Frontiers in Protein and Peptide Sciences

Volume: 1

Prediction of Golgi-Resident Protein Types Using Computational Method

Author(s): Hao Lin, Hui Ding and Wei Chen

Pp: 174-193 (20)

DOI: 10.2174/9781608058624114010011

* (Excluding Mailing and Handling)

Abstract

The Golgi apparatus plays a key role in sorting, modifying, packaging and distributing proteins. Thus, correct identification of the type of a Golgi-resident protein will provide in-depth insights into its function involved in various biological processes. In this article, we will briefly outline the prediction of protein subGolgi localizations using bioinformatics method. We introduced the available databases for training predicted models. Moreover, three kinds of methods were presented for discriminating between cis-Golgi and trans-Golgi proteins.


Keywords: Cis-Golgi proteins, trans-Golgi proteins, benchmark dataset, information parameter, feature selection, increment of diversity, analysis of variance, binomial distribution, support vector machine, cross-validation.

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      • 16. app/Models/Subject.php:255
      • 17. app/Http/Controllers/ChapterController.php:1435
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      • 13. vendor/laravel/framework/src/Illuminate/Routing/Controller.php:54
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      • 11. app/Models/ContentAccess.php:647
      • 12. app/Http/Controllers/ChapterController.php:1478
      • 13. vendor/laravel/framework/src/Illuminate/Routing/Controller.php:54
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      • 13. app/Models/UserAccess/UserAccess.php:1266
      • 14. app/Http/Controllers/ChapterController.php:1518
      • 15. vendor/laravel/framework/src/Illuminate/Routing/Controller.php:54
      • 16. vendor/laravel/framework/src/Illuminate/Routing/ControllerDispatcher.php:43
      • 17. vendor/laravel/framework/src/Illuminate/Routing/Route.php:260
    • (select j.user_access_id,j.volume_id,j.user_id,j.from_ip,j.to_ip,j.type,j.track,"Trial Access" as access_base_text, CASE j.type WHEN 111 THEN true ELSE false END as terms_popup, "S" as content_download_type, null as restricted_user_access_key, null as restricted_user_access_type, CASE j.track WHEN 0 THEN false ELSE true END as tracksAccessByVolume,"chapter" as access_level, j.chapter_id from `user_access_chapter_trail` as `j` inner join `user_access_info` as `info` on `j`.`user_access_id` = `info`.`user_access_id` where ((j.from_ip <= 316498996 and j.to_ip >=316498996 )) and ((j.from_date <= 1740347306 and j.to_date >= 1740347306 and j.perpetual= 0) or (j.from_date is null and j.to_date is null and j.perpetual= 1)) and j.chapter_id = 6552) union (select j.user_access_id,j.volume_id,j.user_id,j.from_ip,j.to_ip,j.type,j.track,"Subscribed" as access_base_text, false as terms_popup, "S" as content_download_type, null as restricted_user_access_key, null as restricted_user_access_type, CASE j.track WHEN 0 THEN false ELSE true END as tracksAccessByVolume,"chapter" as access_level, j.chapter_id from `user_access_chapter_corporate` as `j` inner join `user_access_info` as `info` on `j`.`user_access_id` = `info`.`user_access_id` where ((j.from_ip <= 316498996 and j.to_ip >=316498996 )) and ((j.from_date <= 1740347306 and j.to_date >= 1740347306 and j.perpetual= 0) or (j.from_date is null and j.to_date is null and j.perpetual= 1)) and j.chapter_id = 6552) union (select j.user_access_id,j.volume_id,j.user_id,j.from_ip,j.to_ip,j.type,j.track,"Token Based Access" as access_base_text, false as terms_popup, "R" as content_download_type, j.uc_id as restricted_user_access_key, "v" as restricted_user_access_type, CASE j.track WHEN 0 THEN false ELSE true END as tracksAccessByVolume,"chapter" as access_level, j.chapter_id from `user_access_chapter_token` as `j` inner join `user_access_info` as `info` on `j`.`user_access_id` = `info`.`user_access_id` where ((j.from_ip <= 316498996 and j.to_ip >=316498996 )) and ((j.from_date <= 1740347306 and j.to_date >= 1740347306 and j.perpetual= 0) or (j.from_date is null and j.to_date is null and j.perpetual= 1)) and j.chapter_id = 6552)
      990μsalphaeurekaselec_live_10_06_2022UserAccess.php#1266
      Backtrace
      • 13. app/Models/UserAccess/UserAccess.php:1266
      • 14. app/Http/Controllers/ChapterController.php:1549
      • 15. vendor/laravel/framework/src/Illuminate/Routing/Controller.php:54
      • 16. vendor/laravel/framework/src/Illuminate/Routing/ControllerDispatcher.php:43
      • 17. vendor/laravel/framework/src/Illuminate/Routing/Route.php:260
    • select b.banner_link, b.banner_name, b.banner_script, b.banner_remarks, b.banner_file_name, b.banner_placement, bd.content_type, bd.content_id from `tbl_banner` as `b` inner join `tbl_banner_detail` as `bd` on `bd`.`banner_id` = `b`.`banner_id` inner join `users` as `u` on `u`.`id` = `b`.`updated_by` where `b`.`banner_ebook` = 1 and `bd`.`content_type` = 'B' and `bd`.`content_id` = 1519 and `b`.`banner_from_date` <= 1740347306 and `b`.`banner_to_date` >= 1740347306 and `b`.`banner_status` = 'A' order by `b`.`banner_id` desc
      1.56msalphaeurekaselec_live_10_06_2022Banner.php#95
      Bindings
      • 0: 1
      • 1: B
      • 2: 1519
      • 3: 1740347306
      • 4: 1740347306
      • 5: A
      Backtrace
      • 13. app/Models/Banner.php:95
      • 14. app/Http/helpers.php:404
      • 17. vendor/laravel/framework/src/Illuminate/Filesystem/Filesystem.php:124
      • 18. vendor/laravel/framework/src/Illuminate/View/Engines/PhpEngine.php:58
      • 19. vendor/laravel/framework/src/Illuminate/View/Engines/CompilerEngine.php:73
    • select count(*) as aggregate from `uc_cart_products` where cart_id='7c0d43eaabedb60a23f83c7c7b2aca88'
      300μsalphaeurekaselec_live_10_06_2022Cart.php#271
      Backtrace
      • 15. app/Models/Cart.php:271
      • 16. view::layouts._header:260
      • 18. vendor/laravel/framework/src/Illuminate/Filesystem/Filesystem.php:124
      • 19. vendor/laravel/framework/src/Illuminate/View/Engines/PhpEngine.php:58
      • 20. vendor/laravel/framework/src/Illuminate/View/Engines/CompilerEngine.php:73
    App\Models\Keywords
    10Keywords.php#?
    App\Models\Chapter
    1Chapter.php#?
    App\Models\Ebook
    1Ebook.php#?
        _token
        n94YLqvANEeRuRByvPV1TeHfvetOB4RhUsGIPDoR
        uc_cart_id
        7c0d43eaabedb60a23f83c7c7b2aca88
        _previous
        array:1 [ "url" => "https://alpha.eurekaselect.com/chapter/6552" ]
        _flash
        array:2 [ "old" => [] "new" => [] ]
        PHPDEBUGBAR_STACK_DATA
        []
        path_info
        /chapter/6552
        status_code
        200
        
        status_text
        OK
        format
        html
        content_type
        text/html; charset=UTF-8
        request_query
        []
        
        request_request
        []
        
        request_headers
        0 of 0
        array:16 [ "x-https" => array:1 [ 0 => "1" ] "host" => array:1 [ 0 => "alpha.eurekaselect.com" ] "priority" => array:1 [ 0 => "u=0, i" ] "accept-encoding" => array:1 [ 0 => "gzip, deflate, br, zstd" ] "sec-fetch-dest" => array:1 [ 0 => "document" ] "sec-fetch-user" => array:1 [ 0 => "?1" ] "sec-fetch-mode" => array:1 [ 0 => "navigate" ] "sec-fetch-site" => array:1 [ 0 => "none" ] "accept" => array:1 [ 0 => "text/html,application/xhtml+xml,application/xml;q=0.9,image/avif,image/webp,image/apng,*/*;q=0.8,application/signed-exchange;v=b3;q=0.7" ] "user-agent" => array:1 [ 0 => "Mozilla/5.0 AppleWebKit/537.36 (KHTML, like Gecko; compatible; ClaudeBot/1.0; +claudebot@anthropic.com)" ] "upgrade-insecure-requests" => array:1 [ 0 => "1" ] "sec-ch-ua-platform" => array:1 [ 0 => ""Windows"" ] "sec-ch-ua-mobile" => array:1 [ 0 => "?0" ] "sec-ch-ua" => array:1 [ 0 => ""HeadlessChrome";v="129", "Not=A?Brand";v="8", "Chromium";v="129"" ] "cache-control" => array:1 [ 0 => "no-cache" ] "pragma" => array:1 [ 0 => "no-cache" ] ]
        request_cookies
        []
        
        response_headers
        0 of 0
        array:5 [ "content-type" => array:1 [ 0 => "text/html; charset=UTF-8" ] "cache-control" => array:1 [ 0 => "no-cache, private" ] "date" => array:1 [ 0 => "Sun, 23 Feb 2025 21:48:26 GMT" ] "set-cookie" => array:2 [ 0 => "XSRF-TOKEN=eyJpdiI6IlFuVmFmb1lqZmoxeVg1cXVQMVpxQlE9PSIsInZhbHVlIjoic3VqbDViaDBpTnhha1FUYXB6NGc4bXYrYVZLRWpKTHRtTkhmNmFLd3BqY0NSUmRpUkFad1dVazJNa0JmR1dCZEluNlBYdFBIMWhoS3B3OGFGT09IZDgwSXZJV2QwL09EQzFrQVZoRUVFODNlbmI4b3hCK21RQURvaldsTnd0eE0iLCJtYWMiOiJiODgyZjA5YWJkODE2ZGFjZTM0OTcyNjBkNDdkMDYwNmQzNTJhOGQ2ZmJjYmRlMzU1Yzc4YjBmM2E0M2E4NDk0IiwidGFnIjoiIn0%3D; expires=Wed, 26 Feb 2025 09:48:26 GMT; Max-Age=216000; path=/; secure; samesite=laxXSRF-TOKEN=eyJpdiI6IlFuVmFmb1lqZmoxeVg1cXVQMVpxQlE9PSIsInZhbHVlIjoic3VqbDViaDBpTnhha1FUYXB6NGc4bXYrYVZLRWpKTHRtTkhmNmFLd3BqY0NSUmRpUkFad1dVazJNa0JmR1dCZEluNlBYd" 1 => "alphaeurekaselectnet_session=eyJpdiI6Iml2WjI5aXo5YUVHTG9ibnBaemg2eUE9PSIsInZhbHVlIjoiZE1NdS9aQzlyWkoxbkFuTUNYVFQ2SllOZG5QRmZKV3NWREo5YUcwMWZRd0w5cEliSXA5WVI5M2hUYWdCT09QbnBVQTFuazRMOGpxbVl0VGExdjI0YlgwRmdodzg5dTNZK1ZLOTkvdU9GNmovaWo3d21QTnVNM1ZSclo1citaSTMiLCJtYWMiOiJhNDE1NGZhMTg5Nzg5MTgwMTIzYzcwOWNmMTU3ZjQ1Yjk5ZGE0ZmViYTVhNjAyY2U0ODg1ZmQ2ZmFmN2MzYzI1IiwidGFnIjoiIn0%3D; path=/; secure; httponly; samesite=laxalphaeurekaselectnet_session=eyJpdiI6Iml2WjI5aXo5YUVHTG9ibnBaemg2eUE9PSIsInZhbHVlIjoiZE1NdS9aQzlyWkoxbkFuTUNYVFQ2SllOZG5QRmZKV3NWREo5YUcwMWZRd0w5cEliSXA5WVI5M2h" ] "Set-Cookie" => array:2 [ 0 => "XSRF-TOKEN=eyJpdiI6IlFuVmFmb1lqZmoxeVg1cXVQMVpxQlE9PSIsInZhbHVlIjoic3VqbDViaDBpTnhha1FUYXB6NGc4bXYrYVZLRWpKTHRtTkhmNmFLd3BqY0NSUmRpUkFad1dVazJNa0JmR1dCZEluNlBYdFBIMWhoS3B3OGFGT09IZDgwSXZJV2QwL09EQzFrQVZoRUVFODNlbmI4b3hCK21RQURvaldsTnd0eE0iLCJtYWMiOiJiODgyZjA5YWJkODE2ZGFjZTM0OTcyNjBkNDdkMDYwNmQzNTJhOGQ2ZmJjYmRlMzU1Yzc4YjBmM2E0M2E4NDk0IiwidGFnIjoiIn0%3D; expires=Wed, 26-Feb-2025 09:48:26 GMT; path=/; secureXSRF-TOKEN=eyJpdiI6IlFuVmFmb1lqZmoxeVg1cXVQMVpxQlE9PSIsInZhbHVlIjoic3VqbDViaDBpTnhha1FUYXB6NGc4bXYrYVZLRWpKTHRtTkhmNmFLd3BqY0NSUmRpUkFad1dVazJNa0JmR1dCZEluNlBYd" 1 => "alphaeurekaselectnet_session=eyJpdiI6Iml2WjI5aXo5YUVHTG9ibnBaemg2eUE9PSIsInZhbHVlIjoiZE1NdS9aQzlyWkoxbkFuTUNYVFQ2SllOZG5QRmZKV3NWREo5YUcwMWZRd0w5cEliSXA5WVI5M2hUYWdCT09QbnBVQTFuazRMOGpxbVl0VGExdjI0YlgwRmdodzg5dTNZK1ZLOTkvdU9GNmovaWo3d21QTnVNM1ZSclo1citaSTMiLCJtYWMiOiJhNDE1NGZhMTg5Nzg5MTgwMTIzYzcwOWNmMTU3ZjQ1Yjk5ZGE0ZmViYTVhNjAyY2U0ODg1ZmQ2ZmFmN2MzYzI1IiwidGFnIjoiIn0%3D; path=/; secure; httponlyalphaeurekaselectnet_session=eyJpdiI6Iml2WjI5aXo5YUVHTG9ibnBaemg2eUE9PSIsInZhbHVlIjoiZE1NdS9aQzlyWkoxbkFuTUNYVFQ2SllOZG5QRmZKV3NWREo5YUcwMWZRd0w5cEliSXA5WVI5M2h" ] ]
        session_attributes
        0 of 0
        array:5 [ "_token" => "n94YLqvANEeRuRByvPV1TeHfvetOB4RhUsGIPDoR" "uc_cart_id" => "7c0d43eaabedb60a23f83c7c7b2aca88" "_previous" => array:1 [ "url" => "https://alpha.eurekaselect.com/chapter/6552" ] "_flash" => array:2 [ "old" => [] "new" => [] ] "PHPDEBUGBAR_STACK_DATA" => [] ]
        ClearShow all
        Date ↕MethodURLData
        #12025-02-23 21:48:26GET/chapter/65521121912