Coexpression cluster:C701
From FANTOM5_SSTAR
Full id: C701_Mast_thalamus_globus_middle_substantia_corpus_medial
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:0031116 | positive regulation of microtubule polymerization | 0.0186801036130093 |
| GO:0050998 | nitric-oxide synthase binding | 0.0186801036130093 |
| GO:0031112 | positive regulation of microtubule polymerization or depolymerization | 0.0186801036130093 |
| GO:0030321 | transepithelial chloride transport | 0.0186801036130093 |
| GO:0031113 | regulation of microtubule polymerization | 0.0186801036130093 |
| GO:0046785 | microtubule polymerization | 0.0186801036130093 |
| GO:0032502 | developmental process | 0.0186801036130093 |
| GO:0001937 | negative regulation of endothelial cell proliferation | 0.0186801036130093 |
| GO:0051130 | positive regulation of cellular component organization and biogenesis | 0.0186801036130093 |
| GO:0045178 | basal part of cell | 0.0186801036130093 |
| GO:0009925 | basal plasma membrane | 0.0186801036130093 |
| GO:0001936 | regulation of endothelial cell proliferation | 0.0186801036130093 |
| GO:0019905 | syntaxin binding | 0.0186801036130093 |
| GO:0042311 | vasodilation | 0.0186801036130093 |
| GO:0001935 | endothelial cell proliferation | 0.0186801036130093 |
| GO:0030317 | sperm motility | 0.0186801036130093 |
| GO:0000149 | SNARE binding | 0.0186801036130093 |
| GO:0007595 | lactation | 0.0186801036130093 |
| GO:0043434 | response to peptide hormone stimulus | 0.0186801036130093 |
| GO:0043627 | response to estrogen stimulus | 0.0186801036130093 |
| GO:0016599 | caveolar membrane | 0.0186801036130093 |
| GO:0005901 | caveola | 0.0186801036130093 |
| GO:0031110 | regulation of microtubule polymerization or depolymerization | 0.0186801036130093 |
| GO:0004198 | calcium-dependent cysteine-type endopeptidase activity | 0.0186801036130093 |
| GO:0000245 | spliceosome assembly | 0.0186801036130093 |
| GO:0031109 | microtubule polymerization or depolymerization | 0.0186801036130093 |
| GO:0019861 | flagellum | 0.0186801036130093 |
| GO:0005925 | focal adhesion | 0.0186801036130093 |
| GO:0001764 | neuron migration | 0.0186801036130093 |
| GO:0048545 | response to steroid hormone stimulus | 0.0186801036130093 |
| GO:0048513 | organ development | 0.0186801036130093 |
| GO:0005924 | cell-substrate adherens junction | 0.0186801036130093 |
| GO:0004672 | protein kinase activity | 0.0186801036130093 |
| GO:0006468 | protein amino acid phosphorylation | 0.0186801036130093 |
| GO:0030055 | cell-matrix junction | 0.0186801036130093 |
| GO:0030324 | lung development | 0.0186801036130093 |
| GO:0035150 | regulation of tube size | 0.0186801036130093 |
| GO:0050880 | regulation of blood vessel size | 0.0186801036130093 |
| GO:0030323 | respiratory tube development | 0.0186801036130093 |
| GO:0003018 | vascular process in circulatory system | 0.0186801036130093 |
| GO:0046777 | protein amino acid autophosphorylation | 0.0186801036130093 |
| GO:0045121 | lipid raft | 0.0186801036130093 |
| GO:0016540 | protein autoprocessing | 0.0186801036130093 |
| GO:0044267 | cellular protein metabolic process | 0.019975165662148 |
| GO:0044260 | cellular macromolecule metabolic process | 0.0202967030143573 |
| GO:0005912 | adherens junction | 0.02039706182063 |
| GO:0016310 | phosphorylation | 0.02039706182063 |
| GO:0016773 | phosphotransferase activity, alcohol group as acceptor | 0.02039706182063 |
| GO:0019538 | protein metabolic process | 0.0207095077449335 |
| GO:0048609 | reproductive process in a multicellular organism | 0.0208765004351701 |
| GO:0032504 | multicellular organism reproduction | 0.0208765004351701 |
| GO:0042493 | response to drug | 0.0211450960231025 |
| GO:0016324 | apical plasma membrane | 0.0218118710033986 |
| GO:0000398 | nuclear mRNA splicing, via spliceosome | 0.0218118710033986 |
| GO:0000375 | RNA splicing, via transesterification reactions | 0.0218118710033986 |
| GO:0000377 | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 0.0218118710033986 |
| GO:0048731 | system development | 0.0225153910667357 |
| GO:0009725 | response to hormone stimulus | 0.0228608169243905 |
| GO:0016301 | kinase activity | 0.0233437865526716 |
| GO:0006793 | phosphorus metabolic process | 0.0233437865526716 |
| GO:0006796 | phosphate metabolic process | 0.0233437865526716 |
| GO:0035239 | tube morphogenesis | 0.0233437865526716 |
| GO:0016323 | basolateral plasma membrane | 0.0233437865526716 |
| GO:0045177 | apical part of cell | 0.0233437865526716 |
| GO:0006821 | chloride transport | 0.0233437865526716 |
| GO:0048869 | cellular developmental process | 0.0242610472914439 |
| GO:0030154 | cell differentiation | 0.0242610472914439 |
| GO:0051258 | protein polymerization | 0.0245550436696403 |
| GO:0019900 | kinase binding | 0.0245550436696403 |
| GO:0016485 | protein processing | 0.0245550436696403 |
| GO:0051128 | regulation of cellular component organization and biogenesis | 0.0245550436696403 |
| GO:0000226 | microtubule cytoskeleton organization and biogenesis | 0.0246968259458888 |
| GO:0030659 | cytoplasmic vesicle membrane | 0.0250727235879941 |
| GO:0044433 | cytoplasmic vesicle part | 0.0252035395469867 |
| GO:0016772 | transferase activity, transferring phosphorus-containing groups | 0.0253631517374223 |
| GO:0012506 | vesicle membrane | 0.0258025127592807 |
| GO:0048856 | anatomical structure development | 0.0258025127592807 |
| GO:0035295 | tube development | 0.0261380241335892 |
| GO:0005737 | cytoplasm | 0.0267665293047419 |
| GO:0007420 | brain development | 0.0297900844702313 |
| GO:0022618 | protein-RNA complex assembly | 0.0297900844702313 |
| GO:0043687 | post-translational protein modification | 0.0297900844702313 |
| GO:0004197 | cysteine-type endopeptidase activity | 0.0297900844702313 |
| GO:0007275 | multicellular organismal development | 0.0309125018910617 |
| GO:0008015 | blood circulation | 0.0323781891794638 |
| GO:0003013 | circulatory system process | 0.0323781891794638 |
| GO:0007517 | muscle development | 0.0343943065693929 |
| GO:0006464 | protein modification process | 0.0404822434922459 |
| GO:0043412 | biopolymer modification | 0.0429476695999892 |
| GO:0008285 | negative regulation of cell proliferation | 0.0429476695999892 |
| GO:0008380 | RNA splicing | 0.0429476695999892 |
| GO:0016477 | cell migration | 0.0434120560477655 |
| GO:0005625 | soluble fraction | 0.0434120560477655 |
| GO:0007417 | central nervous system development | 0.0434120560477655 |
| GO:0048699 | generation of neurons | 0.0442254649823763 |
| GO:0022613 | ribonucleoprotein complex biogenesis and assembly | 0.0444829172976253 |
| GO:0015698 | inorganic anion transport | 0.0463873480793026 |
| GO:0022008 | neurogenesis | 0.0463873480793026 |
| GO:0006397 | mRNA processing | 0.0478311459301994 |
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><br>
| Ontology term | p-value | n |
|---|---|---|
| histamine secreting cell | 7.56e-09 | 5 |
| biogenic amine secreting cell | 7.56e-09 | 5 |
| granulocytopoietic cell | 7.56e-09 | 5 |
| mast cell | 7.56e-09 | 5 |
| mast cell progenitor | 7.56e-09 | 5 |
| basophil mast progenitor cell | 7.56e-09 | 5 |
| endocrine cell | 7.27e-08 | 9 |
| melanocyte | 3.03e-07 | 10 |
| melanoblast | 3.03e-07 | 10 |
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 | 1.34964 |
| MA0004.1 | 0.32225 |
| MA0006.1 | 0.188769 |
| MA0007.1 | 0.305951 |
| MA0009.1 | 0.756202 |
| MA0014.1 | 0.657865 |
| MA0017.1 | 0.220105 |
| MA0019.1 | 0.45566 |
| MA0024.1 | 0.654931 |
| MA0025.1 | 0.886436 |
| MA0027.1 | 2.35633 |
| MA0028.1 | 0.583404 |
| MA0029.1 | 0.673506 |
| MA0030.1 | 0.662482 |
| MA0031.1 | 0.600685 |
| MA0038.1 | 1.87299 |
| MA0040.1 | 0.67914 |
| MA0041.1 | 0.338572 |
| MA0042.1 | 0.310552 |
| MA0043.1 | 0.756508 |
| MA0046.1 | 0.745626 |
| MA0048.1 | 1.4241 |
| MA0050.1 | 0.311321 |
| MA0051.1 | 0.410316 |
| MA0052.1 | 3.99404 |
| MA0055.1 | 0.107116 |
| MA0056.1 | 0 |
| MA0057.1 | 0.0373953 |
| MA0058.1 | 0.240796 |
| MA0059.1 | 0.239727 |
| MA0060.1 | 0.103131 |
| MA0061.1 | 0.0856761 |
| MA0063.1 | 0 |
| MA0066.1 | 0.414559 |
| MA0067.1 | 1.06751 |
| MA0068.1 | 0.0633085 |
| MA0069.1 | 0.741884 |
| MA0070.1 | 0.731026 |
| MA0071.1 | 0.379038 |
| MA0072.1 | 0.726666 |
| MA0073.1 | 1.83363e-05 |
| MA0074.1 | 0.40963 |
| MA0076.1 | 0.254045 |
| MA0077.1 | 0.719193 |
| MA0078.1 | 0.502027 |
| MA0081.1 | 0.239862 |
| MA0083.1 | 0.763502 |
| MA0084.1 | 1.25286 |
| MA0087.1 | 0.724294 |
| MA0088.1 | 0.0178242 |
| MA0089.1 | 0 |
| MA0090.1 | 0.266215 |
| MA0091.1 | 0.324543 |
| MA0092.1 | 0.291716 |
| MA0093.1 | 0.191154 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.426863 |
| MA0101.1 | 0.19375 |
| MA0103.1 | 0.181541 |
| MA0105.1 | 0.0320473 |
| MA0106.1 | 0.452066 |
| MA0107.1 | 0.137948 |
| MA0108.2 | 0.597764 |
| MA0109.1 | 0 |
| MA0111.1 | 0.277713 |
| MA0113.1 | 0.467266 |
| MA0114.1 | 0.418165 |
| MA0115.1 | 0.992167 |
| MA0116.1 | 0.433848 |
| MA0117.1 | 0.792789 |
| MA0119.1 | 0.226505 |
| MA0122.1 | 0.818044 |
| MA0124.1 | 0.951337 |
| MA0125.1 | 0.868909 |
| MA0130.1 | 0 |
| MA0131.1 | 0.519055 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 0.785738 |
| MA0136.1 | 0.420617 |
| MA0139.1 | 0.0781324 |
| MA0140.1 | 0.376643 |
| MA0141.1 | 0.238287 |
| MA0142.1 | 0.570448 |
| MA0143.1 | 0.467429 |
| MA0144.1 | 0.124153 |
| MA0145.1 | 0.0212759 |
| MA0146.1 | 0.000996775 |
| MA0147.1 | 0.143012 |
| MA0148.1 | 0.344198 |
| MA0149.1 | 0.367947 |
| MA0062.2 | 0.280813 |
| MA0035.2 | 0.376007 |
| MA0039.2 | 0.0117227 |
| MA0138.2 | 0.503176 |
| MA0002.2 | 0.0954816 |
| MA0137.2 | 0.20663 |
| MA0104.2 | 0.102626 |
| MA0047.2 | 0.440861 |
| MA0112.2 | 0.0192555 |
| MA0065.2 | 0.0221687 |
| MA0150.1 | 0.261236 |
| MA0151.1 | 0 |
| MA0152.1 | 0.382565 |
| MA0153.1 | 0.852412 |
| MA0154.1 | 3.33201 |
| MA0155.1 | 0.0793743 |
| MA0156.1 | 0.208455 |
| MA0157.1 | 0.544523 |
| MA0158.1 | 0 |
| MA0159.1 | 0.441451 |
| MA0160.1 | 0.357736 |
| MA0161.1 | 0 |
| MA0162.1 | 0.138499 |
| MA0163.1 | 0.0909552 |
| MA0164.1 | 0.478818 |
| MA0080.2 | 0.191221 |
| MA0018.2 | 0.453345 |
| MA0099.2 | 0.382887 |
| MA0079.2 | 0.0178219 |
| MA0102.2 | 1.28978 |
| MA0258.1 | 0.754226 |
| MA0259.1 | 0.149181 |
| 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 |
|---|---|---|---|---|
| CTCF#10664 | 10 | 4.46688031089586 | 2.32271458385553e-06 | 8.25389548905367e-05 |
| RAD21#5885 | 9 | 7.76627542159225 | 1.22173700731638e-07 | 7.02626604114072e-06 |
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.
