
|---|---|---|
| umbilical cord | 2.06e-30 | 10 |
| blastocyst | 2.06e-30 | 10 |
| blastula | 2.06e-30 | 10 |
| bilaminar disc | 2.06e-30 | 10 |
| inner cell mass | 2.06e-30 | 10 |
| cleaving embryo | 2.06e-30 | 10 |
| connecting stalk | 2.06e-30 | 10 |
| inner cell mass derived epiblast | 2.06e-30 | 10 |
| extraembryonic mesoderm | 2.06e-30 | 10 |
| blood | 1.37e-20 | 15 |
| haemolymphatic fluid | 1.37e-20 | 15 |
| organism substance | 1.37e-20 | 15 |
| extraembryonic structure | 3.48e-13 | 24 |
| Ontology term | p-value | n |
|---|---|---|
| non-Hodgkin lymphoma | 2.58e-34 | 1 |
| cutaneous T cell lymphoma | 2.58e-34 | 1 |
| mycosis fungoides | 2.58e-34 | 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 | 0.213534 |
| MA0004.1 | 0.502801 |
| MA0006.1 | 0.904424 |
| MA0007.1 | 0.483857 |
| MA0009.1 | 0.973289 |
| MA0014.1 | 0.912418 |
| MA0017.1 | 0.380797 |
| MA0019.1 | 0.652951 |
| MA0024.1 | 0.867125 |
| MA0025.1 | 1.10816 |
| MA0027.1 | 2.59001 |
| MA0028.1 | 0.35747 |
| MA0029.1 | 0.886702 |
| MA0030.1 | 0.875089 |
| MA0031.1 | 0.809638 |
| MA0038.1 | 0.60704 |
| MA0040.1 | 0.892629 |
| MA0041.1 | 0.521615 |
| MA0042.1 | 0.48922 |
| MA0043.1 | 0.973609 |
| MA0046.1 | 0.962263 |
| MA0048.1 | 0.382278 |
| MA0050.1 | 0.490116 |
| MA0051.1 | 0.602745 |
| MA0052.1 | 0.896548 |
| MA0055.1 | 0.649431 |
| MA0056.1 | 0 |
| MA0057.1 | 0.369442 |
| MA0058.1 | 0.406232 |
| MA0059.1 | 1.04442 |
| MA0060.1 | 0.224688 |
| MA0061.1 | 0.198335 |
| MA0063.1 | 0 |
| MA0066.1 | 0.607474 |
| MA0067.1 | 1.29359 |
| MA0068.1 | 0.162298 |
| MA0069.1 | 0.958358 |
| MA0070.1 | 0.947018 |
| MA0071.1 | 0.567661 |
| MA0072.1 | 0.942461 |
| MA0073.1 | 0.126287 |
| MA0074.1 | 0.60198 |
| MA0076.1 | 0.422297 |
| MA0077.1 | 0.934645 |
| MA0078.1 | 0.703614 |
| MA0081.1 | 0.405093 |
| MA0083.1 | 0.980893 |
| MA0084.1 | 1.48179 |
| MA0087.1 | 0.939982 |
| MA0088.1 | 0.252594 |
| MA0089.1 | 0 |
| MA0090.1 | 0.436918 |
| MA0091.1 | 0.505453 |
| MA0092.1 | 0.467172 |
| MA0093.1 | 0.344385 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.621149 |
| MA0101.1 | 0.347695 |
| MA0103.1 | 0.88373 |
| MA0105.1 | 0.104569 |
| MA0106.1 | 0.648997 |
| MA0107.1 | 0.274127 |
| MA0108.2 | 0.806528 |
| MA0109.1 | 0 |
| MA0111.1 | 0.45062 |
| MA0113.1 | 0.665691 |
| MA0114.1 | 0.269076 |
| MA0115.1 | 1.21667 |
| MA0116.1 | 1.39213 |
| MA0117.1 | 1.01134 |
| MA0119.1 | 0.388712 |
| MA0122.1 | 1.03753 |
| MA0124.1 | 1.17486 |
| MA0125.1 | 1.0901 |
| MA0130.1 | 0 |
| MA0131.1 | 0.722072 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 1.00402 |
| MA0136.1 | 0.614215 |
| MA0139.1 | 0.547495 |
| MA0140.1 | 0.564957 |
| MA0141.1 | 1.83545 |
| MA0142.1 | 0.777365 |
| MA0143.1 | 0.66587 |
| MA0144.1 | 0.254954 |
| MA0145.1 | 0.980834 |
| MA0146.1 | 0.0127148 |
| MA0147.1 | 0.768766 |
| MA0148.1 | 1.30922 |
| MA0149.1 | 0.555119 |
| MA0062.2 | 0.563664 |
| MA0035.2 | 0.564239 |
| MA0039.2 | 0.0170091 |
| MA0138.2 | 0.704862 |
| MA0002.2 | 0.213296 |
| MA0137.2 | 0.36398 |
| MA0104.2 | 0.636673 |
| MA0047.2 | 0.636643 |
| MA0112.2 | 0.0758925 |
| MA0065.2 | 0.282161 |
| MA0150.1 | 0.430951 |
| MA0151.1 | 0 |
| MA0152.1 | 0.571637 |
| MA0153.1 | 1.07307 |
| MA0154.1 | 0.335384 |
| MA0155.1 | 1.36741 |
| MA0156.1 | 0.36627 |
| MA0157.1 | 0.749547 |
| MA0158.1 | 0 |
| MA0159.1 | 0.281681 |
| MA0160.1 | 1.34201 |
| MA0161.1 | 0 |
| MA0162.1 | 0.780982 |
| MA0163.1 | 0.632664 |
| MA0164.1 | 0.678332 |
| MA0080.2 | 0.344472 |
| MA0018.2 | 0.650405 |
| MA0099.2 | 0.572 |
| MA0079.2 | 0.184526 |
| MA0102.2 | 1.51913 |
| MA0258.1 | 0.245543 |
| MA0259.1 | 0.289405 |
| 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.
