Difference between revisions of "Event.ini"

Latest revision as of 19:52, 22 June 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.

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.

• 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

• 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

• 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). <p>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.

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.

<p>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&equals;0, VLOW&equals;1, LOW&equals;2, OK/SOK&equals;3. For information on other quality scores associated with each sample's PSI in the plot, please visit the FAQ section.

Biotic stress conditions in A. thaliana. Sample information is available in the Supplemental Table 1 of Martín et al.

Responses to light changes in A. thaliana. Sample information is available in the Supplemental Table 1 of Martín et al.

Experimental manipulation of various regulators in A. thaliana. Sample information is available in the Supplemental Table 1 of Martín et al.