Coexpression cluster:C261
From FANTOM5_SSTAR
Full id: C261_locus_medial_parietal_pons_diencephalon_olfactory_spinal
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
| p.value | FDR | nGenes | nPathway | Name |
|---|---|---|---|---|
| 2.4140612493822e-08 | 1.52810077085894e-05 | 3 | 53 | Amyotrophic lateral sclerosis (ALS) (KEGG):05014 |
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:0060053 | neurofilament cytoskeleton | 4.23101610269649e-09 |
| GO:0005883 | neurofilament | 4.23101610269649e-09 |
| GO:0030424 | axon | 4.81680398255976e-07 |
| GO:0045110 | intermediate filament bundle assembly | 6.84538130668057e-07 |
| GO:0043005 | neuron projection | 3.91095559129903e-06 |
| GO:0060052 | neurofilament cytoskeleton organization and biogenesis | 3.91095559129903e-06 |
| GO:0045109 | intermediate filament organization | 3.91095559129903e-06 |
| GO:0008088 | axon cargo transport | 9.580148792241e-06 |
| GO:0031175 | neurite development | 1.07113664769344e-05 |
| GO:0048666 | neuron development | 1.38193985235911e-05 |
| GO:0007399 | nervous system development | 1.38193985235911e-05 |
| GO:0045104 | intermediate filament cytoskeleton organization and biogenesis | 2.07496567459559e-05 |
| GO:0045103 | intermediate filament-based process | 2.08846379961956e-05 |
| GO:0032990 | cell part morphogenesis | 2.08846379961956e-05 |
| GO:0048858 | cell projection morphogenesis | 2.08846379961956e-05 |
| GO:0030030 | cell projection organization and biogenesis | 2.08846379961956e-05 |
| GO:0030182 | neuron differentiation | 2.14453827583458e-05 |
| GO:0044430 | cytoskeletal part | 2.27522652460715e-05 |
| GO:0005882 | intermediate filament | 2.5883240202762e-05 |
| GO:0045111 | intermediate filament cytoskeleton | 2.5883240202762e-05 |
| GO:0048699 | generation of neurons | 2.65804079784278e-05 |
| GO:0022008 | neurogenesis | 3.2199136132167e-05 |
| GO:0050770 | regulation of axonogenesis | 3.86366421737609e-05 |
| GO:0042995 | cell projection | 4.92236542123348e-05 |
| GO:0007017 | microtubule-based process | 4.92236542123348e-05 |
| GO:0050767 | regulation of neurogenesis | 7.38786335274999e-05 |
| GO:0005856 | cytoskeleton | 8.52699397135336e-05 |
| GO:0048731 | system development | 0.000133838498078037 |
| GO:0044446 | intracellular organelle part | 0.000133838498078037 |
| GO:0044422 | organelle part | 0.000133838498078037 |
| GO:0000902 | cell morphogenesis | 0.000133838498078037 |
| GO:0032989 | cellular structure morphogenesis | 0.000133838498078037 |
| GO:0048856 | anatomical structure development | 0.000275992745606819 |
| GO:0005200 | structural constituent of cytoskeleton | 0.000286103611385618 |
| GO:0007010 | cytoskeleton organization and biogenesis | 0.000359040506163476 |
| GO:0000226 | microtubule cytoskeleton organization and biogenesis | 0.000389482381163675 |
| GO:0007275 | multicellular organismal development | 0.000422578373894008 |
| GO:0007409 | axonogenesis | 0.000461063935069976 |
| GO:0048667 | neuron morphogenesis during differentiation | 0.00048537342180161 |
| GO:0048812 | neurite morphogenesis | 0.00048537342180161 |
| GO:0000904 | cellular morphogenesis during differentiation | 0.000522096502794062 |
| GO:0008090 | retrograde axon cargo transport | 0.000528510109930102 |
| GO:0033693 | neurofilament bundle assembly | 0.000528510109930102 |
| GO:0033596 | TSC1-TSC2 complex | 0.000528510109930102 |
| GO:0043232 | intracellular non-membrane-bound organelle | 0.00087136633023563 |
| GO:0043228 | non-membrane-bound organelle | 0.00087136633023563 |
| GO:0007018 | microtubule-based movement | 0.00091716122221323 |
| GO:0009653 | anatomical structure morphogenesis | 0.00091716122221323 |
| GO:0031133 | regulation of axon diameter | 0.000930123030426531 |
| GO:0019896 | axon transport of mitochondrion | 0.000930123030426531 |
| GO:0030705 | cytoskeleton-dependent intracellular transport | 0.00101433288656327 |
| GO:0016043 | cellular component organization and biogenesis | 0.00121196012980163 |
| GO:0032502 | developmental process | 0.00126827491445492 |
| GO:0019987 | negative regulation of anti-apoptosis | 0.00126827491445492 |
| GO:0030517 | negative regulation of axon extension | 0.00126827491445492 |
| GO:0048468 | cell development | 0.00130133684677868 |
| GO:0050793 | regulation of developmental process | 0.00131382944009915 |
| GO:0032501 | multicellular organismal process | 0.00197025161148262 |
| GO:0008089 | anterograde axon cargo transport | 0.00197025161148262 |
| GO:0006996 | organelle organization and biogenesis | 0.00222492379745686 |
| GO:0031594 | neuromuscular junction | 0.00224976776725475 |
| GO:0050771 | negative regulation of axonogenesis | 0.00224976776725475 |
| GO:0001578 | microtubule bundle formation | 0.00258291462092895 |
| GO:0048869 | cellular developmental process | 0.00338391799232485 |
| GO:0030154 | cell differentiation | 0.00338391799232485 |
| GO:0050768 | negative regulation of neurogenesis | 0.00404163294447627 |
| GO:0016358 | dendrite development | 0.00404163294447627 |
| GO:0045767 | regulation of anti-apoptosis | 0.00404163294447627 |
| GO:0030516 | regulation of axon extension | 0.00404163294447627 |
| GO:0048675 | axon extension | 0.00564219054121416 |
| GO:0005829 | cytosol | 0.00600575663579328 |
| GO:0043229 | intracellular organelle | 0.00681287527294214 |
| GO:0043226 | organelle | 0.00681287527294214 |
| GO:0007026 | negative regulation of microtubule depolymerization | 0.00681287527294214 |
| GO:0031114 | regulation of microtubule depolymerization | 0.00681287527294214 |
| GO:0031111 | negative regulation of microtubule polymerization or depolymerization | 0.00693714164661611 |
| GO:0007019 | microtubule depolymerization | 0.00693714164661611 |
| GO:0031110 | regulation of microtubule polymerization or depolymerization | 0.00863164222565041 |
| GO:0031109 | microtubule polymerization or depolymerization | 0.00940234569647014 |
| GO:0022607 | cellular component assembly | 0.0107676993146376 |
| GO:0051261 | protein depolymerization | 0.013087176159772 |
| GO:0046907 | intracellular transport | 0.013087176159772 |
| GO:0051129 | negative regulation of cellular component organization and biogenesis | 0.0145253696570421 |
| GO:0030176 | integral to endoplasmic reticulum membrane | 0.0146275959853866 |
| GO:0044424 | intracellular part | 0.0150008238923059 |
| GO:0030334 | regulation of cell migration | 0.016167772421178 |
| GO:0031227 | intrinsic to endoplasmic reticulum membrane | 0.0162473449589946 |
| GO:0051649 | establishment of cellular localization | 0.0175591055910402 |
| GO:0051270 | regulation of cell motility | 0.0179566926436438 |
| GO:0051641 | cellular localization | 0.0180258923310935 |
| GO:0048523 | negative regulation of cellular process | 0.0181232143219493 |
| GO:0040012 | regulation of locomotion | 0.0181232143219493 |
| GO:0040011 | locomotion | 0.0181762756204863 |
| GO:0008022 | protein C-terminus binding | 0.0182281790107758 |
| GO:0048519 | negative regulation of biological process | 0.018568730079944 |
| GO:0051093 | negative regulation of developmental process | 0.018568730079944 |
| GO:0051128 | regulation of cellular component organization and biogenesis | 0.0238343265402459 |
| GO:0051248 | negative regulation of protein metabolic process | 0.0245289866141991 |
| GO:0005622 | intracellular | 0.0259452798575701 |
| GO:0051179 | localization | 0.0294502339281616 |
| GO:0044444 | cytoplasmic part | 0.0312111074793519 |
| GO:0031301 | integral to organelle membrane | 0.0314334501173939 |
| GO:0031300 | intrinsic to organelle membrane | 0.0340135051096874 |
| GO:0006916 | anti-apoptosis | 0.0376357318201396 |
| GO:0005875 | microtubule associated complex | 0.0394468473645381 |
| GO:0044445 | cytosolic part | 0.0412212483758672 |
| GO:0005635 | nuclear envelope | 0.0416858902861601 |
| GO:0043066 | negative regulation of apoptosis | 0.0482313546818419 |
| GO:0043069 | negative regulation of programmed cell death | 0.0484118847156383 |
| GO:0016477 | cell migration | 0.0485889128549148 |
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 |
|---|---|---|
| Merkel cell | 5.10e-07 | 2 |
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 | 5.78061e-12 |
| MA0004.1 | 0.0287532 |
| MA0006.1 | 0.0290142 |
| MA0007.1 | 0.024623 |
| MA0009.1 | 0.252434 |
| MA0014.1 | 1.14887e-11 |
| MA0017.1 | 0.00870385 |
| MA0019.1 | 0.0757474 |
| MA0024.1 | 0.183969 |
| MA0025.1 | 2.4963 |
| MA0027.1 | 1.73105 |
| MA0028.1 | 0.0348968 |
| MA0029.1 | 1.08244 |
| MA0030.1 | 0.188804 |
| MA0031.1 | 0.150659 |
| MA0038.1 | 0.213125 |
| MA0040.1 | 0.199633 |
| MA0041.1 | 0.0332488 |
| MA0042.1 | 0.264815 |
| MA0043.1 | 0.252653 |
| MA0046.1 | 0.685727 |
| MA0048.1 | 0.00351449 |
| MA0050.1 | 0.109642 |
| MA0051.1 | 0.0572096 |
| MA0052.1 | 0.202085 |
| MA0055.1 | 1.0756 |
| MA0056.1 | 0 |
| MA0057.1 | 0.0812865 |
| MA0058.1 | 0.0568651 |
| MA0059.1 | 0.0561949 |
| MA0060.1 | 0.000588275 |
| MA0061.1 | 0.0687895 |
| MA0063.1 | 0 |
| MA0066.1 | 1.23063 |
| MA0067.1 | 0.49981 |
| MA0068.1 | 8.92408e-05 |
| MA0069.1 | 0.242306 |
| MA0070.1 | 0.234718 |
| MA0071.1 | 0.0459331 |
| MA0072.1 | 0.231695 |
| MA0073.1 | 1.15334e-13 |
| MA0074.1 | 0.0569489 |
| MA0076.1 | 0.0138475 |
| MA0077.1 | 0.226543 |
| MA0078.1 | 0.321356 |
| MA0081.1 | 7.9135 |
| MA0083.1 | 0.25765 |
| MA0084.1 | 0.664025 |
| MA0087.1 | 0.230056 |
| MA0088.1 | 0.00767257 |
| MA0089.1 | 0 |
| MA0090.1 | 0.191226 |
| MA0091.1 | 0.289788 |
| MA0092.1 | 1.4496 |
| MA0093.1 | 0.0300741 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.227752 |
| MA0101.1 | 0.200267 |
| MA0103.1 | 0.318689 |
| MA0105.1 | 0.00563636 |
| MA0106.1 | 0.0741862 |
| MA0107.1 | 0.496379 |
| MA0108.2 | 0.14894 |
| MA0109.1 | 0 |
| MA0111.1 | 0.082444 |
| MA0113.1 | 0.0808928 |
| MA0114.1 | 0.179021 |
| MA0115.1 | 0.436009 |
| MA0116.1 | 0.729675 |
| MA0117.1 | 0.27892 |
| MA0119.1 | 0.274103 |
| MA0122.1 | 0.297683 |
| MA0124.1 | 1.03875 |
| MA0125.1 | 0.336564 |
| MA0130.1 | 0 |
| MA0131.1 | 0.10574 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 0.27375 |
| MA0136.1 | 1.25703 |
| MA0139.1 | 0.000203372 |
| MA0140.1 | 0.389168 |
| MA0141.1 | 0.0552982 |
| MA0142.1 | 0.133251 |
| MA0143.1 | 0.582117 |
| MA0144.1 | 2.10189 |
| MA0145.1 | 1.47713e-05 |
| MA0146.1 | 9.46233e-10 |
| MA0147.1 | 0.00196312 |
| MA0148.1 | 0.0348816 |
| MA0149.1 | 0.0422402 |
| MA0062.2 | 0.122451 |
| MA0035.2 | 0.171459 |
| MA0039.2 | 2.7447e-11 |
| MA0138.2 | 0.0978028 |
| MA0002.2 | 0.00348218 |
| MA0137.2 | 0.905104 |
| MA0104.2 | 0.0005775 |
| MA0047.2 | 0.0694194 |
| MA0112.2 | 7.01122e-07 |
| MA0065.2 | 0.206774 |
| MA0150.1 | 0.0151269 |
| MA0151.1 | 0 |
| MA0152.1 | 2.05334 |
| MA0153.1 | 0.865299 |
| MA0154.1 | 1.15244 |
| MA0155.1 | 0.0317588 |
| MA0156.1 | 0.408437 |
| MA0157.1 | 0.119034 |
| MA0158.1 | 0 |
| MA0159.1 | 0.00198615 |
| MA0160.1 | 0.152819 |
| MA0161.1 | 0 |
| MA0162.1 | 7.17851e-09 |
| MA0163.1 | 0.000201516 |
| MA0164.1 | 3.3867 |
| MA0080.2 | 5.41959 |
| MA0018.2 | 0.0747401 |
| MA0099.2 | 0.0472524 |
| MA0079.2 | 1.90069e-13 |
| MA0102.2 | 0.697711 |
| MA0258.1 | 0.0254544 |
| MA0259.1 | 0.0144768 |
| 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
