Coexpression cluster:C38
From FANTOM5_SSTAR
Full id: C38_extraskeletal_rhabdomyosarcoma_adrenal_rectal_mesothelioma_lung_Wilms
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:0032502 | developmental process | 1.09100664697505e-13 |
GO:0032501 | multicellular organismal process | 4.45904962569228e-11 |
GO:0007275 | multicellular organismal development | 3.47214716850796e-09 |
GO:0048856 | anatomical structure development | 4.62125968221429e-07 |
GO:0065007 | biological regulation | 6.2823496025851e-07 |
GO:0048731 | system development | 2.67773238184643e-06 |
GO:0048513 | organ development | 6.12784147594054e-05 |
GO:0050789 | regulation of biological process | 8.58829632794838e-05 |
GO:0050794 | regulation of cellular process | 0.000216011211722171 |
GO:0005886 | plasma membrane | 0.000856511431827884 |
GO:0048869 | cellular developmental process | 0.001126820399881 |
GO:0030154 | cell differentiation | 0.001126820399881 |
GO:0044464 | cell part | 0.00201353519325747 |
GO:0006366 | transcription from RNA polymerase II promoter | 0.00302836234527874 |
GO:0005624 | membrane fraction | 0.00444605892563611 |
GO:0000267 | cell fraction | 0.00496552476370926 |
GO:0007399 | nervous system development | 0.00543314345098537 |
GO:0009790 | embryonic development | 0.00584583574569698 |
GO:0008188 | neuropeptide receptor activity | 0.00589413314273301 |
GO:0042923 | neuropeptide binding | 0.00595581333628997 |
GO:0030594 | neurotransmitter receptor activity | 0.00829124062051489 |
GO:0042165 | neurotransmitter binding | 0.00864618647898194 |
GO:0006357 | regulation of transcription from RNA polymerase II promoter | 0.00864618647898194 |
GO:0048518 | positive regulation of biological process | 0.0111561806845732 |
GO:0007517 | muscle development | 0.0142835205673985 |
GO:0005515 | protein binding | 0.0142835205673985 |
GO:0045449 | regulation of transcription | 0.0162615220682648 |
GO:0006355 | regulation of transcription, DNA-dependent | 0.0171668228962938 |
GO:0050679 | positive regulation of epithelial cell proliferation | 0.0178534419604711 |
GO:0019219 | regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 0.0186416492512965 |
GO:0008584 | male gonad development | 0.0186416492512965 |
GO:0048522 | positive regulation of cellular process | 0.019653068386465 |
GO:0006351 | transcription, DNA-dependent | 0.0204062398746496 |
GO:0008283 | cell proliferation | 0.0204062398746496 |
GO:0032774 | RNA biosynthetic process | 0.0204062398746496 |
GO:0016010 | dystrophin-associated glycoprotein complex | 0.0215411414047579 |
GO:0003700 | transcription factor activity | 0.0215411414047579 |
GO:0006350 | transcription | 0.0219594121522814 |
GO:0019222 | regulation of metabolic process | 0.0228104234583783 |
GO:0010468 | regulation of gene expression | 0.0235792095927749 |
GO:0001649 | osteoblast differentiation | 0.024531124103968 |
GO:0046546 | development of primary male sexual characteristics | 0.0259081324404001 |
GO:0009880 | embryonic pattern specification | 0.0278004416641354 |
GO:0044424 | intracellular part | 0.0278004416641354 |
GO:0031323 | regulation of cellular metabolic process | 0.0278004416641354 |
GO:0005634 | nucleus | 0.0278004416641354 |
GO:0050678 | regulation of epithelial cell proliferation | 0.0278004416641354 |
GO:0035295 | tube development | 0.0278004416641354 |
GO:0042391 | regulation of membrane potential | 0.0278004416641354 |
GO:0046661 | male sex differentiation | 0.0278004416641354 |
GO:0043231 | intracellular membrane-bound organelle | 0.0278004416641354 |
GO:0043227 | membrane-bound organelle | 0.0278004416641354 |
GO:0042026 | protein refolding | 0.0278004416641354 |
GO:0045743 | positive regulation of fibroblast growth factor receptor signaling pathway | 0.0278004416641354 |
GO:0043257 | laminin-8 complex | 0.0278004416641354 |
GO:0060045 | positive regulation of cardiac muscle cell proliferation | 0.0278004416641354 |
GO:0005607 | laminin-2 complex | 0.0278004416641354 |
GO:0016913 | follicle-stimulating hormone activity | 0.0278004416641354 |
GO:0007267 | cell-cell signaling | 0.0278004416641354 |
GO:0003779 | actin binding | 0.0278004416641354 |
GO:0030326 | embryonic limb morphogenesis | 0.0278004416641354 |
GO:0035113 | embryonic appendage morphogenesis | 0.0278004416641354 |
GO:0050673 | epithelial cell proliferation | 0.0278004416641354 |
GO:0048523 | negative regulation of cellular process | 0.0298416882710965 |
GO:0048736 | appendage development | 0.0323157930315383 |
GO:0060173 | limb development | 0.0323157930315383 |
GO:0035107 | appendage morphogenesis | 0.0323157930315383 |
GO:0035108 | limb morphogenesis | 0.0323157930315383 |
GO:0031175 | neurite development | 0.0331103674160884 |
GO:0048519 | negative regulation of biological process | 0.0346241126411889 |
GO:0007268 | synaptic transmission | 0.0354221120952876 |
GO:0005605 | basal lamina | 0.0354221120952876 |
GO:0045595 | regulation of cell differentiation | 0.0354221120952876 |
GO:0030324 | lung development | 0.0354221120952876 |
GO:0065008 | regulation of biological quality | 0.0354221120952876 |
GO:0007167 | enzyme linked receptor protein signaling pathway | 0.0354221120952876 |
GO:0030323 | respiratory tube development | 0.0354221120952876 |
GO:0008528 | peptide receptor activity, G-protein coupled | 0.0354221120952876 |
GO:0001653 | peptide receptor activity | 0.0354221120952876 |
GO:0043229 | intracellular organelle | 0.0354221120952876 |
GO:0022610 | biological adhesion | 0.0354221120952876 |
GO:0007155 | cell adhesion | 0.0354221120952876 |
GO:0043226 | organelle | 0.0354221120952876 |
GO:0016070 | RNA metabolic process | 0.0354221120952876 |
GO:0048666 | neuron development | 0.0354221120952876 |
GO:0045880 | positive regulation of smoothened signaling pathway | 0.0354221120952876 |
GO:0042745 | circadian sleep/wake cycle | 0.0354221120952876 |
GO:0002053 | positive regulation of mesenchymal cell proliferation | 0.0354221120952876 |
GO:0060043 | regulation of cardiac muscle cell proliferation | 0.0354221120952876 |
GO:0031290 | retinal ganglion cell axon guidance | 0.0354221120952876 |
GO:0010464 | regulation of mesenchymal cell proliferation | 0.0354221120952876 |
GO:0047372 | acylglycerol lipase activity | 0.0354221120952876 |
GO:0045475 | locomotor rhythm | 0.0354221120952876 |
GO:0004572 | mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity | 0.0354221120952876 |
GO:0010463 | mesenchymal cell proliferation | 0.0354221120952876 |
GO:0043259 | laminin-10 complex | 0.0354221120952876 |
GO:0005654 | nucleoplasm | 0.0371680897574866 |
GO:0008015 | blood circulation | 0.0371680897574866 |
GO:0003013 | circulatory system process | 0.0371680897574866 |
GO:0019226 | transmission of nerve impulse | 0.0392981478635945 |
GO:0006936 | muscle contraction | 0.0392981478635945 |
GO:0003012 | muscle system process | 0.0392981478635945 |
GO:0048608 | reproductive structure development | 0.041239537551561 |
GO:0008406 | gonad development | 0.041239537551561 |
GO:0009653 | anatomical structure morphogenesis | 0.0446982945743933 |
GO:0005887 | integral to plasma membrane | 0.0446982945743933 |
GO:0007411 | axon guidance | 0.0446982945743933 |
GO:0030911 | TPR domain binding | 0.0446982945743933 |
GO:0060011 | Sertoli cell proliferation | 0.0446982945743933 |
GO:0048512 | circadian behavior | 0.0446982945743933 |
GO:0007622 | rhythmic behavior | 0.0446982945743933 |
GO:0001757 | somite specification | 0.0446982945743933 |
GO:0030297 | transmembrane receptor protein tyrosine kinase activator activity | 0.0446982945743933 |
GO:0040036 | regulation of fibroblast growth factor receptor signaling pathway | 0.0446982945743933 |
GO:0016043 | cellular component organization and biogenesis | 0.0448526907092937 |
GO:0031226 | intrinsic to plasma membrane | 0.0453829723111605 |
GO:0044459 | plasma membrane part | 0.0480055673039496 |
GO:0045137 | development of primary sexual characteristics | 0.0480055673039496 |
GO:0010467 | gene expression | 0.0491999571696071 |
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 |
---|---|---|
collagen secreting cell | 4.27e-34 | 6 |
chondroblast | 4.27e-34 | 6 |
chondrocyte | 4.27e-34 | 6 |
GAG secreting cell | 2.62e-23 | 9 |
carbohydrate secreting cell | 2.62e-23 | 9 |
extracellular matrix secreting cell | 1.22e-14 | 15 |
stromal cell | 1.52e-08 | 28 |
secretory cell | 5.81e-07 | 36 |
Ontology term | p-value | n |
---|---|---|
cartilage tissue | 2.39e-66 | 3 |
skeletal tissue | 2.39e-66 | 3 |
Ontology term | p-value | n |
---|---|---|
chondrosarcoma | 5.42e-195 | 1 |
extraosseous chondrosarcoma | 5.42e-195 | 1 |
myxoid chondrosarcoma | 5.42e-195 | 1 |
extraskeletal myxoid chondrosarcoma | 5.42e-195 | 1 |
connective tissue cancer | 4.27e-34 | 6 |
musculoskeletal system cancer | 4.27e-34 | 6 |
sarcoma | 2.29e-11 | 20 |
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 |
MA0004.1 | 0.00644352 |
MA0006.1 | 0.129559 |
MA0007.1 | 0.00328009 |
MA0009.1 | 0.106606 |
MA0014.1 | 1.33318e-13 |
MA0017.1 | 0.0489001 |
MA0019.1 | 0.25255 |
MA0024.1 | 0.106616 |
MA0025.1 | 0.0932021 |
MA0027.1 | 0.790244 |
MA0028.1 | 7.28261e-06 |
MA0029.1 | 0.314087 |
MA0030.1 | 0.907895 |
MA0031.1 | 0.425506 |
MA0038.1 | 0.501401 |
MA0040.1 | 2.40833 |
MA0041.1 | 2.58041 |
MA0042.1 | 0.977245 |
MA0043.1 | 0.0227983 |
MA0046.1 | 0.269117 |
MA0048.1 | 4.39114e-09 |
MA0050.1 | 0.133566 |
MA0051.1 | 0.05339 |
MA0052.1 | 2.45203 |
MA0055.1 | 4.57129e-07 |
MA0056.1 | 0 |
MA0057.1 | 0.446247 |
MA0058.1 | 0.00145589 |
MA0059.1 | 0.026756 |
MA0060.1 | 0.00180568 |
MA0061.1 | 4.80918e-05 |
MA0063.1 | 0 |
MA0066.1 | 0.403145 |
MA0067.1 | 0.158043 |
MA0068.1 | 0.115688 |
MA0069.1 | 0.162324 |
MA0070.1 | 0.0394406 |
MA0071.1 | 0.126828 |
MA0072.1 | 0.343508 |
MA0073.1 | 2.96601e-07 |
MA0074.1 | 0.0191864 |
MA0076.1 | 0.00167077 |
MA0077.1 | 0.0133614 |
MA0078.1 | 0.186391 |
MA0081.1 | 0.168011 |
MA0083.1 | 1.33897 |
MA0084.1 | 0.17385 |
MA0087.1 | 0.479396 |
MA0088.1 | 0.0328874 |
MA0089.1 | 0 |
MA0090.1 | 0.655271 |
MA0091.1 | 0.0122919 |
MA0092.1 | 0.109032 |
MA0093.1 | 0.0018435 |
MA0095.1 | 0 |
MA0098.1 | 0 |
MA0100.1 | 0.112812 |
MA0101.1 | 0.155327 |
MA0103.1 | 0.0307417 |
MA0105.1 | 0.000597185 |
MA0106.1 | 0.00900761 |
MA0107.1 | 0.196198 |
MA0108.2 | 0.702271 |
MA0109.1 | 0 |
MA0111.1 | 0.0998599 |
MA0113.1 | 0.0250621 |
MA0114.1 | 0.00367943 |
MA0115.1 | 0.0322933 |
MA0116.1 | 0.182027 |
MA0117.1 | 0.00306131 |
MA0119.1 | 0.0844557 |
MA0122.1 | 0.654177 |
MA0124.1 | 0.287789 |
MA0125.1 | 0.437162 |
MA0130.1 | 0 |
MA0131.1 | 0.685517 |
MA0132.1 | 0 |
MA0133.1 | 0 |
MA0135.1 | 0.0747319 |
MA0136.1 | 0.344841 |
MA0139.1 | 0.0569225 |
MA0140.1 | 0.221705 |
MA0141.1 | 0.0365903 |
MA0142.1 | 3.5728 |
MA0143.1 | 0.911113 |
MA0144.1 | 0.0978679 |
MA0145.1 | 2.29194e-05 |
MA0146.1 | 0 |
MA0147.1 | 0.000461844 |
MA0148.1 | 0.338213 |
MA0149.1 | 1.86637 |
MA0062.2 | 2.32794e-07 |
MA0035.2 | 0.362694 |
MA0039.2 | 9.00682e-14 |
MA0138.2 | 0.0157017 |
MA0002.2 | 0.0139997 |
MA0137.2 | 0.0934672 |
MA0104.2 | 0.000426209 |
MA0047.2 | 0.691662 |
MA0112.2 | 9.99864e-08 |
MA0065.2 | 1.65583e-06 |
MA0150.1 | 0.291299 |
MA0151.1 | 0 |
MA0152.1 | 0.245957 |
MA0153.1 | 0.796407 |
MA0154.1 | 0.0341189 |
MA0155.1 | 4.43543e-05 |
MA0156.1 | 0.0414293 |
MA0157.1 | 0.698797 |
MA0158.1 | 0 |
MA0159.1 | 0.000829049 |
MA0160.1 | 0.154276 |
MA0161.1 | 0 |
MA0162.1 | 5.05367e-06 |
MA0163.1 | 0.000132239 |
MA0164.1 | 1.3916 |
MA0080.2 | 0.176991 |
MA0018.2 | 1.26667e-05 |
MA0099.2 | 0.24732 |
MA0079.2 | 0 |
MA0102.2 | 0.0560451 |
MA0258.1 | 0.0509692 |
MA0259.1 | 0.148396 |
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 |
---|---|---|---|---|
SUZ12#23512 | 43 | 4.48020494631124 | 6.44925774245506e-16 | 1.23136019993467e-13 |
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