常用数据库 - HGNC

常见的 Gene ID 官网

这个标准比较多，有Ensembl ID，HGNC ID，Entrez ID（NCBI），Refseq ID

数据库	链接地址
Ensembl	https://asia.ensembl.org/index.html
HGNC	https://www.genenames.org/
Entrez	https://www.ncbi.nlm.nih.gov/gene/672 【案例】
Refseq	https://www.ncbi.nlm.nih.gov/nuccore/NM_031991.4【所有物种，很少用】

https://www.genenames.org/about/guidelines/

基因命名映射关系建立

由于面向临床生产过程中的基因名称，参考相关指南和质评规范，统一以HGNC命名为统一参考。
HGNC官网是随时都在进行更新的，没有固定的更新周期。
但是本身每个月会保留一次版本镜像快照。所以日常更新建议使用快照版本，以便后续数据的相关回溯。

快照记录索引链接

快照记录的包含所有基因的名称映射（包含假基因，非编码RNA等）可以根据需要进行筛选以提高后续效率。

关注基因的基因ID获取

针对关注的转录本及基因信息，获取现有注释体系下，基因ID和注释基因名称之间的对应关系

# 基于目前版本提报的基因和转录本信息，通过注释配置文件，获取基因ID和基因名称的对应关系总列表文件
grep -w -f /jdfstj1/B2C_COM_P1/PipeAdmin/04.Pipeline/aio.v2.Dev.liubo/chip_info/PanCancer_IDT_v1/PanCancer.v1.Trans.list  /jdfstj1/B2C_COM_P1/PipeAdmin/04.Pipeline/aio.v2.Dev.liubo/database/Ref104/ncbi_anno_rel104.dbref > ncbi_ref104.geneSymble2ID

#基于NCBI生成的ncbi_ref104.geneSymble2ID 文件中，其中第9、10两列为后续用于映射的列
第9列： ncbi注释的基因symble
第10列：entrez_id

HGNC数据整理准备

# 首先下载HGNC官方对应名称信息，根据需要调整相应的文件日期

wget http://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/archive/monthly/tsv/hgnc_complete_set_2021-06-01.txt

其中重要的列为第1,2,9,19,24列。
# 提取其中的映射相关的重要信息示例如下：
awk -F '\t' '{print $1"\t"$19"\t"$2"\t"$9"\t"$24}' /jdfstj1/B2C_COM_P1/Research_and_Development/Database/HGNC/hgnc_complete_set_2021-06-01.txt  |head 
head hgnc_complete_set_2021-06-01.fit.tsv
hgnc_id	entrez_id	symbol	alias_symbol	refseq_accession
HGNC:5	1	A1BG		NM_130786
HGNC:37133	503538	A1BG-AS1	FLJ23569	NR_015380
HGNC:24086	29974	A1CF	"ACF|ASP|ACF64|ACF65|APOBEC1CF"	NM_014576

#其中比较主要的信息分别如下
#第1洌hgnc_id：HGNC的基因ID
#entrez_id：NCBI的基因ID
#symbol：基因统一命名
#alias_symbol：基因历史别名
#

所在列数	字段头	官方含义	字段信息
1	hgnc_id	ID used to designate a gene family or group the gene has been assigned to.	HGNC对应的基因ID
2	symbol	Status of the symbol report, which can be either “Approved” or “Entry Withdrawn”.	基因命名
3	name	miRBase ID
4	locus_group	Same as “location” but single digit chromosomes are prefixed with a 0 enabling them to be sorted in correct numerical order (e.g. 02q34).
5	locus_type	A group name for a set of related locus types as defined by the HGNC (e.g. non-coding RNA).
6	status	snoRNABase ID
7	location	lncRNA Database ID
8	location_sortable	Cytogenetic location of the gene (e.g. 2q34).
9	alias_symbol	Other names used to refer to this gene as seen in the “SYNONYMS” field in the gene symbol report.	基因曾用名
10	alias_name	The HGNC ID that the Alliance of Genome Resources (AGR) have linked to their record of the gene. Use the HGNC ID to link to the AGR.
11	prev_symbol	Gene names previously approved by the HGNC for this gene. Equates to the “PREVIOUS SYMBOLS & NAMES” field within the gene symbol report.
12	prev_name	Orphanet ID
13	gene_group	The HGNC ID used within the GenCC database as the unique identifier of their gene reports within the GenCC database.
14	gene_group_id	Name given to a gene family or group the gene has been assigned to. Equates to the “GENE FAMILY” field within the gene symbol report.
15	date_approved_reserved	Symbol used within the Catalogue of somatic mutations in cancer for the gene.
16	date_symbol_changed	The date the gene name was last changed.
17	date_name_changed	Date the entry was last modified.
18	date_modified	The date the entry was first approved.
19	entrez_id	Ensembl gene ID. Found within the “GENE RESOURCES” section of the gene symbol report.
20	ensembl_gene_id	International Nucleotide Sequence Database Collaboration (GenBank, ENA and DDBJ) accession number(s). Found within the “NUCLEOTIDE SEQUENCES” section of the gene symbol report.
21	vega_id	UniProt protein accession. Found within the “PROTEIN RESOURCES” section of the gene symbol report.
22	ucsc_id	The HGNC approved gene symbol. Equates to the “APPROVED SYMBOL” field within the gene symbol report.
23	ena	The date the gene symbol was last changed.
24	refseq_accession	Pubmed and Europe Pubmed Central PMID(s).	HGNC提供的转录本ID
25	ccds_id	Symbol used to link to the SLC tables database at bioparadigms.org for the gene
26	uniprot_ids	UCSC gene ID. Found within the “GENE RESOURCES” section of the gene symbol report.
27	pubmed_id	Pseudogene.org
28	mgd_id	ID used to link to the MEROPS peptidase database
29	rgd_id	RefSeq nucleotide accession(s). Found within the “NUCLEOTIDE SEQUENCES” section of the gene symbol report.
30	lsdb	The locus type as defined by the HGNC (e.g. RNA, transfer).
31	cosmic	Symbol used within the Human Cell Differentiation Molecule database for the gene
32	omim_id	HGNC approved name for the gene. Equates to the “APPROVED NAME” field within the gene symbol report.
33	mirbase	Mouse genome informatics database ID. Found within the “HOMOLOGS” section of the gene symbol report.
34	homeodb	HGNC ID. A unique ID created by the HGNC for every approved symbol.
35	snornabase	Rat genome database gene ID. Found within the “HOMOLOGS” section of the gene symbol report.
36	bioparadigms_slc	Other symbols used to refer to this gene as seen in the “SYNONYMS” field in the symbol report.
37	orphanet	Online Mendelian Inheritance in Man (OMIM) ID
38	pseudogene.org	Symbols previously approved by the HGNC for this gene. Equates to the “PREVIOUS SYMBOLS & NAMES” field within the gene symbol report.
39	horde_id	Homeobox Database ID
40	merops	NCBI and Ensembl transcript IDs/acessions including the version number for one high-quality representative transcript per protein-coding gene that is well-supported by experimental data and represents the biology of the gene. The IDs are delimited by	.
41	imgt	Symbol used within HORDE for the gene
42	iuphar	ID used to link to the Human Intermediate Filament Database
43	kznf_gene_catalog	The objectId used to link to the IUPHAR/BPS Guide to PHARMACOLOGY database. To link to IUPHAR/BPS Guide to PHARMACOLOGY database only use the number (only use 1 from the result objectId:1)
44	mamit-trnadb	The name of the Locus Specific Mutation Database and URL for the gene separated by a	character
45	cd	Consensus CDS ID. Found within the “NUCLEOTIDE SEQUENCES” section of the gene symbol report.
46	lncrnadb	The gene symbol used to link to LNCipedia - a comprehensive compendium of human long non-coding RNAs.
47	enzyme_id	Entrez gene ID. Found within the “GENE RESOURCES” section of the gene symbol report.	ncbi的基因symbol
48	intermediate_filament_db	Symbol used within international ImMunoGeneTics information system
49	rna_central_ids	Rat genome database gene ID. Found within the “HOMOLOGS” section of the gene symbol report.
50	lncipedia	ID used to link to the Human KZNF Gene Catalog
51	gtrnadb	ID used to designate a gene family or group the gene has been assigned to.
52	agr	The HGNC ID that the Alliance of Genome Resources (AGR) have linked to their record of the gene. Use the HGNC ID to link to the AGR.
53	mane_select	ID to link to the Mamit-tRNA database
54	gencc	ENZYME EC accession number

信息来源

进行HGNC映射文件更新

# 生成HGNC基因名称转换文件
 perl /jdfstj1/B2C_COM_P1/Research_and_Development/Database/HGNC/creat.change_genelist.pl 
 -hgnc hgnc_complete_set_2021-06-01.txt 
 -ncbi ncbi_ref104.geneSymble2ID 
 -o change_gene.list.tmp

结果文件示例如下（change_gene.list.tmp）：

entrez_id	HGNC_symble	NCBI_symble	Tag
1	A1BG	A1BG	Match
29974	A1CF	A1CF	Match
2	A2M	A2M	Match
144568	A2ML1	A2ML1	Match
53947	A4GALT	A4GALT	Match
51146	A4GNT	A4GNT	Match
8086	AAAS	AAAS	Match
65985	AACS	AACS	Match
13	AADAC	AADAC	Match

前三列为基因对应的信息，第四列tag为示例信息，提示是否能匹配上：

如果标记为match，则表明HGNC和NCBI的对应基因ID可以匹配。

如果标记为MisMatch，则表明两个数据对应的基因ID无法进行匹配，

更新后，在目录下readme中记录数据库的更新日期和操作人员。

1 2	eg： # liubo4 @ 20210616