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How to Curate a Gene Page (view source)

Revision as of 16:56, 5 December 2018

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''TO DO: create a tutorial video based on this script''

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The basic logic for CCGA pages is that there is basic Gene and Protein molecular biology-type information on the “Gene Pages”, and that there is Disease and clinical-type information type on the “Disease pages”. However, the dividing line between ~~these types of~~ information is sometime hard to determine. These guidelines will help you determine what information goes where. Please note that you should plan to spend between 4-8 hours in curating the information onto a single gene page, more if you are unfamiliar with the gene.

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The basic logic for CCGA pages is that there is basic Gene and Protein (and mutation) molecular biology-type information on the “Gene Pages”, and that there is Disease and clinical-type information type on the “Disease pages”. The CCGA is especially interested in curation the fusion genes/mutations that arise in disease, esp. in the hematological cancers. However, the dividing line between "Gene/Protein/Mutation" information and "Disease" information is sometime hard to determine. These guidelines will help you determine what information goes where. Please note that you should plan to spend between 4-8 hours in curating the information onto a single gene page, more if you are unfamiliar with the gene.

==Editor:==

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==Wiki Pages:==

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The CCGA web site is here : http://www.ccga.io/index.php/Main_Page ~~The CCGA is based on wiki pages~~. The functionality of the wiki pages are described in brief, at MediaWiki, see here: https://www.mediawiki.org/wiki/MediaWiki.

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The CCGA web site is based on wiki pages and can be accessed here : http://www.ccga.io/index.php/Main_Page. please ask your editor for write premissions.

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There are also short videos available on youtube that describe MediaWiki functionality here: https://www.youtube.com/watch?v=F8irbbwNo2E&list=PLAagofQWV6pf0xFyUw7gJg2yYYB-nCS4l

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The functionality of the wiki pages are described in brief, at MediaWiki, see here: https://www.mediawiki.org/wiki/MediaWiki.

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There are also short videos available on youtube that describe MediaWiki functionality here: https://www.youtube.com/watch?v=F8irbbwNo2E&list=PLAagofQWV6pf0xFyUw7gJg2yYYB-nCS4l. Others are available, by searching youtube for "MediaWiki tutorial".

==Gene Pages:==

You will be asked to choose from a number gene pages that you would like to curate. See list here: http://www.ccga.io/index.php/List_of_Gene_Pages

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A “Gene specific Template” has been produced which provides you with ~~Very~~ nice Media Wiki Template to fill in with information you have curated. It is shown here. http://www.ccga.io/index.php/Gene-Specific_Template

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A “Gene specific Template” has been produced which provides you with very nice Media Wiki Template to fill in with information you have curated. It is shown here. http://www.ccga.io/index.php/Gene-Specific_Template.

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Note that the Template already has the markup language you will need for headers, links, and other syntax to be used in the Gene Paes. Please do not change the syntax of the template, so users of the CCGA pages will want to see the same format from page to page.

==Gene curation using the “Gene specific Template” MediaWiki Template in CCGA==

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===Curating the Template with Gene Information===

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~~====Describing the Template information.====~~

The template provides an easy "fill in the blanks" WikiMedia page which already has formatted markups (for headers) and has examples for you to follow. The Template is described briefly, below.

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The sections of the Template are for ease of reading for the USER: HOWEVER, as a curator, you will want to curate and load information in the WIKI in a non-linear fashion. This is the suggested workflow:

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===== 1. PRIMARY AUTHORS section. =====

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==== 1. PRIMARY AUTHORS section. ====

By adding your name to the PRIMARY AUTHORS section you can make sure that no-one else is curating this gene now, and so you will get credit for curating this information by your peers.

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===== 2. EXTERNAL LINKS Section. =====

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==== 2. EXTERNAL LINKS Section. ====

To familiarize yourself with the latest information on the Gene you are curating, “Your Gene of Interest” (designated YGI throughout), please start with one of the last sections of the Template, the EXTERNAL LINKS Section. The listed resources will provide exhaustive (but not necessarily recent) molecular information about YGI, its mutations and its place in disease and cancer and treatment. The resources suggested as EXTERNAL LINKS as of Dec 2018 are as follows:

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<big>'''''PLEASE NOTE: DO NOT PLAGIARIZE. You can borrow phrases here or there without attribution. Yo can even use a sentence here and there if you attribute the quote directly ( eg: "From NCBI"). However, you CANNOT cut and paste whole paragraphs from other resources into the CCGA pages.'''''</big>

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===== 3. SYNONYMS Section =====

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==== 3. SYNONYMS Section ====

As you read though the EXTERNAL LINKS resources, you will find many of them have lists of synonyms, esp. NCBI Gene and GeneCards. Please italicize the alternative gene names (synonyms).

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==== 4. GENOMIC LOCATION Section. ====

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<big>Appendix</big>

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This information is most easily obtained from GeneCards, in the GeneCards section "Genomics" and subsection "Genomic Locations for YFG" and subsection "Genomic View for YFG"and sub-subsection "Cytogenetic band"

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==== 5. Gene Overview ====

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This section should describe in 1 paragraph (approx 5-7 sentences):

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# the molecular function of the gene/protein

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# its normal cellular role

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# its role in diseases, esp. cancer diseases in the CCGA.

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# interesting or frequent mutations and their effects on specific cancers.

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# role in drug resistance, if any.

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A few examples are shown below.

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"The protein encoded by ''RUNX1'' can bind the protein encoded by ''CBFB'' to form "Core Binding Factor", a hetero-dimeric transcription factor which regulates a number of genes responsible for hematopoiesis and osteogenesis [2]. Runx1 protein can bind to DNA as a monomer through the Runt domain within the Runx1 protein. ''RUNX1'' is the most frequent target for chromosomal translocation in leukemia [1]. Alterations of ''RUNX1'' are typically loss-of-function or decreased function, and are considered "secondary driver mutations" (disease progression) in sporadic leukemias [2]; however, germline ''RUNX1'' mutations contribute to a lifetime risk for myeloid malignancy of about 44% [2]. ''RUNX1'' mutations (loss-of-function or decreased function) have been associated with decreased P53 activity and increased DNA repair defects and increased inflammation [2]. ''RUNX1'' mutations are associated with gene mutations in ''ASXL1'', ''MLLPTD'', and ''IDH1''/''IDH2'', and are mutually exclusive with ''NPM1'' mutations [3]. Non-complex ''RUNX1'' mutations were found to be associated with resistance to chemotherapy, decreased disease free survival (DFS), event free survival (EFS) and overall survival (OS) [3]."

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The ''ABL1'' gene encodes a non-receptor tyrosine kinase that is ubiquitously expressed and involved in a large number of cellular processes (see '''[https://www.ncbi.nlm.nih.gov/gene/25#reference-sequences "NCBI Gene]'''). By far the most prevalent ''ABL1'' alteration associated with cancer are the fusions of the ''ABL1'' gene with a number of partners, but especially with the ''BCR'' gene in CML [1,2] and to a lesser extent in B-ALL and T-ALL. The head to tail arrangement of the BCR-ABL1 fusion gene results in an activated tyrosine kinase activity [6]. It appears that the N-terminal domain of ''BCR'' can cause oligomerization of the BCR-ABL1 protein product, thus activating the ''ABL1'' tyrosine kinase domain of the fusion protein [6,10,11]. The ''ABL1'' and ''ABL2'' genes encode tyrosine kinases which share overlapping physiological roles, and ''ABL2'' somatic or amplification mutations are more common than similar mutations in ''ABL1'' [6].

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See the '''[http://www.ccga.io/index.php/BCR "BCR gene"]''' for additional details of the BCR-ABL1 gene fusion.

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For molecular information and some disease and mutation information, this section is most informed by reading the EXTERNAL LINKS resources of:

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# UniProt

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# GeneCards

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# NCBI Gene

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# CIViC

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# Cancer Index

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# My Cancer Genome

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# Pfam

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For mutational information, this section is most informed by

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# Atlas of Genetics and Cytogenetics in Oncology and Haematology

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# COSMIC

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# LOVD(3)

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# TICdb

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# St. Jude ProteinPaint

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# Precision Medicine Knowledgebase (Weill Cornell)

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# OncoKB

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For Disease information, the best resources are:

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# OMIM

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# WHO Classification of Tumours of Haematopoietic and Lymphoid Tissues (download from http://publications.iarc.fr/_publications/media/download/1511/700ac655d7f248cf1044efd985275086ed4f341f.pdf)

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# Pubmed (search for YFG, esp. in o=context of "cancer" or specific cancers.

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Note that in this section, you mauch

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== <big>Appendix</big> ==

==Resources:==

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#YouTube videos for how to use MediaWiki: https://www.youtube.com/watch?v=F8irbbwNo2E&list=PLAagofQWV6pf0xFyUw7gJg2yYYB-nCS4l

#The CCGA web site is here : http://www.ccga.io/index.php/Main_Page

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#~~Download~~ “WHO Classification of Tumours of Haematopoietic and Lymphoid Tissues.pdf” from http://publications.iarc.fr/_publications/media/download/1511/700ac655d7f248cf1044efd985275086ed4f341f.pdf

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#“WHO Classification of Tumours of Haematopoietic and Lymphoid Tissues.pdf” Download from http://publications.iarc.fr/_publications/media/download/1511/700ac655d7f248cf1044efd985275086ed4f341f.pdf

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~~#Search for your YGI to see which cancer is associated with mutations in YGI. Read and collect annotations for YGI.~~

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#

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<big>FAQ (Frequently Asked Questions)</big>

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== <big>FAQ (Frequently Asked Questions)</big> ==

Brian.Davis

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