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NCHlab / RTPEA

Retroelement Protein Expression Atlas
http://www.rtpea.com
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major protvista revamp #50

Open Nazrath10R opened 5 years ago

Nazrath10R commented 5 years ago

MAJOR new feature!

inspired by expression atlas for gene expression https://www.ebi.ac.uk/gxa/experiments/E-GEOD-26284/Results

create a small table that can be used to filter main consequence criteria for protvista

Naz will come up with an exact table layout after a working template has been implemented

the idea is to use dropdown boxes for tissues, radio buttons for ORF1p and ORF2p, tickboxes to show only high confident results etc.

ProtVista should load up after these have been selected

This will make it easier for a user to explore all the mutations

Nazrath10R commented 4 years ago

add PTM info - Naz to generate

NCHlab commented 4 years ago

{ "_id" : ObjectId("5dcc34de95d15c0ba817c693"), "PXD" : "ORF1P", "sequence" : "MGKKQNRKTGNSKTQSASPPPKERSSSPATEQSWMENDFDELREEGFRRSNYSELREDIQTKGKEVENFEKNLEECITRITNTEKCLKELMELKTKARELREECRSLRSRCDQLEERVSAMEDEMNEMKREGKFREKRIKRNEQSLQEIWDYVKRPNLRLIGVPESDVENGTKLENTLQDIIQENFPNLARQANVQIQEIQRTPQRYSSRRATPRHIIVRFTKVEMKEKMLRAAREKGRVTLKGKPIRLTADLSAETLQARREWGPIFNILKEKNFQPRISYPAKLSFISEGEIKYFIDKQMLRDFVTTRPALKELLKEALNMERNNRYQPLQNHAKM", "features" : [ { "type" : "act_site", "category" : "PTM", "tissue" : "breast", "begin" : 157, "description" : "test" }, { "type" : "act_site", "category" : "PTM", "tissue" : "breast", "begin" : 130, "description" : "test", "color" : "#f00" }, { "type" : "mod_res", "category" : "PTM", "tissue" : "breast", "begin" : 111, "description" : "wesd", "color" : "#000" }, { "type" : "DOMAIN", "category" : "DOMAINS_AND_SITES", "begin" : 253, "end" : 317, "description" : "C-terminal domain (CTD)" }, { "type" : "COILED", "category" : "DOMAINS_AND_SITES", "begin" : 45, "end" : 753, "description" : "Coiled coil domain mediates homotrimerization" }, { "type" : "VARIANT", "category" : "VARIATION", "description" : "HOT_4", "alternativeSequence" : "M", "begin" : "14", "end" : "14", "Family" : "HOT", "wildType" : "T", "consequence" : "breast", "consequence2" : "breast diseased", "consequence3" : "breast cancer", "polyphenPrediction" : "unknown", "polyphenScore" : 0, "siftPrediction" : "not tolerated, low value", "siftScore" : 0.15 },

NCHlab commented 4 years ago

PTM should contain tissue as an extra field