Additional file 2. Table S1. Ubiquitination annotation. Table S2. Protein annotation. Table S3. 42 proteins having ten or more than ten ubiquitination modifications. Table S4. 20 ubiquitin-binding motifs. Table S5. 2242 proteins with an upregulated ubiquitination and 1204 proteins with a down-regulated ubiquitination. Table S6. 1172 up-regulated proteins and 1700 down-regulated proteins. Table S7. 646 Secretory proteins. Table S8. 53 proteins having an upregulated expression simultaneously with a down-regulated ubiquitination and 116 proteins having down-regulated...

The incidence of cervical cancer ranks third among all female tumours globally and second in developing countries. However, the role of eukaryotic translation initiation factor 3 subunit D (EIF3D) in cervical carcinoma is unknown. This study investigated the effects of EIF3D on cell progression of cervical carcinoma and its underlying mechanism in vivo and vitro models. There were increases of EIF3D expression mRNA and protein expression levels in patients with cervical carcinoma. Disease-free survival (DFS)...

The incidence of cervical cancer ranks third among all female tumours globally and second in developing countries. However, the role of eukaryotic translation initiation factor 3 subunit D (EIF3D) in cervical carcinoma is unknown. This study investigated the effects of EIF3D on cell progression of cervical carcinoma and its underlying mechanism in vivo and vitro models. There were increases of EIF3D expression mRNA and protein expression levels in patients with cervical carcinoma. Disease-free survival (DFS)...

PCGEM1 facilitates prostate cancer (PCa) progression. This study aimed to elucidate the mechanism of action of PCGEM1 in PCa. The expression of PCGEM1, microRNA miR-129-5p, chromatin licensing, and DNA replication factor 1 (CDT1) was detected by quantitative reverse transcription-PCR (qRT-PCR). A series of function experiments including cell counting kit-8 (CCK-8), caspase-3 activity, and cell cycle assays were performed to evaluate the influence of PCGEM1, miR-129-5p, and CDT1 on the biological processes of PCa cells. CyclinD1,...

Esophageal cancer (EC) is one type of aggressive gastrointestinal cancers. The treatment of EC is challenging. Effective therapeutic targets require development. Long non-coding RNA TRPM2 antisense RNA (LncRNA TRPM2-AS) is considering a novel biomarker and therapeutic target for various types of cancer. However, the role of lncRNA TRPM2-AS in EC remains unknown. This study aimed to illustrate effects of LncRNA TRPM2-AS on EC growth and metastasis and potential underlying molecular mechanisms. LncRNA TRPM2-AS expression was...

Zaire ebolavirus (EBOV) causes a severe hemorrhagic fever in humans and non-human primates with high morbidity and mortality. EBOV infection is dependent on its structural glycoprotein (GP), but high levels of GP expression also trigger cell rounding, detachment, and downregulation of many surface molecules that is thought to contribute to its high pathogenicity. Thus, EBOV has evolved an RNA editing mechanism to reduce its GP expression and increase its fitness. We now report that the...

In this work, the asymmetric weld fusion geometry in oscillating laser beam welding (OLBW) of aluminium alloy was reported and investigated using a numerical approach. A multi-physics heat transfer and fluid flow model of OLBW was developed and validated with the corresponding experimental results. The weld fusion geometry, temperature fields, and fluid flow behaviours for four commonly used oscillation modes, line, circle, eight, and infinity, were calculated to analyse the origin of the asymmetric weld...

Recent research unveiled that LINC00857 plays a regulatory role in multiple human cancers, such as lung adenocarcinoma and gastric cancer. Nevertheless, the function of LINC00857 in pancreatic adenocarcinoma (PAAD) remains unclear. This study concentrates on LINC00857 to discuss the relevant molecular mechanism of this gene in PAAD. Quantitative reverse transcription polymerase chain reaction (RT-qPCR) and western blot were implemented for measuring the expressions of RNAs and proteins. Wound healing and Transwell assays were used to...

The DEAD-box family has been shown to play an important role in a variety of abiotic stresses, but little is known in studies of mangrove plants. Here, the effects of cold stress on various physiological changes and the role of the DEAD-box RNA helicase family in response to cold stress were determined. First, we identified 73 DEAD-box RNA helicase family members in L. littorea. Second, the evolutionary relationships between the DEAD family in L. littorea...

Collaborative geographic analysis can lead to better outcomes but requires complicated interactions among participants, support resources and analytic tools. A process expression with explicit structure and content can help coordinate and guide these interactions. For different geographic problems, the structure and content of collaborative geographic analysis are generally distinct. Since the process structure embodies the pathway of problem-solving and the process content contains the information flow and internal interactions, both the structure and the content...

Hsa_circ_0101432 promotes the development of hepatocellular carcinoma (HCC) by adsorbing miR-1258 and miR-622 We, the Editors and Publisher of the journal Cell Cycle, have retracted the following article: Haibo Zou, Xiangang Xu, Lanyun Luo, Yu Zhang, Le Luo, Yutong Yao, Guangming Xiang, Xiaolun Huang, and Guan Wang. Hsa_circ_0101432 promotes the development of hepatocellular carcinoma (HCC) by adsorbing miR-1258 and miR-622. Cell Cycle. 2019;18(19):2398-2413. doi: 10.1080/15384101.2019.1618120. Since publication, significant concerns have been raised about the integrity...

High-grade serous ovarian cancer (HGSOC) is the most common and malignant type of ovarian cancer, accounting for 70%–80% of mortality. However, the treatment of HGSOC has improved little in the past few decades. Metformin is the first-line medication for the treatment of type 2 diabetes and has now gained more attention in cancer treatment. In this study, we sought to identify potential hub genes that metformin could target in the treatment of HGSOC. We downloaded...

Accumulating evidence has unfolded the significance of extracellular vesicles (EVs) in diseases and cancers. Here, we attempted to discuss the role of cancer-associated fibroblasts (CAFs)-derived EVs containing miR-199a-5p in gastric tumorigenesis. Upregulated miR-199a-5p was first identified in cancer cells. Then, we selected CAFs for isolation of EVs which were co-cultured with AGS cells. We observed successful delivery of miR-199a-5p via CAF-derived EVs. Besides, miR-199a-5p promoted malignant properties of AGS cells. Moreover, miR-199a-5p downregulated FKBP5, leading...

Sucrose transporters (SUCs/SUTs) play crucial roles in apoplast transport and long-distance distribution of sucrose throughout the whole plant. However, whether and how the Arabidopsis AtSUC4 modulates sucrose import from apoplast to cytosol remains unclear. In the present study, we found that AtSUC4 protein was localized to the plasma membrane in the root. Expression of AtSUC4 in roots was gradually induced with the increasing sucrose concentrations (0%, 2%, 4% and 6%). When feeding high concentrations (4%...

Combining individual p-values to perform an overall test is often encountered in statistical applications. The Cauchy combination test (CCT) (Journal of the American Statistical Association, 2020, 115, 393–402) is a powerful and computationally efficient approach to integrate individual p-values under arbitrary dependence structures for sparse signals. We revisit this test to additionally show that (i) the tail probability of the CCT can be approximated just as well when more relaxed assumptions are imposed on individual...

A stereo interplanting system with foxtail millet beneath chestnut trees is an effective planting method to raise the utilization of land in chestnut orchards, increase yields and improve quality of chestnut nuts. Consequently, exploration of genes involved in shade tolerance response in foxtail millet and breeding shade-tolerant varieties have become urgent issues. In this study, RNA-seq of leaf samples from two shade-tolerant varieties and three shade-intolerant varieties of foxtail millet at the booting stage was...

A stereo interplanting system with foxtail millet beneath chestnut trees is an effective planting method to raise the utilization of land in chestnut orchards, increase yields and improve quality of chestnut nuts. Consequently, exploration of genes involved in shade tolerance response in foxtail millet and breeding shade-tolerant varieties have become urgent issues. In this study, RNA-seq of leaf samples from two shade-tolerant varieties and three shade-intolerant varieties of foxtail millet at the booting stage was...

A stereo interplanting system with foxtail millet beneath chestnut trees is an effective planting method to raise the utilization of land in chestnut orchards, increase yields and improve quality of chestnut nuts. Consequently, exploration of genes involved in shade tolerance response in foxtail millet and breeding shade-tolerant varieties have become urgent issues. In this study, RNA-seq of leaf samples from two shade-tolerant varieties and three shade-intolerant varieties of foxtail millet at the booting stage was...

A stereo interplanting system with foxtail millet beneath chestnut trees is an effective planting method to raise the utilization of land in chestnut orchards, increase yields and improve quality of chestnut nuts. Consequently, exploration of genes involved in shade tolerance response in foxtail millet and breeding shade-tolerant varieties have become urgent issues. In this study, RNA-seq of leaf samples from two shade-tolerant varieties and three shade-intolerant varieties of foxtail millet at the booting stage was...

Additional file 7: Supplementary Data 7. GSEA in males.

Additional file 1: Table S1. Summary of sequencing quality.

Additional file 3: Table S3. The KEGG enrichment analysis of comparison analysis.

Additional file 4: Table S4. The gene description list of the model.

Additional file 3: Table S3. The KEGG enrichment analysis of comparison analysis.

Additional file 6: Table S6. The KEGG enrichment analysis of coexpression modules.