Abstract With the accumulation of massive data sets from high-throughput experiments and rapid emergence new types omics data, gene have become more diverse essential for refinement annotation at multidimensional levels. Accordingly, we collected defined 236 007 across different categories 44 plant species in Plant Gene Set Annotation Database (PlantGSAD). These were divided into nine main covering many functional subcategories, such as trait ontology, co-expression modules, chromatin...

Genetic and epigenetic changes after polyploidization events could result in variable gene expression modified regulatory networks. Here, using large-scale transcriptome data, we constructed co-expression networks for diploid, tetraploid, hexaploid wheat species, built a platform comparing of allohexaploid its progenitors, named WheatCENet. WheatCENet is searching specific functional networks, as well identifying the related functions genes clustered therein. Functional annotations like...

Subtilases (SBTs), which belong to the serine peptidases, control plant development by regulating cell wall properties and activity of extracellular signaling molecules, affect all stages life cycle, such as seed germination, responses biotic abiotic environments. In this study, 146 Gossypium hirsutum, 138 barbadense, 89 arboreum 84 raimondii SBTs were identified divided into six subfamilies. Cotton are unevenly distributed on chromosomes. Synteny analysis showed that members SBT1 SBT4...

Plant Knotted1-like homeobox (KNOX) genes encode homeodomain-containing transcription factors. In rice (Oryza sativa L.), little is known about the downstream target of KNOX Class II subfamily proteins. Here we generated chromatin immunoprecipitation (ChIP)-sequencing datasets for HOS59, a member subfamily, and characterized genome-wide binding sites HOS59. We conducted trait ontology (TO) analysis 9705 identified genes, found that multiple TO terms are related to plant structure morphology...

Abstract Lamins are the major components of nuclear lamina, which regulate chromatin structure and gene expression. KAKU4 is a unique lamina component in periphery, modulates shape size Arabidopsis. The knowledge about regulatory role leaf development remains limited. Here we found that knockdown resulted an accelerated senescence phenotype, with elevated levels H 2 O hormones, particularly SA, JA, ABA. Our results demonstrated importance as potential negative regulator age-triggered...

Lonicera japonica Thunb., a traditional Chinese herb, has been used for treating human diseases thousands of years. Recently, the genome L. decoded, providing valuable information research into gene function. However, no comprehensive database functional analysis and mining is available japonica. We therefore constructed LjaFGD (www.gzybioinformatics.cn/LjaFGD bioinformatics.cau.edu.cn/LjaFGD), analyzing comparing function in co-expression network based on 77 RNA-seq samples, then annotated...

Tomato (Solanum lycopersicum), belonging to the Solanaceae family, holds distinction of being second most important vegetable crop on a global scale. As model plant renowned for its insights into fruit ripening and disease resistance, collaborative analysis multi-omics data takes an indispensable role in advancing flavor genetic traits this vital crop. In our endeavor, we have seamlessly integrated staggering 343 transcriptome sets create co-expression network. This network encompasses...

Abstract Background The nuclear lamina links the membrane to chromosomes and plays a crucial role in regulating chromatin states gene expression. However, current knowledge of plants is limited compared animals humans. Results This study mainly focused on elucidating mechanism through which putative component protein KAKU4 regulates expression Arabidopsis leaves. Thus, we constructed network using association proteins lamin-like proteins, revealing that strongly associated with or epigenetic...

The Min pig is a famous native breed in northeast China, which has the special genetic character of villi hair growth cold seasons. At present, little research focused on mechanism pigs. Copy number variations (CNVs) are type variant that may influence many traits. In this study, we first investigated phenotype Large White × pigs' F2 detail and then performed CNV-based genome-wide association study (GWAS) between CNVs appearance. Finally, total 15 significant CNVRs were found to be...

Summary Transgenes integrated into mammalian cells are silenced rapidly. This phenomenon correlates with repressed chromatin structure marked by histone hypoacetylation. study investigated the effect of trichostatin A (TSA; a histone-deacetylase inhibitor) on EGFP expression in transfected and embryonic development after somatic cell nuclear transfer (SCNT). Porcine adult fibroblasts were pEGFP-C1 vector. Then cells, donor for SCNT, pretreated TSA, untreated being used as control. Expression...

Min Pig (Sus scrofa) is a northern Chinese domestic pig breed, whose cold resistance remarkable. However, the cold-resistant phenotype of unclear. Our studies showed that in long-term exposure, death rate Pigs significantly lower than control Large White (LW) Pigs. The ear tissue freezing for 0%, but LW 100%. shivering time and frequency are both at 5 months (P < .005) 80–90 kg pigs .001). results indicated more resistant exposure. These findings provided important reference data field...

Rattan is regarded as one of the major non-timber forest products, second only to wood and bamboo, worldwide. Although published genomes Calamus simplicifolius Daemonorops jenkinsiana have facilitated genome-wide gene functional analyses, coexpression networks (CENs) provide more comprehensive complete annotations function at transcriptome level. Thus, we analyzed CENs two rattans, C. D. jenkinsiana, by integrating genome sequences analyzing in-house data from different development stages...

Abstract Genetic and epigenetic changes after polyploidization events could result in variable gene expression modified regulatory networks. Here, using large-scale transcriptome data, we constructed co-expression networks for diploid, tetraploid, hexaploid wheat species, built a platform comparing of allohexaploid its progenitors, named ccnWheat. ccnWheat is searching specific functional networks, as well identifying the related functions genes clustered therein. Functional annotations like...

Cold stress can promote fat metabolism and reduce deposition. The present study compared differentially expressed (DE) lncRNAs mRNAs in the subcutaneous back of Min pigs subjected to 24 h acute cold stress. Transcriptome sequencing was used identify DE mRNAs. A lncRNA mRNA co expression network constructed using confirmed lncRNAs. GO KEGG analyses were performed investigate biological processes involved response total 166 269 found. Several genes such as ANGPTL4, KLF11 NUPR1 related lipid...

To investigate the mechanism of Coptidis Rhizoma-Pinelliae Rhizoma in treatment gastric cancer based on syste-matic pharmacology and data mining. The chemical constituents Pinelliae were obtained from Traditio-nal Chinese Medicine Systems Pharmacology Database(TCMSP) Shanghai Institute Organic Chemistry database Academy Sciences by Then active ingredients screened ADME, targets predicted chemometrics. Molecular docking free energy analysis used to verify screen targets, so as obtain...

The efficiency of producing porcine transgenic cloned embryos is still low due to lower developmental competence compared in vivo-fertilized/cultured embryos. This phenomenon may correlates with poor culture condition. Energy substrate medium play an important role optimizing study pertain investigate the effect replacing pyruvate and lactate glucose PZM-3 at rest part period on embryonic development after SCNT. Porcine adult fibroblasts cells were transfected pEGFP-C1 vector. Then used as...

Osteosarcoma is one of the most serious primary malignant bone tumors that threaten lives children and adolescents. However, mechanism underlying how to prevent or treat disease have not been well understood.This aim present study was identify key genes explore novel insights into molecular miR-542-3p over-expressed Osteosarcoma.Gene expression profile data GDS5367 downloaded from Gene Expression Omnibus (GEO) database. The differentially expressed (DEGs) were screened using GEO2R, Ontology...