Difference between revisions of "Event.ini"

Latest revision as of 17:23, 21 December 2020

event-coords=Genomic coordinates of the AS event (1-based).

event-length=Length of the alternatively spliced sequence.
In ALTD/ALTA events, the most internal splice site within each event (indicated as 1/N) has a length of 0 nt, by definition.

event-splice=Nucleotide sequences at the intron-exon boundaries. 5' splice site sequences include three exonic and six intronic positions, whereas 3' splice site sequences include 20 intronic and 3 exonic positions. Splice-site scores were calculated using MaxEntScan for the human models (more information in FAQs).

event-exon=Nucleotide sequences of the C1, A and C2 exons. Click on the arrow to reveal the sequences.

event-vastdbfeatures=Click on the arrow to reveal more information. event-internal=Internal vast-tools ID for the event. More information in FAQs.

event-complexity=Detailed classification of the AS event (including exon skipping, intron retention and alternative splice sites) based on its associated transcriptomic complexity. It has implication for PCR validations. See FAQs for more information.

event-mappability=Estimate of the percent of possible closest exon-exon junctions that can be mapped uniquely using RNA-seq (ideally 100%=100%=100%, for exclusion junctions, upstream inclusion junctions, and downstream inclusion junctions, respectively). For a cassette exon to be included in vast-tools their reference exon-exon junctions (those formed by the neighboring exons [C1,C2] and the alternative [A] exon) must be uniquely mappable.

event-impact=

Effect of the exon inclusion on the open reading frame of the transcript. Ref or No Ref indicates whether the exon is included in the reference mRNA of the gene. More information in the FAQ.

event-disorder=Fraction of residues predicted as disordered by disopred2 in the C1, A and C2 exons.

event-prosite=The field follows the scheme: Dom_ID=Dom_Name=Type_Overlap(%Dom_Overlap=%Exon_Overlap), where:

Dom_ID is the domain ID in either PROSITE or PFAM databases. For PROSITE, domains with high frequency motifs (i.e. those starting with P0*) are excluded.
Dom_Name is the domain name as provided by PROSITE or PFAM databases.
Type_Overlap describes the way in whcih an exon can overlap a protein domain. The possible values are:
- FE (Full Exon): The whole exonic sequence fully overlaps with a domain
- WD (Whole Domain): The whole domain is fully encoded within an exon
- PU (Partial Upstream): The upstream (5') of the exon overlaps the domain
- PD (Partial Downstream): The downstream (3') of the exon overlaps the domain
%Dom_Overlap is the percentage of the domain encoded by the exon
%Exon_Overlap is the percentage of the exon that overlaps the domain

event-pfam=The field follows the scheme: Dom_ID=Dom_Name=Type_Overlap(%Dom_Overlap=%Exon_Overlap), where:

Dom_ID is the domain ID in either PROSITE or PFAM databases. For PROSITE, domains with high frequency motifs (i.e. those starting with P0*) are excluded.
Dom_Name is the domain name as provided by PROSITE or PFAM databases.
Type_Overlap describes the way in whcih an exon can overlap a protein domain. The possible values are:
- FE (Full Exon): The whole exonic sequence fully overlaps with a domain
- WD (Whole Domain): The whole domain is fully encoded within an exon
- PU (Partial Upstream): The upstream (5') of the exon overlaps the domain
- PD (Partial Downstream): The downstream (3') of the exon overlaps the domain
%Dom_Overlap is the percentage of the domain encoded by the exon
%Exon_Overlap is the percentage of the exon that overlaps the domain

event-degree=

The degree is defined as the number of interactions of a protein. It defines how connected, and hence important a protein is in the network. These degree values were obtained for each protein using BioGrid data.
The betweenness is defined as the number of pairwise shortest paths between all pairs of nodes in a PPI network that go through a protein, and therefore reflects the extent of centrality or hubness of the protein. Hub proteins have much higher betweenness, as they connect multiple parts within a PPI network. In contrast, peripheral proteins that sit on the borders of a PPI network have lower betweenness.

Data source: Ellis et al., Mol Cell (2012). For non-human and non-mouse data, the degree and betweenness corresponds to that of the human ortholog.

event-associated=AS events in the same assembly, with coordinates overlapping with this event.

event-conservation=Orthologous events in other species, obtained by synteny conservation using LiftOver.

event-primers=Designed in C1 and C2 exons. The band sizes correspond to the size of the two predicted bands for the specific AS event, and are optimized to reduce the impact of PCR amplification biases (more information in FAQs). Please note that if there are associated events (particularly Alt3 or Alt5) and/or the event is composed by multiple AS exons, the resulting PCR product may be much more complex and thus RT-PCR validations may not be informative. It is suggested you always take a look at the genome browser to know what it is being amplified.

event-browser=

Genomic context of the event. Click on the image to view the event 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.

event-tissuevalue=Each of the dots in this plot represents the average PSI of the AS event 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.

Read coverage stringency is increasingly strict from 0 to 3 (PSIs for '0' are NOT reliable). This refers to the first coverage score in the vast-tools output (see the FAQ section for details). N=0, VLOW=1, LOW=2, OK/SOK=3. For information on other quality scores associated with each sample's PSI in the plot, please visit the FAQ section. event-specialpsi-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.

event-specialpsi-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

event-specialpsi-tcga=

Data from the The Cancer Genome Atlas (TCGA) project

Note: PSI values were only calculated using vast-tools hg38 libraries (Hs2)

event-specialpsi-gtex=

Data from the Genotype-Tissue Expresssion project

Note: PSI values were only calculated using vast-tools hg19 libraries (Hsa)

event-specialpsi-pancreas=

Data from RNA-Seq experiments performed in pancreatic cell types isolated by FACS.

Sample source: Arda et al., Cell Metab. (2016). PMID: 27133132

event-specialpsi-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.

event-specialpsi-myoblast=

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.

event-specialpsi-spermatogenesis=

Data from diverse cell types from testis, isolated from C57BL/6J mice.

Sample source: Soumillon et al., Cell Rep. (2013). PMID: 23791531.

event-specialpsi-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.

event-specialpsi-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

More than 70% of the data is from Yan et al.

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

More than 70% of the data is from Deng et al. and from Biase et al.

Note: PSI values were only calculated using vast-tools hg19, mm9 or bosTau6 libraries (Hsa, Mmu, Bta)

event-specialpsi-vicky=

Three independent cell lines were grown in three cell culture conditions:

ESCs were grown in 2i Lif or Serum Lif supplemented media.
EpiSCs were grown in Fgf and Activin supplemented media.

event-specialpsi-abiotic=

Abiotic stress conditions in A. thaliana

event-specialpsi-biotic=

Biotic stress conditions in A. thaliana

event-specialpsi-light=

Responses to light changes in A. thaliana

event-specialpsi-spl_factors=

Experimental manipulation of various regulators in A. thaliana

event-specialpsi-neural_diversity=

Multiple neuronal populations in D. melanogaster

Datasets: SRP153159 (optic lobe), SRP160109, SRP012051, SRP078048, SRP132957, SRP108664

event-specialpsi-neurogenesis=

Differentiation time course in the neuronal and glial lineages

Datasets: SRP121281 (progenitors at different developmental stages), SRP061327 (differentiated neurons and glia)

event-specialpsi-neuronal_act=

Neuronal activity time courses in fly brains upon KCl depolarization or optogenetic activation

Datasets: SRP077742 (optogenetics), SRP077739 (KCl)

event-specialpsi-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

event-specialpsi-regulation_rbp_sl2=

Experimental manipulation of various splicing factors in fly SL2 cells

Datasets: SRP001537 (modENCODE, main dataset), SRP056965 (u2af), SRP149913 (human SRRM4 OE)

event-specialpsi-scheiffele=

Ribosome-engaged transcriptomes of neuronal types

Datasets from Furlanis et al (PMID: 31451803): GSE133291

Note: PSI values were only calculated using vast-tools mm10 libraries (Mm2)

@@ Line 38: / Line 38: @@
 event-specialpsi-neudif=<p>Samples selected from a differentiation experiment from murine ESCs to glutamatergic cortical neurons.</p><p>DIV: Days In Vitro.</p><p><b>Sample source:</b> Hubbard <i>et al.</i>, F1000 (2013). PMID: 24358889</p>
-event-specialpsi-tcga=<p>Data from the The Cancer Genome Atlas (TCGA) project</p>
+event-specialpsi-tcga=<p>Data from the The Cancer Genome Atlas (TCGA) project</p><p>Note: PSI values were only calculated using vast-tools hg38 libraries (Hs2)</p>
-event-specialpsi-gtex=<p>Data from the Genotype-Tissue Expresssion project</p>
+event-specialpsi-gtex=<p>Data from the Genotype-Tissue Expresssion project</p><p>Note: PSI values were only calculated using vast-tools hg19 libraries (Hsa)</p>
 event-specialpsi-pancreas=<p>Data from RNA-Seq experiments performed in pancreatic cell types isolated by FACS.</p><p><b>Sample source:</b> Arda <i>et al.</i>, Cell Metab. (2016). PMID: 27133132</p>
@@ Line 52: / Line 52: @@
 event-specialpsi-reprogr_carstens=<p>Time-course data from a reprogramming process from mouse embryonic fibroblasts to iPSCs</p><p><b>Sample source:</b> Cieply <i>et al.</i>, Cell Rep. (2016). PMID: 27050523.</p>
-event-specialpsi-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>
+event-specialpsi-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: PSI values were only calculated using vast-tools hg19, mm9 or bosTau6 libraries (Hsa, Mmu, Bta)</p>
 event-specialpsi-vicky=<p>Three independent cell lines were grown in three cell culture conditions:</p><ul><li>ESCs were grown in 2i Lif or Serum Lif supplemented media.</li><li>EpiSCs were grown in Fgf and Activin supplemented media.</li></ul>
@@ Line 73: / Line 73: @@
 event-specialpsi-regulation_rbp_sl2=<p>Experimental manipulation of various splicing factors in fly SL2 cells</p><p>Datasets: SRP001537 (modENCODE, main dataset), SRP056965 (u2af), SRP149913 (human SRRM4 OE)</p>
+event-specialpsi-scheiffele=<p>Ribosome-engaged transcriptomes of neuronal types</p><p>Datasets from Furlanis et al (PMID: 31451803): GSE133291</p><p>Note: PSI values were only calculated using vast-tools mm10 libraries (Mm2)</p>

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Difference between revisions of "Event.ini"

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Latest revision as of 17:23, 21 December 2020