Difference between revisions of "Gene.ini"
From VastDB
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gene-browser=<p>Genomic context of the gene. Click on the image to view the gene, its events and its context in the UCSC website</p><p>Track colors:</p><ul><li><b>Black:</b> Group of neighboring cassette exon events (no link to VASTDB)</li><li><b>Blue:</b> Simple cassette exon events</li><li><b>Purple:</b> Cassette exon events of intermediate complexity</li><li><b>Red:</b> Complex cassette exon events</li><li><b>Orange:</b> Intron retention events</li><li><b>Dark green:</b>Alternative 3' splice site choice event.</li><li><b>Light green:</b>Alternative 5' splice site choice event.</li></ul><p>See the FAQ section for further explanation.</p> | gene-browser=<p>Genomic context of the gene. Click on the image to view the gene, its events and its context in the UCSC website</p><p>Track colors:</p><ul><li><b>Black:</b> Group of neighboring cassette exon events (no link to VASTDB)</li><li><b>Blue:</b> Simple cassette exon events</li><li><b>Purple:</b> Cassette exon events of intermediate complexity</li><li><b>Red:</b> Complex cassette exon events</li><li><b>Orange:</b> Intron retention events</li><li><b>Dark green:</b>Alternative 3' splice site choice event.</li><li><b>Light green:</b>Alternative 5' splice site choice event.</li></ul><p>See the FAQ section for further explanation.</p> | ||
| − | gene-expression=<p>Each of the dots in this plot represents the average expression of the gene across several related samples. Put your mouse on each dot to see the individual values for each sample.</p><p>Dot colors represent sample groups from a similar biological origin (see legend below).</p><p> Samples can be included/excluded from the plot using the buttons "Show All","Show None","Select All","Select None", or clicking on the sample groups below.</p> | + | gene-expression=<p>Each of the dots in this plot represents the average expression of the gene across several related samples. Put your mouse on each dot to see the individual values for each sample.</p><p>Dot colors represent sample groups from a similar biological origin (see legend below).</p><p> Samples can be included/excluded from the plot using the buttons "Show All","Show None","Select All","Select None", or clicking on the sample groups below.</p><p> cRPKM can be converted to TPMs applying the following formula: TPM = 10^6 * cRPKM/sum_all(cRPKM).</p> |
| − | gene-specialdataset-tcga=<p>Data from the The Cancer Genome Atlas (TCGA) project</p> | + | gene-specialdataset-tcga=<p>Data from the The Cancer Genome Atlas (TCGA) project</p><p>Note: Expression values were only calculated for hg38 annotations.</p> |
| − | gene-specialdataset-gtex=<p>Data from the Genotype-Tissue Expresssion project</p> | + | gene-specialdataset-gtex=<p>Data from the Genotype-Tissue Expresssion project</p><p>Note: Expression values were only calculated using vast-tools hg19 libraries (Hsa)</p> |
gene-specialdataset-asducla=<p>Samples from BA41_42_22 and BA9 brain regions from individuals with autism spectrum disorder (ASD) and matched controls ("Cont", blue). ASD samples include idiopatic cases ("ASD", red) and carriers of a 15q duplication ("Dup15q", orange).</p><p>Each sample corresponds to a group of 4 individuals to increase coverage; the grouping were made based on age ("a" younger, "c" older), and the selected ASD samples correspond to those showing the strongest gene expression signature for diagnosis (see Irimia et al, Cell 2014 for details).</p><p><b>Sample source:</b> Parikshak <i>et al.</i>, Nature (2016). PMID: 27919067</p><p>RNA-Seq specifics: 50nt single end; Ribo-Seq libraries.</p> | gene-specialdataset-asducla=<p>Samples from BA41_42_22 and BA9 brain regions from individuals with autism spectrum disorder (ASD) and matched controls ("Cont", blue). ASD samples include idiopatic cases ("ASD", red) and carriers of a 15q duplication ("Dup15q", orange).</p><p>Each sample corresponds to a group of 4 individuals to increase coverage; the grouping were made based on age ("a" younger, "c" older), and the selected ASD samples correspond to those showing the strongest gene expression signature for diagnosis (see Irimia et al, Cell 2014 for details).</p><p><b>Sample source:</b> Parikshak <i>et al.</i>, Nature (2016). PMID: 27919067</p><p>RNA-Seq specifics: 50nt single end; Ribo-Seq libraries.</p> | ||
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gene-specialdataset-hemato=<p>Recopilation of RNA-Seq experiments in hematopoietic cell types from the SRA.</p><p><b>Sample sources:</b></p><ul><li><b>MSC:</b> SRR1825654, SRR1825655, SRR1825642, SRR1825641, SRR4448546, SRR4448542, SRR4448538, SRR2982412, SRR2982411.</li><li><b>HSC_a:</b> SRR5272995, SRR5272994, SRR5272993, SRR3180533, SRR3180532.</li><li><b>HSC_b:</b> SRR1535691, SRR1535692, SRR1535693</li><li><b>HSC_c:</b> SRR3192579, SRR3192578.</li><li><b>CLP_a:</b> SRR2031874, SRR3157474, SRR3157473, SRR3157472, SRR3157471.</li><li><b>CLP_b:</b> SRR3152878, SRR3152879, SRR1536385, ERR674977, SRR1373358.</li><li><b>CMP_a:</b> SRR5273012, SRR5273011, SRR5273010, SRR2079145.</li><li><b>CMP_b:</b> SRR3192652, SRR3192651.</li><li><b>CMP_c:</b> SRR2927369, SRR2927370, SRR2927371, SRR2927372, SRR2927373.</li><li><b>MEP_a:</b> SRR3192624, SRR3192625.</li><li><b>MEP_b:</b> SRR5272980, SRR5272979, SRR5272978, SRR3479226, SRR3479225, SRR3479224, SRR3479223, SRR3479222, SRR3479221, SRR3479219.</li><li><b>Erythroblasts_a:</b> SRR4422111.</li><li><b>Erythroblasts_b:</b> SRR4422110.</li><li><b>GMP_a:</b> SRR3192676, SRR3192675</li><li><b>GMP_b:</b> SRR5272999, SRR5273000, SRR5272998, SRR2079146, ERR674985.</li><li><b>MDP:</b> SRR5272983, SRR5272982, SRR5272981, SRR1629218.</li><li><b>Monocytes_ab:</b> SRR2047009, SRR2047008, ERR674981.</li><li><b>BM_DM_a:</b> SRR1634674, SRR1634708, SRR1514123, SRR1514122, SRR1514121.</li><li><b>BM_DM_b:</b> SRR3586229, SRR3586202, SRR3586201, SRR502948, SRR1999896, SRR1999895.</li></ul> | gene-specialdataset-hemato=<p>Recopilation of RNA-Seq experiments in hematopoietic cell types from the SRA.</p><p><b>Sample sources:</b></p><ul><li><b>MSC:</b> SRR1825654, SRR1825655, SRR1825642, SRR1825641, SRR4448546, SRR4448542, SRR4448538, SRR2982412, SRR2982411.</li><li><b>HSC_a:</b> SRR5272995, SRR5272994, SRR5272993, SRR3180533, SRR3180532.</li><li><b>HSC_b:</b> SRR1535691, SRR1535692, SRR1535693</li><li><b>HSC_c:</b> SRR3192579, SRR3192578.</li><li><b>CLP_a:</b> SRR2031874, SRR3157474, SRR3157473, SRR3157472, SRR3157471.</li><li><b>CLP_b:</b> SRR3152878, SRR3152879, SRR1536385, ERR674977, SRR1373358.</li><li><b>CMP_a:</b> SRR5273012, SRR5273011, SRR5273010, SRR2079145.</li><li><b>CMP_b:</b> SRR3192652, SRR3192651.</li><li><b>CMP_c:</b> SRR2927369, SRR2927370, SRR2927371, SRR2927372, SRR2927373.</li><li><b>MEP_a:</b> SRR3192624, SRR3192625.</li><li><b>MEP_b:</b> SRR5272980, SRR5272979, SRR5272978, SRR3479226, SRR3479225, SRR3479224, SRR3479223, SRR3479222, SRR3479221, SRR3479219.</li><li><b>Erythroblasts_a:</b> SRR4422111.</li><li><b>Erythroblasts_b:</b> SRR4422110.</li><li><b>GMP_a:</b> SRR3192676, SRR3192675</li><li><b>GMP_b:</b> SRR5272999, SRR5273000, SRR5272998, SRR2079146, ERR674985.</li><li><b>MDP:</b> SRR5272983, SRR5272982, SRR5272981, SRR1629218.</li><li><b>Monocytes_ab:</b> SRR2047009, SRR2047008, ERR674981.</li><li><b>BM_DM_a:</b> SRR1634674, SRR1634708, SRR1514123, SRR1514122, SRR1514121.</li><li><b>BM_DM_b:</b> SRR3586229, SRR3586202, SRR3586201, SRR502948, SRR1999896, SRR1999895.</li></ul> | ||
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gene-specialdataset-myoblast=<p>RNA-Seq data collected from murine C2C12 skeletal muscle cells induced to undergo myogenic differentiation.</p><p> <b>Sample source:</b> Trapnell <i>et al.</i>, Nat. Biotechnol. (2010). PMID: 20436464.</p> | gene-specialdataset-myoblast=<p>RNA-Seq data collected from murine C2C12 skeletal muscle cells induced to undergo myogenic differentiation.</p><p> <b>Sample source:</b> Trapnell <i>et al.</i>, Nat. Biotechnol. (2010). PMID: 20436464.</p> | ||
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gene-specialdataset-vicky=<p>Vicky EXP tooltip goes here</p> | gene-specialdataset-vicky=<p>Vicky EXP tooltip goes here</p> | ||
| − | gene-specialdataset-earlydev=<p>Single and pooled cell data from multiple sources, representing Oocyte to Blastocyst embryo development.</p><p><b>Sample sources (Hsa):</b><ul><li>Xue <i>et al.</i>, Nature. (2013). PMID: 23892778</li><li>Yan <i>et al.</i>, Nat Struct Mol Biol. (2013). PMID: 23934149</li></ul><p>More than 70% of the data is from <i>Yan et al.</i></p><p><b>Sample sources (Mmu):</b><ul><li>MacFarlen <i>et al.</i>, Nature. (2012). PMID: 22722858</li><li>Biase <i>et al.</i>, Genome Res. (2014). PMID: 25096407</li><li>Deng <i>et al.</i>, Science. (2014). PMID: 24408435</li><li>Abe <i>et al.</i>, EMBO J. (2015). PMID: 25896510</li><li> Hamazaki <i>et al.</i>, Development. (2015). PMID: 25633350</li></ul><p>More than 70% of the data is from Deng <i>et al.</i> and from Biase <i>et al.</i></p> | + | gene-specialdataset-earlydev=<p>Single and pooled cell data from multiple sources, representing Oocyte to Blastocyst embryo development.</p><p><b>Sample sources (Hsa):</b><ul><li>Xue <i>et al.</i>, Nature. (2013). PMID: 23892778</li><li>Yan <i>et al.</i>, Nat Struct Mol Biol. (2013). PMID: 23934149</li></ul><p>More than 70% of the data is from <i>Yan et al.</i></p><p><b>Sample sources (Mmu):</b><ul><li>MacFarlen <i>et al.</i>, Nature. (2012). PMID: 22722858</li><li>Biase <i>et al.</i>, Genome Res. (2014). PMID: 25096407</li><li>Deng <i>et al.</i>, Science. (2014). PMID: 24408435</li><li>Abe <i>et al.</i>, EMBO J. (2015). PMID: 25896510</li><li> Hamazaki <i>et al.</i>, Development. (2015). PMID: 25633350</li></ul><p>More than 70% of the data is from Deng <i>et al.</i> and from Biase <i>et al.</i></p><p>Note: Expression values were only calculated using vast-tools hg19, mm9 or bosTau6 libraries (Hsa, Mmu, Bta)</p> |
event-specialdataset-abiotic=<p>Abiotic stress conditions in <i>A. thaliana</i></p> | event-specialdataset-abiotic=<p>Abiotic stress conditions in <i>A. thaliana</i></p> | ||
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gene-specialdataset-scheiffele=<p>Ribosome-engaged transcriptomes of neuronal types</p><p>Datasets from Furlanis et al (PMID: 31451803): GSE133291</p><p>Note: Expression values were only calculated using vast-tools mm10 libraries (Mm2)</p> | gene-specialdataset-scheiffele=<p>Ribosome-engaged transcriptomes of neuronal types</p><p>Datasets from Furlanis et al (PMID: 31451803): GSE133291</p><p>Note: Expression values were only calculated using vast-tools mm10 libraries (Mm2)</p> | ||
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gene-associatedevents=<p>Events belonging to the gene of interest. You can click on each of the table columns to sort the events by this column or on each of the events to access to detailed information. <li>PSI Average: average for all the samples included in the plot. </li><li>PSI Range: difference between the maximum and minimum PSIs for all the samples displayed in the plot.</li><li> Each of the dots in the plot represents the average PSI of the AS event across several related samples. Hover the mouse over each dot to see the individual values for each sample. Dot colors represent sample groups from a similar biological origin (see legend below). </li><li>Samples can be included/excluded from the plot using the buttons “Show All Tissues”,”Show None Tissues”,”Select All Tissues”,”Select None Tissues”, or clicking on the sample groups below. To access to each sample information, click on the sample name of the “Show All” section.</li></p> | gene-associatedevents=<p>Events belonging to the gene of interest. You can click on each of the table columns to sort the events by this column or on each of the events to access to detailed information. <li>PSI Average: average for all the samples included in the plot. </li><li>PSI Range: difference between the maximum and minimum PSIs for all the samples displayed in the plot.</li><li> Each of the dots in the plot represents the average PSI of the AS event across several related samples. Hover the mouse over each dot to see the individual values for each sample. Dot colors represent sample groups from a similar biological origin (see legend below). </li><li>Samples can be included/excluded from the plot using the buttons “Show All Tissues”,”Show None Tissues”,”Select All Tissues”,”Select None Tissues”, or clicking on the sample groups below. To access to each sample information, click on the sample name of the “Show All” section.</li></p> | ||
Latest revision as of 17:49, 21 December 2020
gene-coords=Genomic coordinates of the gene (1-based).
gene-browser=Genomic context of the gene. Click on the image to view the gene, its events and its context in the UCSC website
Track colors:
- Black: Group of neighboring cassette exon events (no link to VASTDB)
- Blue: Simple cassette exon events
- Purple: Cassette exon events of intermediate complexity
- Red: Complex cassette exon events
- Orange: Intron retention events
- Dark green:Alternative 3' splice site choice event.
- Light green:Alternative 5' splice site choice event.
See the FAQ section for further explanation.
gene-expression=Each of the dots in this plot represents the average expression of the gene across several related samples. Put your mouse on each dot to see the individual values for each sample.
Dot colors represent sample groups from a similar biological origin (see legend below).
Samples can be included/excluded from the plot using the buttons "Show All","Show None","Select All","Select None", or clicking on the sample groups below.
cRPKM can be converted to TPMs applying the following formula: TPM = 10^6 * cRPKM/sum_all(cRPKM).
gene-specialdataset-tcga=Data from the The Cancer Genome Atlas (TCGA) project
Note: Expression values were only calculated for hg38 annotations.
gene-specialdataset-gtex=Data from the Genotype-Tissue Expresssion project
Note: Expression values were only calculated using vast-tools hg19 libraries (Hsa)
gene-specialdataset-asducla=Samples from BA41_42_22 and BA9 brain regions from individuals with autism spectrum disorder (ASD) and matched controls ("Cont", blue). ASD samples include idiopatic cases ("ASD", red) and carriers of a 15q duplication ("Dup15q", orange).
Each sample corresponds to a group of 4 individuals to increase coverage; the grouping were made based on age ("a" younger, "c" older), and the selected ASD samples correspond to those showing the strongest gene expression signature for diagnosis (see Irimia et al, Cell 2014 for details).
Sample source: Parikshak et al., Nature (2016). PMID: 27919067
RNA-Seq specifics: 50nt single end; Ribo-Seq libraries.
gene-specialdataset-neudif=Samples selected from a differentiation experiment from murine ESCs to glutamatergic cortical neurons.
DIV: Days In Vitro.
Sample source: Hubbard et al., F1000 (2013). PMID: 24358889
gene-specialdataset-pancreas=Data from RNA-Seq experiments performed in pancreatic cell types isolated by FACS.
Sample source: Arda et al., Cell Metab. (2016). PMID: 27133132
gene-specialdataset-hemato=Recopilation of RNA-Seq experiments in hematopoietic cell types from the SRA.
Sample sources:
- MSC: SRR1825654, SRR1825655, SRR1825642, SRR1825641, SRR4448546, SRR4448542, SRR4448538, SRR2982412, SRR2982411.
- HSC_a: SRR5272995, SRR5272994, SRR5272993, SRR3180533, SRR3180532.
- HSC_b: SRR1535691, SRR1535692, SRR1535693
- HSC_c: SRR3192579, SRR3192578.
- CLP_a: SRR2031874, SRR3157474, SRR3157473, SRR3157472, SRR3157471.
- CLP_b: SRR3152878, SRR3152879, SRR1536385, ERR674977, SRR1373358.
- CMP_a: SRR5273012, SRR5273011, SRR5273010, SRR2079145.
- CMP_b: SRR3192652, SRR3192651.
- CMP_c: SRR2927369, SRR2927370, SRR2927371, SRR2927372, SRR2927373.
- MEP_a: SRR3192624, SRR3192625.
- MEP_b: SRR5272980, SRR5272979, SRR5272978, SRR3479226, SRR3479225, SRR3479224, SRR3479223, SRR3479222, SRR3479221, SRR3479219.
- Erythroblasts_a: SRR4422111.
- Erythroblasts_b: SRR4422110.
- GMP_a: SRR3192676, SRR3192675
- GMP_b: SRR5272999, SRR5273000, SRR5272998, SRR2079146, ERR674985.
- MDP: SRR5272983, SRR5272982, SRR5272981, SRR1629218.
- Monocytes_ab: SRR2047009, SRR2047008, ERR674981.
- BM_DM_a: SRR1634674, SRR1634708, SRR1514123, SRR1514122, SRR1514121.
- BM_DM_b: SRR3586229, SRR3586202, SRR3586201, SRR502948, SRR1999896, SRR1999895.
RNA-Seq data collected from murine C2C12 skeletal muscle cells induced to undergo myogenic differentiation.
Sample source: Trapnell et al., Nat. Biotechnol. (2010). PMID: 20436464.
gene-specialdataset-spermatogenesis=Data from diverse cell types from testis, isolated from C57BL/6J mice.
Sample source: Soumillon et al., Cell Rep. (2013). PMID: 23791531.
gene-specialdataset-reprogr_carstens=Time-course data from a reprogramming process from mouse embryonic fibroblasts to iPSCs
Sample source: Cieply et al., Cell Rep. (2016). PMID: 27050523.
gene-specialdataset-vicky=Vicky EXP tooltip goes here
gene-specialdataset-earlydev=Single and pooled cell data from multiple sources, representing Oocyte to Blastocyst embryo development.
Sample sources (Hsa):
- Xue et al., Nature. (2013). PMID: 23892778
- Yan et al., Nat Struct Mol Biol. (2013). PMID: 23934149
Sample sources (Mmu):
- MacFarlen et al., Nature. (2012). PMID: 22722858
- Biase et al., Genome Res. (2014). PMID: 25096407
- Deng et al., Science. (2014). PMID: 24408435
- Abe et al., EMBO J. (2015). PMID: 25896510
- Hamazaki et al., Development. (2015). PMID: 25633350
Note: Expression values were only calculated using vast-tools hg19, mm9 or bosTau6 libraries (Hsa, Mmu, Bta)
event-specialdataset-abiotic=Abiotic stress conditions in A. thaliana
event-specialdataset-biotic=Biotic stress conditions in A. thaliana
event-specialdataset-light=Responses to light changes in A. thaliana
event-specialdataset-spl_factors=Experimental manipulation of various regulators in A. thaliana
gene-specialdataset-neural_diversity=Multiple neuronal populations in D. melanogaster
Datasets: SRP153159 (optic lobe), SRP160109, SRP012051, SRP078048, SRP132957, SRP108664
gene-specialdataset-neurogenesis=Differentiation time course in the neuronal and glial lineages
Datasets: SRP121281 (progenitors at different developmental stages), SRP061327 (differentiated neurons and glia)
gene-specialdataset-neuronal_act=Neuronal activity time courses in fly brains upon KCl depolarization or optogenetic activation
Datasets: SRP077742 (optogenetics), SRP077739 (KCl)
gene-specialdataset-regulation_rbp_brain=Knock down of various splicing factors in fly brains
Datasets: SRP186005 (main dataset), SRP171625 (upf1), SRP072850 (psi), Torres-Mendez et al, submitted
gene-specialdataset-regulation_rbp_sl2=Experimental manipulation of various splicing factors in fly SL2 cells
Datasets: SRP001537 (modENCODE, main dataset), SRP056965 (u2af), SRP149913 (human SRRM4 OE)
gene-specialdataset-scheiffele=Ribosome-engaged transcriptomes of neuronal types
Datasets from Furlanis et al (PMID: 31451803): GSE133291
Note: Expression values were only calculated using vast-tools mm10 libraries (Mm2)
gene-associatedevents=Events belonging to the gene of interest. You can click on each of the table columns to sort the events by this column or on each of the events to access to detailed information.
Each colored line corresponds to one of the AS events in this gene (see "Associated Events", above). Each dot corresponds to the average PSI value of the event across several related samples (as in the Gene Expression section, above). To see the individual values for an event, click on the event ID
Events can be toggled on and off with the buttons "Select All Events" and "Select No Events", or by clicking on the boxes next to the event names.
Samples can be toggled on and off with the buttons "Select All Tissues" and "Select No Tissues", or by clicking on the sample groups below.
gene-homology=Homologous genes listed in Ensembl