一种面向功能基因挖掘的动物多组学数据集

doi:10.19788/j.issn.2096-6369.100039

摘要/Abstract

摘要：

单一的组学数据难以全面揭示基因调控性状的复杂分子机制，整合不同类型和层次的生物组学数据对于理解生物体内复杂的分子网络具有重要的意义。本数据集提供了包含21个动物物种的61191个个体水平组学数据（WGS、RNA-Seq、ChIP-Seq和ATAC-Seq）和基因组注释信息，有效数据规模为2.8 TB。此外，本数据集还收录了基于深度学习算法得到的基因与表型实体识别数据。总的来说，该多组学数据集可用于农业重要性状的基因发掘和功能验证，能够为跨物种比较研究提供有价值的资源，也可更好地服务于动物经济性状关键基因识别模型构建以及算法研究。

数据摘要：

项目	描述
数据库（集）名称	一种面向功能基因挖掘的动物多组学数据集
所属学科	农学
研究主题	动物多组学数据集
数据时间范围	2000-2022年
数据类型与技术格式	.txt，.vcf，ped，map，bed，bim，fam
数据库（集）组成	数据集由五部分组成： 21个物种403216个基因的功能注释信息。 21个物种10835个个体的基因组变异数据，共包含877.59M变异。 21个物种44638个个体的基因表达矩阵数据。 21个物种5718个个体的表观信号矩阵数据，包含H3K27ac等124个marker。 21个物种2794237篇文献的基因、表型预标注数据。
数据量	2.8 TB
主要数据指标	基因功能注释、基因组变异信息、基因表达矩阵、表观信号矩阵、基因和表型预标注数据
数据可用性	https://cstr.cn/17058.11.sciencedb.agriculture.00024 https://doi.org/10.57760/sciencedb.agriculture.00024
经费支持	国家自然科学基金面上项目（32272841）；湖北国际科技合作项目（2022EHB055）

关键词: 多组学数据, 跨物种, 功能基因挖掘, 个体水平, 深度学习

Abstract:

Single-omics data alone is insufficient to comprehensively reveal the complex molecular mechanisms of gene regulation traits. Integrating different types and levels of biological omics data is of great significance for understanding the complex molecular networks within organisms. This dataset provides individual-level omics data (WGS, RNA-Seq, ChIP-Seq, and ATAC-Seq) and genome annotation information for 61,191 individuals from 21 animal species, with an effective data size of 2.8 TB. Additionally, this dataset includes gene and phenotype entity recognition data obtained through deep learning algorithms. Overall, this multi-omics dataset can be used for gene discovery and functional validation of agriculturally important traits, offering valuable resources for cross-species comparative studies. It also supports the construction of models for identifying key genes associated with economic traits in animals and facilitates algorithm research.

Data summary:

Item	Description
Dataset name	A Multi-Omics Dataset for Functional Gene Mining in Animals
Specific subject area	Agronomy
Research topic	Animal Multi-Omics Dataset
Time range	2000-2022
Data types and technical formats	.txt,.vcf, ped, map, bed, bim, fam
Dataset stucture	The dataset consists of five parts: Functional annotation information for 403,216 genes across 21 species. Genomic variation data for 10,835 individuals from 21 species, encompassing 877.59 million variations. Gene expression matrix data for 44,638 individuals from 21 species. Epigenetic signal matrix data for 5,718 individuals from 21 species, including 124 markers such as H3K27ac. The pre-labeled gene and phenotype data of 2794237 articles from 21 species.
Volume of dataset	2.8 TB
Key index in dataset	Gene functional annotation, genomic variation information, gene expression matrices, epigenetic signal matrices, gene and phenotypic pre-labeled data
Data accessibility	https://cstr.cn/17058.11.sciencedb.agriculture.00024 https://doi.org/10.57760/sciencedb.agriculture.00024 PUBLIC, CC BY-NC 4.0
Financial support	National Natural Science Foundation of China General Program (32272841); Hubei International Science and technology cooperation project (2022EHB055)

Key words: multi-omics data, cross-species, functional gene mining, individual level, deep learning

刘洪, 窦婧文, 王越, 廖勇, 刘小磊, 李新云, 赵书红, 付玉华. 一种面向功能基因挖掘的动物多组学数据集[J]. 农业大数据学报, 2025, 7(1): 96-106.

LIU Hong, DOU JingWen, WANG Yue, LIAO Yong, LIU XiaoLei, LI XinYun, ZHAO ShuHong, FU YuHua. A Multi-Omics Dataset for Functional Gene Mining in Animals[J]. Journal of Agricultural Big Data, 2025, 7(1): 96-106.

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物种	WGS	RNA	ChIP	ATAC	文献	组织	变异数（M）	碱基（TB）
Ailuropoda melanoleuca	58	133	0	0	2534	21	12.42	2.49
Anas platyrhynchos	1162	819	0	4	1408	30	44.27	18.38
Anser cygnoides	283	134	0	8	130	10	22.67	5.31
Balaenoptera musculus	1	2	0	0	629	3	6.17	0.13
Bos taurus	983	3995	216	158	291242	85	52.71	76.89
Camelus dromedarius	38	28	0	0	4197	10	10.17	1.7
Canis lupus familiaris	2116	2581	95	9	225467	126	47.57	134.04
Capra hircus	961	1355	0	5	1015	60	65.66	64.24
Equus asinus	189	61	8	0	53280	14	16	2.66
Equus caballus	538	2192	135	18	58089	95	35.71	42.64
Felis catus	311	180	0	0	92331	46	79.49	25.91
Gallus gallus	1108	4098	533	161	108208	111	37.16	53.26
Loxodonta africana	11	23	0	0	567	6	14.3	1.55
Macaca mulatta	696	7318	222	149	37963	127	107.18	129.66
Mus musculus	80	8983	2499	544	1644283	132	16.47	77.99
Oryctolagus cuniculus	49	1424	67	12	234595	45	106.05	12.33
Ovis aries	877	2682	90	8	8715	75	71.91	61.83
Panthera leo	41	2	0	0	5439	6	13.93	1.14
Panthera tigris	8	2	0	0	914	4	12.11	0.99
Sus scrofa	1311	8626	647	130	23092	218	95.2	132.92
Ursus thibetanus	14	0	0	0	139	1	10.44	0.4
ALL	10853	44638	4512	1206	2794237	256	877.6	846.46

物种	基因数	Swiss-Prot	KEGG	GO	Pfam	InterPro	KOG
Ailuropoda melanoleuca	24463	20295	15775	14847	18915	19596	18246
Anas platyrhynchos	18491	15871	12099	11811	15235	15779	14433
Anser cygnoides	19449	14734	11593	11032	14010	14524	13405
Balaenoptera musculus	22592	19038	14746	13724	17599	18245	16980
Bos taurus	27608	21224	16772	15410	19968	20612	19096
Camelus dromedarius	22445	18878	14801	13762	17604	18195	16862
Canis lupus familiaris	30952	19760	15442	14255	18483	19104	17837
Capra hircus	27272	20923	16621	15502	19620	20291	18872
Equus asinus	22929	19425	15053	14114	18043	18685	17453
Equus caballus	30372	20367	16038	14696	19292	19851	18334
Felis catus	29551	19019	15183	13989	17858	18452	17053
Gallus gallus	24357	15920	12269	11799	15252	15842	14465
Loxodonta africana	23246	19793	15739	14685	18491	19081	17938
Macaca mulatta	35433	21036	15102	13646	18250	18802	19161
Mus musculus	55417	21373	17288	15889	20606	21156	18964
Oryctolagus cuniculus	29588	19997	14793	14064	18576	19250	18082
Ovis aries	26479	19959	15808	14758	18724	19338	17955
Panthera leo	22744	19054	15091	13893	17831	18438	17056
Panthera tigris	22120	17231	13084	12454	15867	16491	15450
Sus scrofa	31909	20041	15562	14436	18871	19453	18202
Ursus thibetanus	23211	19560	15553	14234	18380	18942	17525
All	570628	403498	314412	293000	377475	390127	363369

物种	个体	品种	分组	平均深度	变异数（M）
Ailuropoda melanoleuca	58	2	4	7.04	12.42
Anas platyrhynchos	1162	27	4	6.86	44.27
Anser cygnoides	283	8	5	9.55	22.67
Balaenoptera musculus	1	1	1	40.72	6.17
Bos taurus	983	36	10	17.01	52.71
Camelus dromedarius	38	11	11	15.27	10.17
Canis lupus familiaris	2116	301	11	20.63	47.57
Capra hircus	961	108	6	15.32	65.66
Equus asinus	189	5	5	3.62	16
Equus caballus	538	61	7	18.21	35.71
Felis catus	311	54	9	26.84	79.49
Gallus gallus	1108	148	10	14.92	37.16
Loxodonta africana	11	3	3	19.82	14.3
Macaca mulatta	696	9	6	26.86	107.18
Mus musculus	80	15	10	29.99	16.47
Oryctolagus cuniculus	49	14	4	11.29	106.05
Ovis aries	877	149	6	13.35	71.91
Panthera leo	41	4	3	9.28	13.93
Panthera tigris	8	2	2	33.18	12.11
Sus scrofa	1311	65	9	14.89	95.2
Ursus thibetanus	14	2	2	8.50	10.44
ALL	10835	1025	128	17.30	877.60

物种	脂肪	骨	血管	胚胎	免疫	肌肉	神经	器官	其他
Ailuropoda melanoleuca	0	0	80	0	5	2	2	39	5
Anas platyrhynchos	42	6	129	36	55	134	12	357	48
Anser cygnoides	12	0	0	0	3	6	0	104	9
Balaenoptera musculus	1	0	0	0	0	0	0	0	1
Bos taurus	94	43	689	222	464	365	74	1626	418
Camelus dromedarius	0	0	12	0	0	0	10	0	6
Canis lupus familiaris	36	29	261	14	145	78	139	940	939
Capra hircus	17	6	136	12	63	140	42	641	298
Equus asinus	0	0	12	3	1	6	2	32	5
Equus caballus	1	82	751	196	23	234	75	377	453
Felis catus	9	1	5	4	38	4	26	50	43
Gallus gallus	167	22	306	453	650	269	346	1272	613
Loxodonta africana	0	0	19	1	0	0	0	0	3
Macaca mulatta	143	16	3569	529	422	94	1553	791	201
Mus musculus	636	286	706	443	705	653	2450	1836	1268
Oryctolagus cuniculus	61	0	354	138	12	19	151	446	243
Ovis aries	242	0	319	57	83	366	126	1057	432
Panthera leo	0	0	0	0	0	0	0	2	0
Panthera tigris	0	0	1	0	0	0	0	1	0
Sus scrofa	395	39	1251	719	415	1663	573	3051	520
Ursus thibetanus	0	0	0	0	0	0	0	0	0