因為在Review中砲聲隆隆, 眾老師認為我的自吹自擂缺乏數據基礎,所以我最近在補幾個圖來証明,我的BFO方法比較靈敏及廣泛性。抓對斯殺的對象是大家最常用的功能註解軟體，NIH 的DAVID ,用同樣的資料作分析,比較 Gene ontology 的分析結果。因為DAVID 沒有提供 GO access id, 所以我就直接用 GO term 作key 把兩組結果對上，可是很奇怪的有很多筆對不上，許多DAVID抓出的GOTERM在我的database 裡找不到，讓我冷汗直流，難道是我的GO 資料來源出了問題嗎？於是我把有爭議GOTERM 貼上Geneontology 的官網去查了一下! 竟然沒有! 看來不是我的問題，難道是DAVID用來分析的GO term 有問題嗎?還是沒有跟上 Geneontology DB update 的速度，所以剛剛去DAVID的官網去貼了問題，過兩天就知道了。官方說是因為沒更新，所以用的是舊版本。（官方答覆見下文）
這是DAVID的分析結果，你可以試著去QuickGO 查一下"cellular physiological process"
就會發現這個 GO term 在資料庫裡不存在，在我的結果中，這個比例還蠻高的，大概有近五成，大家在使用時，還是要小心一點。
##ReadMore##hi,
I found many Go-term used in DAVID function annotation tools were not found in GO database(QuickGO), such as "cellular catabolism", "aromatic compound metabolism", "cellular physiological process"....
Does DAVID use special ontology system or old version?
Lucas
DAVID does use the standard Gene Ontology terminology. This difference is most likely due to a database update disconnect. Many terms have been slightly changed lately, such as "cellular catabolism" which is now "cellular catabolic process". This should not affect your analysis as the biological meaning has not changed. In future releases we will include and link to the GO id in order to direct the user to the most updated term. We are currently working on the newest update which will be available in February.
DAVID Team
照他們的說法，在二月份釋出的新版，而且會有GO id，那就可以用GO accession number 作key接回GO db, 解決大部份的問題。
這是DAVID的分析結果，你可以試著去QuickGO 查一下"cellular physiological process"
就會發現這個 GO term 在資料庫裡不存在，在我的結果中，這個比例還蠻高的，大概有近五成，大家在使用時，還是要小心一點。
##ReadMore##hi,
I found many Go-term used in DAVID function annotation tools were not found in GO database(QuickGO), such as "cellular catabolism", "aromatic compound metabolism", "cellular physiological process"....
Does DAVID use special ontology system or old version?
Lucas
DAVID does use the standard Gene Ontology terminology. This difference is most likely due to a database update disconnect. Many terms have been slightly changed lately, such as "cellular catabolism" which is now "cellular catabolic process". This should not affect your analysis as the biological meaning has not changed. In future releases we will include and link to the GO id in order to direct the user to the most updated term. We are currently working on the newest update which will be available in February.
DAVID Team
照他們的說法，在二月份釋出的新版，而且會有GO id，那就可以用GO accession number 作key接回GO db, 解決大部份的問題。
lucast您好:
回覆刪除偶然搜尋到您的這篇不錯的文章，啟發我ㄧ些新的靈感，謝謝!
另外可否請問一下，我現在想ㄧ次取得所有NCBI上gene ID對應的GO ID，有任何方法可以快速取得嗎?
謝啦!
Jeremy Liu
Lucas您好:
回覆刪除很感謝您精闢的解說, 讓我有了新的思考方向,我想詢問一下, common ID是否可使用 gene ID而非
uniprot ID, 或者有轉換系統.
我需要processed table , 麻煩您了.
真的非常非常感謝您
轉換 ID 可以使用 Gene Name Service.
回覆刪除http://bioagent.iis.sinica.edu.tw/GeneAlias/
板主回覆：
回覆刪除hi,
Dumping NCBI? its GO id is incorrect. I suggest U to get the official edition. GO annotation files can be downloaded from official websit. see http://www.geneontology.org/GO.current.annotations.shtml. But it is not your answer. this file still need some process for the Gene-to-GO mapping.
1. U need convert Ur gene id to common id used in this annotation tables (Uniprot id, IPI id ....)
2. GO term have a hierarchive struture. the parent GO term will included all genes of its child GO term. You need to process the annoation table to fit this relationship. This required some skill for database handling.
I am not sure if anybody can do it convienently, but If U need help. I can pass the processed table to U.
Just left a message here to me. :-)
板主回覆：
回覆刪除有空會去看看，謝謝你的資訊。