Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:
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Story Points:1
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Epic Link:
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Sprint:Spring 4 2023 Feb 21, Spring 5 2023 Mar 6
Description
[~aloraine] agreed to review an article that describes a new iteration of "CHESS" annotations for human genome. Review is due 19 Feb 2023. Article info:
- Web site with annotations: http://ccb.jhu.edu/chess/
- Article draft on BioRxiv: https://www.biorxiv.org/content/10.1101/2022.12.21.521274v1
Preliminary scan of the article shows that these new annotations could be very useful for understanding human transcriptome, so this task also includes deploying the annotations into IGB Quickload site.
Proposed strategy for reviewing this work:
- Try to deploy the annotations onto an IGB Quickload site
- If that goes well, use IGB to make interesting and/or artistic screen shots of genomic scenes showing the CHESS data
- Submit a review that describes observations made
Possible benefits of proposed strategy:
- Helps bioinformatics scientists by pointing out a useful dataset or helping to improve a work in progress
- Try out a possible new use case for IGB (dataset review tool?)
- Provide access to possibly very useful gene models that can benefit our field, and others
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Activity
I'm pretty happy with how the gene models look in IGB. I am going to move the work needed to set up CHESS for CHM13 into a new ticket linked with this one.
Added chess 3.0 BED-detail file to svn repository, updated to revision 170.
See: https://svn.bioviz.org/viewvc/genomes/quickload/H_sapiens_Dec_2013/
Updated igbquickload at RENCI:
[aloraine@lorainelab-quickload quickload]$ svn up Updating '.': A H_sapiens_Dec_2013/chess3.0.GRCh38.p12.bed.gz U H_sapiens_Dec_2013/annots.xml A H_sapiens_Dec_2013/chess3.0.GRCh38.p12.bed.gz.tbi Updated to revision 170.
See: http://lorainelab-quickload.scidas.org/quickload/H_sapiens_Dec_2013/
Committed new version of GFF3 / BED parsing / writing code.
Repository: https://bitbucket.org/lorainelab/genomesource/src/master/
Commit: https://bitbucket.org/lorainelab/genomesource/commits/92eb0500f7cefd7b86ecbefa3d763a4d1e5f5c34
Made BED14 file as follows:
local aloraine$ CHESSgff3ToBedDetail.py -g chess3.0.gff.gz -b chess3.0.GRCh38.p12.bed local aloraine$ wc -l chess3.0.GRCh38.p12.bed 168475 chess3.0.GRCh38.p12.bed local aloraine$ sort -k1,1 -k2,2n chess3.0.GRCh38.p12.bed | bgzip > chess3.0.GRCh38.p12.bed.gz local aloraine$ tabix -s 1 -b 2 -e 3 chess3.0.GRCh38.p12.bed.gz [W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option? [W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option? [W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option? [W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option? [W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option? [W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option? [W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option? [W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option? [W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option? [W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option? [W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option? [W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option? [W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option? [W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option? local aloraine$ tabix -0 -s 1 -b 2 -e 3 -f chess3.0.GRCh38.p12.bed.gz
In CHESS, RAP1GAP on chromosome 1 has lots of splice variants. The NCBI Gene record (abstract is below) mentions expression and mis-regulation in diverse cancer types. Also, looks like the UCSC reference annotations IGB shows probably need to be updated, as IGB does not show nearly as many gene models as visible and mentioned in the Entrez Gene record.
This gene encodes a type of GTPase-activating-protein (GAP) that down-regulates the activity of the ras-related RAP1 protein. RAP1 acts as a molecular switch by cycling between an inactive GDP-bound form and an active GTP-bound form. The product of this gene, RAP1GAP, promotes the hydrolysis of bound GTP and hence returns RAP1 to the inactive state whereas other proteins, guanine nucleotide exchange factors (GEFs), act as RAP1 activators by facilitating the conversion of RAP1 from the GDP- to the GTP-bound form. In general, ras subfamily proteins, such as RAP1, play key roles in receptor-linked signaling pathways that control cell growth and differentiation. RAP1 plays a role in diverse processes such as cell proliferation, adhesion, differentiation, and embryogenesis. Alternative splicing results in multiple transcript variants encoding distinct proteins. [provided by RefSeq, Aug 2011]
Contacted authors to find out location of reference assembly used to generate the annotations. Answer is:
Hi Ann and Steven,
We used CHM13 2.0 as our target sequence, which you can find here: https://github.com/marbl/CHM13.
All chromosomes except chromosome Y in CHM13 v1.1 are the same as CHM13 v2.0. ("Changes from v1.1 is the addition of a finished chromosome Y from the GIAB HG002/NA24385 sample, sequenced both by GIAB and HPRC.")Best regards,
Kuan-Hao
Wrote and submitted review. I liked the article and recommended to "accept". I also mentioned my confusion about the GFF producer and extra feature fields, and suggested adding more documentation to the Web site.