Coexpression cluster:C41
From FANTOM5_SSTAR
Full id: C41_retina_eye_medulla_Retinal_medulloblastoma_kidney_pineal
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 |
|---|---|---|---|---|
| 2.67418142040755e-06 | 0.000846378419558991 | 4 | 29 | Phototransduction (KEGG):04744 |
| 0.000308510542242841 | 0.0390574346479436 | 3 | 39 | Vitamin A and carotenoid metabolism (Wikipathways):WP716 |
| 1.11054433107064e-07 | 7.02974561567715e-05 | 11 | 401 | Transmembrane transport of small molecules (Reactome):REACT_15518 |
| 0.000278915193463015 | 0.0390574346479436 | 6 | 265 | Axon guidance (Reactome):REACT_18266 |
| 2.42202453492495e-05 | 0.00511047176869165 | 3 | 17 | {CNGB1,17} (Static Module):NA |
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:0007601 | visual perception | 9.81064457375546e-31 |
| GO:0050953 | sensory perception of light stimulus | 9.81064457375546e-31 |
| GO:0032501 | multicellular organismal process | 3.08510962248049e-22 |
| GO:0007600 | sensory perception | 3.26189058192588e-17 |
| GO:0003008 | system process | 1.26111358163529e-16 |
| GO:0050877 | neurological system process | 1.26111358163529e-16 |
| GO:0044459 | plasma membrane part | 1.78753219018382e-10 |
| GO:0005887 | integral to plasma membrane | 3.48236554855786e-09 |
| GO:0031226 | intrinsic to plasma membrane | 3.82694137065199e-09 |
| GO:0005886 | plasma membrane | 1.10604557177807e-08 |
| GO:0009584 | detection of visible light | 1.14514516990045e-08 |
| GO:0009583 | detection of light stimulus | 1.21800691734385e-08 |
| GO:0016020 | membrane | 1.21800691734385e-08 |
| GO:0051606 | detection of stimulus | 5.28086257607399e-08 |
| GO:0009416 | response to light stimulus | 5.38462326854317e-08 |
| GO:0009582 | detection of abiotic stimulus | 5.65792470998684e-08 |
| GO:0050906 | detection of stimulus during sensory perception | 6.11213327574056e-08 |
| GO:0009581 | detection of external stimulus | 9.71823187771387e-08 |
| GO:0016021 | integral to membrane | 1.18976350754503e-07 |
| GO:0031224 | intrinsic to membrane | 1.37309308415663e-07 |
| GO:0009314 | response to radiation | 1.83030242100536e-07 |
| GO:0051179 | localization | 2.5065367989969e-07 |
| GO:0044425 | membrane part | 2.61038036091781e-07 |
| GO:0022857 | transmembrane transporter activity | 2.74197624924218e-07 |
| GO:0007602 | phototransduction | 2.87293679057931e-07 |
| GO:0050962 | detection of light stimulus during sensory perception | 3.74486102475781e-07 |
| GO:0050908 | detection of light stimulus during visual perception | 3.74486102475781e-07 |
| GO:0006811 | ion transport | 5.92245011953541e-07 |
| GO:0022892 | substrate-specific transporter activity | 7.77852834846723e-07 |
| GO:0006810 | transport | 1.75099921659154e-06 |
| GO:0015075 | ion transmembrane transporter activity | 2.18226246992338e-06 |
| GO:0022891 | substrate-specific transmembrane transporter activity | 2.48960658892293e-06 |
| GO:0051234 | establishment of localization | 3.37262948252363e-06 |
| GO:0009628 | response to abiotic stimulus | 3.37262948252363e-06 |
| GO:0031404 | chloride ion binding | 7.22496996755269e-06 |
| GO:0043168 | anion binding | 7.22496996755269e-06 |
| GO:0000267 | cell fraction | 3.39085306567683e-05 |
| GO:0044464 | cell part | 7.74935097155196e-05 |
| GO:0006776 | vitamin A metabolic process | 0.000113042067013674 |
| GO:0006775 | fat-soluble vitamin metabolic process | 0.000196630872701977 |
| GO:0008509 | anion transmembrane transporter activity | 0.000213168768062022 |
| GO:0006820 | anion transport | 0.000236212476668935 |
| GO:0043195 | terminal button | 0.000571118476344432 |
| GO:0033267 | axon part | 0.000571118476344432 |
| GO:0005216 | ion channel activity | 0.000640543268030827 |
| GO:0005624 | membrane fraction | 0.000640982667833571 |
| GO:0022838 | substrate specific channel activity | 0.000671170630792134 |
| GO:0022803 | passive transmembrane transporter activity | 0.000697600840236669 |
| GO:0015267 | channel activity | 0.000697600840236669 |
| GO:0005254 | chloride channel activity | 0.000697600840236669 |
| GO:0016323 | basolateral plasma membrane | 0.000787400292004814 |
| GO:0007275 | multicellular organismal development | 0.00114432280767387 |
| GO:0019867 | outer membrane | 0.00121832200935113 |
| GO:0005253 | anion channel activity | 0.00140117869902976 |
| GO:0042461 | photoreceptor cell development | 0.00211882511925589 |
| GO:0015291 | secondary active transmembrane transporter activity | 0.00314933029047855 |
| GO:0046530 | photoreceptor cell differentiation | 0.00327547442681604 |
| GO:0048856 | anatomical structure development | 0.00372423861523655 |
| GO:0015293 | symporter activity | 0.00379722704385757 |
| GO:0005640 | nuclear outer membrane | 0.00379722704385757 |
| GO:0030594 | neurotransmitter receptor activity | 0.0046305457777339 |
| GO:0048513 | organ development | 0.00494388874763118 |
| GO:0042165 | neurotransmitter binding | 0.00498385539098099 |
| GO:0048731 | system development | 0.00522720437998141 |
| GO:0032502 | developmental process | 0.00527176699239718 |
| GO:0045211 | postsynaptic membrane | 0.00527176699239718 |
| GO:0044456 | synapse part | 0.00694711151701581 |
| GO:0045178 | basal part of cell | 0.00704584335409783 |
| GO:0015711 | organic anion transport | 0.00704584335409783 |
| GO:0009925 | basal plasma membrane | 0.00704584335409783 |
| GO:0005509 | calcium ion binding | 0.00769302195183634 |
| GO:0015629 | actin cytoskeleton | 0.00776742014550554 |
| GO:0007166 | cell surface receptor linked signal transduction | 0.0107349223375345 |
| GO:0015464 | acetylcholine receptor activity | 0.0113398407270675 |
| GO:0018298 | protein-chromophore linkage | 0.0113398407270675 |
| GO:0022804 | active transmembrane transporter activity | 0.0113398407270675 |
| GO:0006766 | vitamin metabolic process | 0.0113830076079591 |
| GO:0042166 | acetylcholine binding | 0.0120582613735087 |
| GO:0031968 | organelle outer membrane | 0.013898647321435 |
| GO:0009887 | organ morphogenesis | 0.0170094158627189 |
| GO:0009953 | dorsal/ventral pattern formation | 0.0187450992181296 |
| GO:0001709 | cell fate determination | 0.0187450992181296 |
| GO:0021902 | commitment of a neuronal cell to a specific type of neuron in the forebrain | 0.0187450992181296 |
| GO:0051450 | myoblast proliferation | 0.0187450992181296 |
| GO:0015129 | lactate transmembrane transporter activity | 0.0187450992181296 |
| GO:0021877 | forebrain neuron fate commitment | 0.0187450992181296 |
| GO:0047173 | phosphatidylcholine-retinol O-acyltransferase activity | 0.0187450992181296 |
| GO:0015727 | lactate transport | 0.0187450992181296 |
| GO:0005008 | hepatocyte growth factor receptor activity | 0.0187450992181296 |
| GO:0009288 | flagellin-based flagellum | 0.0187450992181296 |
| GO:0033130 | acetylcholine receptor binding | 0.0187450992181296 |
| GO:0048012 | hepatocyte growth factor receptor signaling pathway | 0.0187450992181296 |
| GO:0006649 | phospholipid transfer to membrane | 0.0187450992181296 |
| GO:0009642 | response to light intensity | 0.0187450992181296 |
| GO:0005548 | phospholipid transporter activity | 0.0209281533410604 |
| GO:0005507 | copper ion binding | 0.0219957603073038 |
| GO:0019861 | flagellum | 0.0228745297614298 |
| GO:0030424 | axon | 0.0228745297614298 |
| GO:0007389 | pattern specification process | 0.0250956803577066 |
| GO:0001764 | neuron migration | 0.0250956803577066 |
| GO:0000904 | cellular morphogenesis during differentiation | 0.025757485968105 |
| GO:0015698 | inorganic anion transport | 0.0263006760497974 |
| GO:0005230 | extracellular ligand-gated ion channel activity | 0.0279803275485031 |
| GO:0006939 | smooth muscle contraction | 0.0279803275485031 |
| GO:0004890 | GABA-A receptor activity | 0.0279803275485031 |
| GO:0009605 | response to external stimulus | 0.02979352862017 |
| GO:0007420 | brain development | 0.0306076284339457 |
| GO:0021872 | generation of neurons in the forebrain | 0.0306076284339457 |
| GO:0021798 | forebrain dorsal/ventral pattern formation | 0.0306076284339457 |
| GO:0007468 | regulation of rhodopsin gene expression | 0.0306076284339457 |
| GO:0022612 | gland morphogenesis | 0.0306076284339457 |
| GO:0005502 | 11-cis retinal binding | 0.0306076284339457 |
| GO:0021879 | forebrain neuron differentiation | 0.0306076284339457 |
| GO:0008525 | phosphatidylcholine transmembrane transporter activity | 0.0306076284339457 |
| GO:0007435 | salivary gland morphogenesis | 0.0306076284339457 |
| GO:0043176 | amine binding | 0.0319321797904677 |
| GO:0008324 | cation transmembrane transporter activity | 0.0319321797904677 |
| GO:0044463 | cell projection part | 0.0355698893762162 |
| GO:0016917 | GABA receptor activity | 0.0355698893762162 |
| GO:0005328 | neurotransmitter:sodium symporter activity | 0.0397857995950336 |
| GO:0004167 | dopachrome isomerase activity | 0.041246130335252 |
| GO:0008273 | calcium, potassium:sodium antiporter activity | 0.041246130335252 |
| GO:0005594 | collagen type IX | 0.041246130335252 |
| GO:0017147 | Wnt-protein binding | 0.041246130335252 |
| GO:0043288 | apocarotenoid metabolic process | 0.041246130335252 |
| GO:0042574 | retinal metabolic process | 0.041246130335252 |
| GO:0046873 | metal ion transmembrane transporter activity | 0.041246130335252 |
| GO:0005326 | neurotransmitter transporter activity | 0.041246130335252 |
| GO:0019748 | secondary metabolic process | 0.041246130335252 |
| GO:0022834 | ligand-gated channel activity | 0.041246130335252 |
| GO:0015276 | ligand-gated ion channel activity | 0.041246130335252 |
| GO:0022836 | gated channel activity | 0.042059685265673 |
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 |
|---|---|---|
| pigment cell | 4.72e-07 | 14 |
| stuff accumulating cell | 4.94e-07 | 39 |
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) |
|---|---|
|
{{{tfbs_overrepresentation_jaspar}}} |
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
"{{{coexpression_dpi_cluster_scores_median}}}" is not a number.
