501 Works

Additional file 1 of Development and validation of an extended Cox prognostic model for patients with ER/PR+ and HER2− breast cancer: a retrospective cohort study

Yiqun Xie, Xizhou Li, Ying Wu, Wenting Cui & Yang Liu
Additional file 1: Appendix 1. Clinicopathologic characteristics of 28 deaths.

LncRNA SNHG16 promotes development of oesophageal squamous cell carcinoma by interacting with EIF4A3 and modulating RhoU mRNA stability

Lihua Ren, Xin Fang, Sachin Mulmi Shrestha, Qinghua Ji, Hui Ye, Yan Liang, Yang Liu, Yadong Feng, Jingwu Dong & Ruihua Shi
Abstract Background Numerous studies have revealed that long noncoding RNAs (lncRNAs) are closely related to the development of many diseases and carcinogenesis. However, their specific biological function and molecular mechanism in oesophageal squamous cell carcinoma (ESCC) remains unclear. Methods RNA-Seq was performed to determine the differential expressions of lncRNAs in ESCC, and the level of SNHG16 expression was detected in ESCC and intraepithelial neoplasia (IEN) samples. In vitro and in vivo experiments were performed to...

Development and validation of an extended Cox prognostic model for patients with ER/PR+ and HER2− breast cancer: a retrospective cohort study

Yiqun Xie, Xizhou Li, Ying Wu, Wenting Cui & Yang Liu
Abstract Background The purpose of this study was to explore a new estrogen receptor (ER) and/or progesterone receptor (PR)+ and human epidermal growth factor receptor 2 (HER2)− breast cancer prognostic model, called the extended Cox prognostic model, for determining the cutoff values for multiple continuous prognostic factors and their interaction via the new model concept and variable selection method. Methods A total of 335 patients with ER/PR+ and HER2− breast cancer were enrolled for the...

Supplementary material from \"Investigation of the photoluminescent properties, scintillation behaviour and toxicological profile of various magnesium tungstate nanoscale motifs\"

Nathaniel Hurley, Sailesh Srinivas, Justin Fang, Manli Sun, Simon Hong, Chia Te Chien, Alan Guo, Tamor A. Khan, Mingxing Li, Mircea Cotlet, Federico Moretti, Edith Bourret-Courchesne, Daniel Radin, Stella E. Tsirka, Maya Shelly & Stanislaus S. Wong
We have synthesized several morphologies and crystal structures of MgWO4 using a one-pot hydrothermal method, producing not only monoclinic stars and large nanoparticles but also triclinic wool balls and sub-10 nm nanoparticles. Herein we describe the importance of reaction parameters in demonstrating morphology control of as-prepared MgWO4. Moreover, we correlate structure and composition with the resulting photoluminescence and radioluminescence properties. Specifically, triclinic-phase samples yielded a photoluminescence emission of 421 nm, whereas monoclinic-phase materials gave rise...

Additional file 5 of Expanding known viral diversity in plants: virome of 161 species alongside an ancient canal

Shixing Yang, Qingqing Mao, Yan Wang, Jingxian He, Jie Yang, Xu Chen, Yuqing Xiao, Yumin He, Min Zhao, Juan Lu, Zijun Yang, Ziyuan Dai, Qi Liu, Yuxin Yao, Xiang Lu, Hong Li, Rui Zhou, Jian Zeng, Wang Li, Chenglin Zhou, Xiaochun Wang, Quan Shen, Hui Xu, Xutao Deng, Eric Delwart … & Wen Zhang
Additional file 5. Fig. S32: The host assignment of plant-associated viruses by using BLASTx searching the contigs assembled from the NGS data of each plant species (those containing possible non-plant-infecting virus) against the total mitochondrial proteome database that were downloaded from GenBank.

Expanding known viral diversity in plants: virome of 161 species alongside an ancient canal

Shixing Yang, Qingqing Mao, Yan Wang, Jingxian He, Jie Yang, Xu Chen, Yuqing Xiao, Yumin He, Min Zhao, Juan Lu, Zijun Yang, Ziyuan Dai, Qi Liu, Yuxin Yao, Xiang Lu, Hong Li, Rui Zhou, Jian Zeng, Wang Li, Chenglin Zhou, Xiaochun Wang, Quan Shen, Hui Xu, Xutao Deng, Eric Delwart … & Wen Zhang
Abstract Background Since viral metagenomic approach was applied to discover plant viruses for the first time in 2006, many plant viruses had been identified from cultivated and non-cultivated plants. These previous researches exposed that the viral communities (virome) of plants have still largely uncharacterized. Here, we investigated the virome in 161 species belonging to 38 plant orders found in a riverside ecosystem. Results We identified 245 distinct plant-associated virus genomes (88 DNA and 157 RNA...

Additional file 3 of Proteogenomic insights into the biology and treatment of pancreatic ductal adenocarcinoma

Yexin Tong, Mingjun Sun, Lingli Chen, Yunzhi Wang, Yan Li, Lingling Li, Xuan Zhang, Yumeng Cai, Jingbo Qie, Yanrui Pang, Ziyan Xu, Jiangyan Zhao, Xiaolei Zhang, Yang Liu, Sha Tian, Zhaoyu Qin, Jinwen Feng, Fan Zhang, Jiajun Zhu, Yifan Xu, Wenhui Lou, Yuan Ji, Jianyuan Zhao, Fuchu He, Yingyong Hou … & Chen Ding
Additional file 3: Fig. S3. The impacts of somatic copy number alterations in PDAC cohort, related to Fig. 2. A Bar plots showing pathway enrichment of cis/trans-effect between CNA and protein (left) or phosphoprotein (right). B Distribution of IRF6 status between the younger patients’ group (≤ 60) and the older patients’ group (> 60) (left). The boxplot reveals the comparison of the mRNA (middle) and protein (right) abundance of IRF6 between the younger patients (≤...

Additional file 4 of Proteogenomic insights into the biology and treatment of pancreatic ductal adenocarcinoma

Yexin Tong, Mingjun Sun, Lingli Chen, Yunzhi Wang, Yan Li, Lingling Li, Xuan Zhang, Yumeng Cai, Jingbo Qie, Yanrui Pang, Ziyan Xu, Jiangyan Zhao, Xiaolei Zhang, Yang Liu, Sha Tian, Zhaoyu Qin, Jinwen Feng, Fan Zhang, Jiajun Zhu, Yifan Xu, Wenhui Lou, Yuan Ji, Jianyuan Zhao, Fuchu He, Yingyong Hou … & Chen Ding
Additional file 4: Fig. S4. Characteristics of PDAC patients with KRASG12D mutations. A The volcano plot showing the phosphosites that significantly altered between tumors with KRASG12D and with other types of KRAS mutations. B The heatmap indicating the phosphorylation abundance of RAF1, MAP2K2, MAPK1 across tumors with different KRAS mutations. C Kaplan-Meier curves for overall survival based on the phosphorylation of E2F1 at S364 (left) and based on the TF activity of E2F1 (right). D...

Additional file 5 of Proteogenomic insights into the biology and treatment of pancreatic ductal adenocarcinoma

Yexin Tong, Mingjun Sun, Lingli Chen, Yunzhi Wang, Yan Li, Lingling Li, Xuan Zhang, Yumeng Cai, Jingbo Qie, Yanrui Pang, Ziyan Xu, Jiangyan Zhao, Xiaolei Zhang, Yang Liu, Sha Tian, Zhaoyu Qin, Jinwen Feng, Fan Zhang, Jiajun Zhu, Yifan Xu, Wenhui Lou, Yuan Ji, Jianyuan Zhao, Fuchu He, Yingyong Hou … & Chen Ding
Additional file 5: Fig. S5. Integrated multi-omics features in tumor tissues compared with NATs of the PDAC, related to Fig. 3. A Principal component analysis (PCA) of RNA-Seq (19,992 genes) in 54 tumors and 51 NATs. Red, tumors; blue, NATs. B PCA of 7,399 phosphoproteins in 113 paired samples. Red, tumors; blue, NATs. C A volcano plot showing the results of a two-tailed Student’s t test comparing tumors and NATs at transcriptome level. D A...

Additional file 7 of Proteogenomic insights into the biology and treatment of pancreatic ductal adenocarcinoma

Yexin Tong, Mingjun Sun, Lingli Chen, Yunzhi Wang, Yan Li, Lingling Li, Xuan Zhang, Yumeng Cai, Jingbo Qie, Yanrui Pang, Ziyan Xu, Jiangyan Zhao, Xiaolei Zhang, Yang Liu, Sha Tian, Zhaoyu Qin, Jinwen Feng, Fan Zhang, Jiajun Zhu, Yifan Xu, Wenhui Lou, Yuan Ji, Jianyuan Zhao, Fuchu He, Yingyong Hou … & Chen Ding
Additional file 7: Fig. S7. The expression of phosphotyrosine in PDAC cohort, related to Fig. 3. A. The proportion of phosphorylation sites S, T and Y in tumors and NATs, respectively. B. The comparison of the percentage of phosphorylation sites S, T and Y in Fudan cohort and other gastrointestinal tumor cohorts. C. The scatter plot demonstrating the T/NAT ratio of phosphotyrosine (y axis) and T/NAT ratio of their corresponding proteins (x axis). D. Heatmap...

Additional file 8 of Proteogenomic insights into the biology and treatment of pancreatic ductal adenocarcinoma

Yexin Tong, Mingjun Sun, Lingli Chen, Yunzhi Wang, Yan Li, Lingling Li, Xuan Zhang, Yumeng Cai, Jingbo Qie, Yanrui Pang, Ziyan Xu, Jiangyan Zhao, Xiaolei Zhang, Yang Liu, Sha Tian, Zhaoyu Qin, Jinwen Feng, Fan Zhang, Jiajun Zhu, Yifan Xu, Wenhui Lou, Yuan Ji, Jianyuan Zhao, Fuchu He, Yingyong Hou … & Chen Ding
Additional file 8: Fig. S8. The effects of diabetes on the proteogenomic characteristics of PDAC, related to Fig. 4. A The boxplot representing the comparison of blood glucose concentration between patients with diabetes and without diabetes. B The Kaplan-Meier curves for overall survival based on diabetic patients with or without medical treatment. C The heatmap showing the distribution of 10q25.3 deletion and MTOR mutations across different samples in TCGA cohort. D The bar plot showing...

Additional file 9 of Proteogenomic insights into the biology and treatment of pancreatic ductal adenocarcinoma

Yexin Tong, Mingjun Sun, Lingli Chen, Yunzhi Wang, Yan Li, Lingling Li, Xuan Zhang, Yumeng Cai, Jingbo Qie, Yanrui Pang, Ziyan Xu, Jiangyan Zhao, Xiaolei Zhang, Yang Liu, Sha Tian, Zhaoyu Qin, Jinwen Feng, Fan Zhang, Jiajun Zhu, Yifan Xu, Wenhui Lou, Yuan Ji, Jianyuan Zhao, Fuchu He, Yingyong Hou … & Chen Ding
Additional file 9: Fig. S9. 8p11.22 amplification is associated with PDAC metastasis, related to Fig. 5. A Western blot assays were conducted for detecting ADAM9 protein in PANC-1 cells after si-ADAM9-1 and si-ADMA9-2 knocked down. B The scatter plot depicting the correlation between ADAM9 expression and expression of ADAM9-interacting proteins (Spearman’s correlation). C The scatter plot depicting the correlation between the abundance of SRC and pathways (GSVA score). D The boxplots indicating the protein expression...

Additional file 24 of Proteogenomic insights into the biology and treatment of pancreatic ductal adenocarcinoma

Yexin Tong, Mingjun Sun, Lingli Chen, Yunzhi Wang, Yan Li, Lingling Li, Xuan Zhang, Yumeng Cai, Jingbo Qie, Yanrui Pang, Ziyan Xu, Jiangyan Zhao, Xiaolei Zhang, Yang Liu, Sha Tian, Zhaoyu Qin, Jinwen Feng, Fan Zhang, Jiajun Zhu, Yifan Xu, Wenhui Lou, Yuan Ji, Jianyuan Zhao, Fuchu He, Yingyong Hou … & Chen Ding
Additional file 24: Table S2. The Impacts of Somatic Copy Number Alterations in PDAC Cohort. Table S2A Matrix of amplification peaks, followed by the genes contained in them, 95% confidence level. Table S2B Matrix of deletion peaks, followed by the genes contained in them, 95% confidence level. Table S2C Matrix of the top 10 mutated genes in PDAC of Fudan cohort. Table S2D Matrix of the 10 mutated genes used in Figure 1C of ICGC,...

Additional file 27 of Proteogenomic insights into the biology and treatment of pancreatic ductal adenocarcinoma

Yexin Tong, Mingjun Sun, Lingli Chen, Yunzhi Wang, Yan Li, Lingling Li, Xuan Zhang, Yumeng Cai, Jingbo Qie, Yanrui Pang, Ziyan Xu, Jiangyan Zhao, Xiaolei Zhang, Yang Liu, Sha Tian, Zhaoyu Qin, Jinwen Feng, Fan Zhang, Jiajun Zhu, Yifan Xu, Wenhui Lou, Yuan Ji, Jianyuan Zhao, Fuchu He, Yingyong Hou … & Chen Ding
Additional file 27: Table S5. 8p11.22 Amplification Associated with PDAC Metastasis. Table S5A The matrix describing mutations in PDAC metastatic patients and non-metastatic patients. Table S5B Matrix of GSVA scores of pathways significantly altered in PDAC metastatic patients and non-metastatic patients, proteome level. Table S5C Matrix of xCell signatures significantly altered in PDAC metastatic patients and non-metastatic patients, transcriptome level. Table S5D Matrix describing the cis-effects of genes located on chromosome 8p11.22. Table S5E Matrix...

Additional file 27 of Proteogenomic insights into the biology and treatment of pancreatic ductal adenocarcinoma

Yexin Tong, Mingjun Sun, Lingli Chen, Yunzhi Wang, Yan Li, Lingling Li, Xuan Zhang, Yumeng Cai, Jingbo Qie, Yanrui Pang, Ziyan Xu, Jiangyan Zhao, Xiaolei Zhang, Yang Liu, Sha Tian, Zhaoyu Qin, Jinwen Feng, Fan Zhang, Jiajun Zhu, Yifan Xu, Wenhui Lou, Yuan Ji, Jianyuan Zhao, Fuchu He, Yingyong Hou … & Chen Ding
Additional file 27: Table S5. 8p11.22 Amplification Associated with PDAC Metastasis. Table S5A The matrix describing mutations in PDAC metastatic patients and non-metastatic patients. Table S5B Matrix of GSVA scores of pathways significantly altered in PDAC metastatic patients and non-metastatic patients, proteome level. Table S5C Matrix of xCell signatures significantly altered in PDAC metastatic patients and non-metastatic patients, transcriptome level. Table S5D Matrix describing the cis-effects of genes located on chromosome 8p11.22. Table S5E Matrix...

Additional file 10 of Proteogenomic insights into the biology and treatment of pancreatic ductal adenocarcinoma

Yexin Tong, Mingjun Sun, Lingli Chen, Yunzhi Wang, Yan Li, Lingling Li, Xuan Zhang, Yumeng Cai, Jingbo Qie, Yanrui Pang, Ziyan Xu, Jiangyan Zhao, Xiaolei Zhang, Yang Liu, Sha Tian, Zhaoyu Qin, Jinwen Feng, Fan Zhang, Jiajun Zhu, Yifan Xu, Wenhui Lou, Yuan Ji, Jianyuan Zhao, Fuchu He, Yingyong Hou … & Chen Ding
Additional file 10: Fig. S10. Protein expression changes in PANC-1 cell lines after ADAM9 knocked down and the co-expressed proteins of ADAM9, related to Fig. 5. A The schematic work flow of validation experiments for the protein expression changes after ADAM9 knocked down. B The volcano plot showed the proteins that significantly altered between PANC-1 cells with ADAM9 KD and Scrambled siRNA. The GO processes enriched by proteins downregulated in ADAM9 KD cell lines are...

Additional file 11 of Proteogenomic insights into the biology and treatment of pancreatic ductal adenocarcinoma

Yexin Tong, Mingjun Sun, Lingli Chen, Yunzhi Wang, Yan Li, Lingling Li, Xuan Zhang, Yumeng Cai, Jingbo Qie, Yanrui Pang, Ziyan Xu, Jiangyan Zhao, Xiaolei Zhang, Yang Liu, Sha Tian, Zhaoyu Qin, Jinwen Feng, Fan Zhang, Jiajun Zhu, Yifan Xu, Wenhui Lou, Yuan Ji, Jianyuan Zhao, Fuchu He, Yingyong Hou … & Chen Ding
Additional file 11: Fig. S11. Multi-omics subtypes of PDAC patients, related to Fig. 6. A Consensus matrices of identified clusters (k = 2 to 4) of transcriptomic, proteomic, and phosphoproteomic subtypes. B The consensus CDF and delta area (change in CDF area) plots, as well as the silhouette plots, are shown. C Heatmaps showing the comparison between transcriptomic and phosphoproteomic subtypes (columns) with proteomic subtypes (rows). Each row sums to one, with different entries showing...

Additional file 12 of Proteogenomic insights into the biology and treatment of pancreatic ductal adenocarcinoma

Yexin Tong, Mingjun Sun, Lingli Chen, Yunzhi Wang, Yan Li, Lingling Li, Xuan Zhang, Yumeng Cai, Jingbo Qie, Yanrui Pang, Ziyan Xu, Jiangyan Zhao, Xiaolei Zhang, Yang Liu, Sha Tian, Zhaoyu Qin, Jinwen Feng, Fan Zhang, Jiajun Zhu, Yifan Xu, Wenhui Lou, Yuan Ji, Jianyuan Zhao, Fuchu He, Yingyong Hou … & Chen Ding
Additional file 12: Fig. S12. Multi-omics characteristics of the three proteomic subtypes, related to Fig. 6. A Bar plot showing the number of overexpressed molecules in each proteomic subtypes at both proteome and transcriptome level. B Heatmap of the characteristic molecules of each proteomic subtypes at proteome (left) and transcriptome (right) level. Molecules previously reported to be associated with PDAC are marked in red. C Scatter plot displaying the significance of molecules that highest expressed...

Additional file 20 of Proteogenomic insights into the biology and treatment of pancreatic ductal adenocarcinoma

Yexin Tong, Mingjun Sun, Lingli Chen, Yunzhi Wang, Yan Li, Lingling Li, Xuan Zhang, Yumeng Cai, Jingbo Qie, Yanrui Pang, Ziyan Xu, Jiangyan Zhao, Xiaolei Zhang, Yang Liu, Sha Tian, Zhaoyu Qin, Jinwen Feng, Fan Zhang, Jiajun Zhu, Yifan Xu, Wenhui Lou, Yuan Ji, Jianyuan Zhao, Fuchu He, Yingyong Hou … & Chen Ding
Additional file 20: Fig. S20. HOGA1 regulated LARP7 expression, related to Fig. 8. A The association of the mRNA expression of HOGA1with prognosis (log-rank test). B Boxplot showing the differential expression of HOGA1 between tumors and NATs in CPTAC cohort (Student’s t test). C Expression of HOGA1, LARP7, CDK1, CCNB1, and CCNB2, in tumor tissues were detected by western blot analysis. N = non-tumor adjacent tissue, T = tumor tissue. D The impacts of HOGA1...

Roles of MEF2A and HOXA5 in the transcriptional regulation of the bovine FoxO1 gene

Dawei Wei, Jin Wang, Zhang Jiupan, Rajwali Khan, Sayed Haidar Abbas Raza, Song Yaping, Jiang Chao, Amel Ayari-Akkari & Dalia Abd El Moneim Ahmed
The Forkhead box factor 1 (FoxO1) gene plays a vital role in the growth and development of skeletal muscle. In the present study, expression analysis of the bovine FoxO1 gene exhibited the highest expression in longissimus dorsi muscle followed by its expression in adipose tissue. Moreover, high mRNA expression of FoxO1 gene was found in differentiated bovine myoblasts and adipocytes at day 6 of induced differentiation (p < 0.05). The regulatory pattern of the bovine...

Additional file 2 of Antibiotic prescribing patterns at children’s outpatient departments of primary care institutions in Southwest China

Wenju Wang, Shitao Yu, Xunrong Zhou, Lei Wang, Xun He, Hanni Zhou & Yue Chang
Additional file 2. National Health Commission of China for Guiding Principle of Clinical Use of Antibiotics.

Antibiotic prescribing patterns at children’s outpatient departments of primary care institutions in Southwest China

Wenju Wang, Shitao Yu, Xunrong Zhou, Lei Wang, Xun He, Hanni Zhou & Yue Chang
Abstract Background Inappropriate use of antibiotics in children is common in many countries. The purpose of the study was to explore patterns of antibiotic prescribing in children’s outpatient clinics in primary care institutions in a province of southwest China. Methods We obtained electronic prescription data from 75 primary care institutions in Guizhou province in 2020. The classification of incorrect spectrum of antibiotics, unnecessary use and combined use of antibiotics was based on the Guiding Principle...

Additional file 1 of Intrauterine growth retardation affects liver bile acid metabolism in growing pigs: effects associated with the changes of colonic bile acid derivatives

Yang Liu, Md. Abul Kalam Azad, Wanghong Zhang, Liang Xiong, Francois Blachier, Zugong Yu & Xiangfeng Kong
Additional file1: Table S1. The composition and nutrient levels of sows' diets (as-fed basis).

Expansion of a vertical effective field-of-view for an optical 360° holographic display

Jun Wang, Jie Zhou, yang wu, XiangLi Lei & Yuqi Zhang
Cylindrical holography, as a promising 360° display technology, has already attracted a lot of attention. In a previous study, an optical 360° cylindrical holography has been achieved in the visible spectrum using a planar spatial light modulator (SLM) and a 45° conical mirror. Although 360° field-of-view (FOV) is successfully achieved in the horizontal direction, in the previous study, the vertical FOV remains as small as the planar holography, and its expansion is not only necessary...

De novo mutations within metabolism networks of amino acid/protein/energy in Chinese autistic children with intellectual disability

Wen-Xiong Chen, Bin Liu, Lijie Zhou, Xiaoli Xiong, Jie Fu, Zhi-Fang Huang, Ting Tan, Mingxi Tang, Jun Wang & Ya-Ping Tang
Abstract Background Autism spectrum disorder (ASD) is often accompanied by intellectual disability (ID). Despite extensive studies, however, the genetic basis for this comorbidity is still not clear. In this study, we tried to develop an analyzing pipeline for de novo mutations and possible pathways related to ID phenotype in ASD. Whole-exome sequencing (WES) was performed to screen de novo mutations and candidate genes in 79 ASD children together with their parents (trios). The de novo...

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  • Stony Brook University
    501
  • Shanghai Jiao Tong University
    384
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  • Sun Yat-sen University
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  • Capital Medical University
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