20 October 2015 PAINT Conference Call

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PAINT conference call minutes, October 20th, 2015

Participants: Psacale, Karen, Donghui, Moni, Paul T., Huaiyu, Suzi


Agenda and Minutes

PAINT svn update

Suzi did an update of all svn families to reflect the changes in PANTHER v.10.0. Pascale and Marc found some issues saving the annotations. Huaiyu also noticed that the annotations can't be loaded to the paint tool for those new families. The problem is probably more complicated, but only affects a very small number of families. The discussion will be taken offline. Pascale and Huaiyu will first find out the exact problems. They will then discuss with Suzi for a possible solution.

PAINT progress

Here is the current PAINT curation status: https://docs.google.com/spreadsheets/d/1eVhVeNq9FEEo-mH9TAa6CaoerUtgVIVrOaA6yodBeOM/edit#gid=859368352b

Family presentation of PTHR12097 (Karen)

PTHR12097 = SPLICING FACTOR 3B, SUBUNIT 1-RELATED

This family contains the spliceosomal protein HSH155 (S. cerevisiae), aka SF3B1 (vertebrates).

In vertebrates, this protein has been characterized as being a member of the SF3b complex, which is part of the U12 snRNP (Will et al. 2004, PMID:15146077; Turunen et al. 2013, PMID:23074130) as well as being part of the U2 snRNP (Turunen et al. 2013, PMID:23074130).

It is believed that the last eukaryotic common ancestor (LECA) possessed both the major (U2-type) and minor (U12-type) spliceosomes and that the current diversity of organisms across multiple taxonomic groups which lack the minor U12-type has been generated by multiple loss events of the minor U12-type spliceosome (Lopez et al. 2008, PMID:18390578; Bartschat & Samuelsson 2010, PMID:20149226; Turunen et al. 2013, PMID:23074130; Irimia and Roy 2014, PMID:24890509).

Comment on annotation propagations:

Based on the current views on the phylogeny of the major U2-type and minor U12-type spliceosomes, I have propagated both the U2-type and the U12-type terms to the root node Eukaryota_PTN000250426 (ignoring the duplication node PTN000949721 that is the actual root of the tree).

Then, I have blocked propagation of the U12-type terms in multiple places based on the phylogenetic analysis in Bartschat & Samuelsson 2010 (PMID:20149226) and Turunen et al. 2013 (PMID:23074130) and the computational work of Lopez et al. 2008 (PMID:18390578) to determine the phylogenetic distribution of the major and minor spliceosomes. - In some places, I have felt confident that I could place the block at the node representing an entire taxonomic group, e.g. Ascomycetes, Chromodorea (a group within Nemotoda), Alveolata (includes Plasmodium & Tetrahymena), Excavarus (includes Trichomonas, Trypanosoma, and Leishmania). - In other places, such as the Basidiomycetes where there are members of this taxonomic group thought to still contain the minor U12-type, I have placed the block on the individual species currently represented in the tree if they are thought to have lost it. - I have also blocked the U12-type terms in several individual species that appear to be the sole representative of their group included in the Panther Tree, e.g. Chlamydomonas reinhardtii (green algae), Entamoeba histolytica, and Thalassiosira pseudonana.


Comment on tree:

There is a duplication node (PTN000949721) at the top of this tree. However, one of the two child nodes, Eukaryota_PTN001739850, contains only two sequences neither of which looks good in the MSA. Therefore, I have pruned this node and considered the other child node Eukaryota_PTN000250426 as the effective root node for all propagations made for this tree.

PTHR12097-tree.jpg