WBConfCall 2019.10.03-Agenda and Minutes
- Faye has responded to this user:
- Does this still require a follow-up?
Standard Strain names for Transgenome project
Daniela: Raymond suggested to obtain standard strain names for Transgenome project. Paul Davis will compile a list of offending names, and Deniela will communicate them to the Transgenome project.
- Paul D: are they generating the file names?
- Karan: some are renames/concatenation
- Paul Davis: will generate a list of offending strain names and might require discussion with them
22G (?) RNA
Chris: A help desk ticket asking about 22G (?) RNA, question for the group if/how we are handling this, since they were brought up by Julie at the IWM? These RNAs are transcribed from other messenger transcripts. Don't always uniquely map to genome because they are small. Questions:
- which class of object do we consider them to be
- how to model the parentage
- Raymond: Biologically do they generate knockdown effect?
- Chris: yes, in conjunction with other RNAs from the same sequence
- Lincoln: are they reagents?
- Chris: no, they are endogenous
- Paul S: how is same protein produced from multiple transcript handled?
- Kevin: one protein with all the genes linking to them
- Paul S: we need something else, since in this case the sequence isn't exactly the same
- Chris: concerned if we model them as transcript, it would imply they are transcribed directly from DNA
- Lincoln: is this comparable to how splice leaders?
- Paul D: they are genomically derived and attached to genes
- Paul S: the effect of each of the RNA might be undetectable, the combined effect is based on contributions of many loci.
- Chris: we might need a set of RNAs that's collectively derived from these loci
- Paul S: would be useful to know what kind of other scenario
- Lincoln: such as histones, requires mapping to an open ended set, outside of central parentage model
- Paul D: proposed to Julie about treating them like non-coding RNA derived from genomic sequence. This is the simplest way to treat them, but she is against it. They agreed to send us data. Will use this as an opportunity to broaden the scenarios we handle.
- Paul S: we should learn about the use cases and the data they have about it.
- Kevin: we are already handling microRNA, pre-miRNA, pri-miRNA, by mapping to the genes
- Paul D: these RNAs don't have identical sequence, with fuzzy edges, additional complication from mRNA editing.
- Chris: could we have them parented by locus, as a distinct class of transcript?
- Kevin: we can treat them as transcript: attached to the genome and use a different Method to describe them. This allows genome browser to display them, potentially on different tracks or colour code them. They needs to be attached to the genome to show in the genome browser.
- Raymond: does this take care of multi-parentage?
- Paul D: hopefully Julie's data anchors the RNAs to particular transcript, hence to the gene
- Chris: will contact Julie about obtaining her data
- Raymond: is it true that transcript cannot handle multi-parentage?
- Kevin: they would be treated as multiple transcripts, one for each gene
- Raymond: How to know where in the genome this affects?
- Chris: will discuss with Julie and others in the field whether it's worthwhile to have a prediction pipeline, similar to RNAi, to predict the effect on regulation of expression
- Sibyl: how will the website and genome browser be affect by this?
- Chris: probably add them to the overall transcripts list, might have different sections and tracks
- Paul: This can be handled at meta-data level, like other non-coding RNA. This likely doesn't require changes to the website. Initially, we aim to get the data in. In the future, we might consider adding additional columns and other data to display
Todd: NAR paper was accepted, minor revisions submitted, and will be published in a few weeks.