Evidence map›Paper›PMID 40827640›Full record

ArticleNucleic acids research2026

The ChickenGTEx portal: a pan-tissue catalogue of regulatory variants shaping transcriptomic and phenotypic diversity.

Yali Hou, Dong Zou, Qin Chu, Bujie Zhan, Ruizhen Wang, Dailu Guan, Wannian Wang, Xiao Feng, Xin Li, Xiaoning Zhu and 10 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nucleic acids research, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.

0numbers the graph read from it
0cells of the map it votes in
7citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

7 citing papers in PubMed.

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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

20 authors.

Yali HouState Key Laboratory of Animal Biotech Breeding; National Germplasm Center of Domestic Animal Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.ORCID 0000-0002-7421-2431
Dong ZouNational Genomics Data Center, China National Center for Bioinformation, Beijing 100101, China.ORCID 0000-0002-7169-4965
Qin ChuInstitute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.ORCID 0000-0001-7669-1440
Bujie ZhanDepartment of Basic Medical Sciences, Medical College, Longdong University, Qingyang 745000, China.
Ruizhen WangAcademy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou 450046, China.
Dailu GuanDepartment of Animal Science, University of California, Davis, CA 95616, United States.
Wannian WangDepartment of Animal Science, Shanxi Agricultural University, Taigu 030801, China.
Xiao FengCollege of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
Xin LiState Key Laboratory of Animal Biotech Breeding; National Germplasm Center of Domestic Animal Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
Xiaoning ZhuCollege of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
Zhonghao BaiState Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193, China.ORCID 0009-0005-8697-1813
Yahui GaoState Key Laboratory of Livestock and Poultry Breeding, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
Hongwei YinShenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China.
Tianyi XuNational Genomics Data Center, China National Center for Bioinformation, Beijing 100101, China.ORCID 0000-0003-4197-8163
Zhixiang YuanNational Genomics Data Center, China National Center for Bioinformation, Beijing 100101, China.
Xiaoxiang HuState Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193, China.ORCID 0000-0001-7045-0283
Ning YangCollege of Animal Science and Technology, China Agricultural University, Beijing 100193, China.ORCID 0000-0001-5772-3320
Huaijun ZhouDepartment of Animal Science, University of California, Davis, CA 95616, United States.
Lingzhao FangCenter for Quantitative Genetics and Genomics (QGG), Aarhus University, Aarhus 8000, Denmark.
Zhang ZhangNational Genomics Data Center, China National Center for Bioinformation, Beijing 100101, China.ORCID 0000-0001-6603-5060

Funding

Agricultural Science and Technology Innovation Program ASTIP-IAS-04-2Central Public-interest Scientific Institution Basal Research Y2025PT02Chinese Academy of Agricultural SciencesChinese Academy of Sciences 153F11KYSB20160008National Key Research and Development Program of China 2024YFF1000100National Natural Science Foundation of China 32030021National Natural Science Foundation of China T2425005Open Biodiversity and Health Big Data Programme of IUBS
6 · The paper itself

Abstract

A systematic dissection of the functional impacts of non-coding variations across diverse tissues and cell types is essential for deciphering the molecular architecture underlying complex traits. Given the significance of chickens as both a key livestock species and a fundamental model organism, the development of an integrative genomics resource is imperative. Leveraging SNP-to-gene-to-trait linking strategies-including molecular quantitative trait loci (molQTL), regulatory elements, and context- or environment-dependent regulatory heterogeneity-we developed the ChickenGTEx portal (http://chicken.farmgtex.org), which provides a comprehensive catalogue of regulatory effects on transcriptomic and phenotypic diversity across tissues, cell types, and sexes. Key features of the resource include a genotype imputation panel of 2869 chickens from 123 breeds worldwide, five types of molecular phenotypes across 28 tissues, ∼2.2 million molQTL, 806 229 fine-mapped molQTL, 1956 context-dependent molQTL, 257 genome-wide profiles of 7 epigenetic marks (representing 15 chromatin states) from 23 tissues, 185 376 single-cell expression profiles across 191 cell clusters from 9 tissues, and 96 386 gene-trait associations covering 108 economically important traits. In summary, the ChickenGTEx portal will serve as an invaluable resource for advancing research in fundamental and evolutionary biology, chicken precision breeding, and eventually human biomedicine.

Indexed as

ChickensDatabases, GeneticQuantitative Trait LociTranscriptomeAnimalsFemaleGenomicsGenotypeMaleOrgan SpecificityPhenotypePolymorphism, Single Nucleotide

Identifiers

PMID40827640
PMCPMC12807649

What OpenQuestion holds

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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.