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22. Additional file 3 of Construction of immune-related signature and identification of S100A14 determining immune-suppressive microenvironment in pancreatic cancer

Author

Wang, Chengcheng, Chen, Yuan, Xinpeng, Yin, Xu, Ruiyuan, Song, Jianlu, Ruze, Rexiati, Xu, Qiang, and Zhao, Yupei

Abstract

Additional file 3: Table S1. Detailed clinical and pathologic information of TCGA entire set. Table S2. Detailed clinical and pathologic information of CRA001160 dataset. Table S3. The imaging channels for each antibody and antibody incubation information in tissue microenvironment landscape imaging. Table S4. Immune-related genes obtained from the ImmPort database.

Published
2022
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23. Additional file 1 of Construction of immune-related signature and identification of S100A14 determining immune-suppressive microenvironment in pancreatic cancer

Author

Wang, Chengcheng, Chen, Yuan, Xinpeng, Yin, Xu, Ruiyuan, Song, Jianlu, Ruze, Rexiati, Xu, Qiang, and Zhao, Yupei

Abstract

Additional file 1: Figure S1. Flowchart of the whole study. Figure S2. The mutation status of the seven hub IRGs in TCGA dataset (A) and ICGC dataset (B). Figure S3. Representative images of hub IRGs expression status except CXCL10 and LIFR in normal pancreas and PC tissues. (The expression information of CXCL10 and LIFR was unavailable in HPA database). Figure S4. Independence of the risk signature and the other clinical variables, including, age, tumor grade, AJCC_stage and gender. (A, C, E) Univariate Cox regression analyses in the training set, testing set and entire set. (B, D, F) Multivariate Cox regression analyses in the training set testing set and entire set. Figure S5. Stratification analyses of all patients using the risk signature. (A-C) The Kaplan-Meier analysis of the younger stratum (age ≤ 65, n=88), older stratum (age >65, n=78) and all patients with PC (n=166). (D-F) The Kaplan-Meier analysis of the male stratum (n=90), female stratum n=76) and all patients with PC (n=166). (G-I) The Kaplan-Meier analysis of the Grade I/II stratum (n=117), Grade III/IV stratum (n=49) and all patients with PC (n=166). (J-L) The Kaplan-Meier analysis of the T1+T2 stratum (n=27), T3+T4 stratum (n=139) and all patients with PC (n=166). Figure S6. The mutation profiles of patients in S100A14 high expression group. Figure S7. The mutation profiles of patients in S100A14 low expression group. Figure S8. Correlation analysis of S100A14 and CD3E in the Bailey P. et al. cohort.

Published
2022
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31. Additional file 8 of Construction of a prognostic model with histone modification-related genes and identification of potential drugs in pancreatic cancer

Author

Chen, Yuan, Xu, Ruiyuan, Ruze, Rexiati, Yang, Jinshou, Wang, Huanyu, Song, Jianlu, You, Lei, Wang, Chengcheng, and Zhao, Yupei

Abstract

Additional file 8: Figure S4. Validation of the nomogram in training set, testing set and entire set. (A–C) Time-dependent ROC analysis of the risk signature in training set, testing set and entire set. (D–L) The calibration plot of the nomogram for agreement test between 1-, 2- and 3-year OS prediction and actual outcome in the training set, testing set and entire set.

Published
2021
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32. Additional file 6 of Construction of a prognostic model with histone modification-related genes and identification of potential drugs in pancreatic cancer

Author

Chen, Yuan, Xu, Ruiyuan, Ruze, Rexiati, Yang, Jinshou, Wang, Huanyu, Song, Jianlu, You, Lei, Wang, Chengcheng, and Zhao, Yupei

Subjects
integumentary system
Abstract

Additional file 6: Figure S2. Stratification analyses of all patients using the risk signature. (A–C) The Kaplan–Meier plot of the younger stratum (age ≤ 65, n = 91), older stratum (age > 65, n = 80) and entire patients with PC (n = 171). (D–F) The Kaplan–Meier plot of the male stratum (n = 93), female stratum n = 78) and entire patients with PC (n = 171). (G–I) The Kaplan–Meier plot of the Grade I/II stratum (n = 121), Grade III/IV stratum (n = 50) and entire patients with PC (n = 171). (J–L) The Kaplan–Meier plot of the T1 + T2 stratum (n = 30), T3 + T4 stratum (n = 141) and entire patients with PC (n = 171).

Published
2021
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33. Additional file 12 of Construction of a prognostic model with histone modification-related genes and identification of potential drugs in pancreatic cancer

Author

Chen, Yuan, Xu, Ruiyuan, Ruze, Rexiati, Yang, Jinshou, Wang, Huanyu, Song, Jianlu, You, Lei, Wang, Chengcheng, and Zhao, Yupei

Subjects
genetic structures, sense organs, psychological phenomena and processes
Abstract

Additional file 12: Figure S8. Differential gene expression in the high- and low-risk group compared with the normal group. (A) Heatmap of DEGs (Top50) between the low-risk pancreatic cancer group and the normal group. (B) Volcanic map of the DEGs between the low-risk pancreatic cancer group and the normal group. (C) Heatmap of DEGs (Top50) between the high-risk pancreatic cancer group and the normal group. (D) Volcanic map of the DEGs between the high-risk pancreatic cancer group and the normal group

Published
2021
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34. Additional file 7 of High-resolution Hi-C maps highlight multiscale 3D epigenome reprogramming during pancreatic cancer metastasis

Author

Ren, Bo, Yang, Jinshou, Wang, Chengcheng, Yang, Gang, Wang, Huanyu, Chen, Yuan, Xu, Ruiyuan, Fan, Xuning, You, Lei, Zhang, Taiping, and Zhao, Yupei

Subjects
ComputingMethodologies_DOCUMENTANDTEXTPROCESSING, ComputingMilieux_COMPUTERSANDEDUCATION, Data_FILES, ComputerApplications_COMPUTERSINOTHERSYSTEMS
Abstract

Additional file 7. Supplementary figures and tables.

Published
2021
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35. Additional file 5 of Construction of a prognostic model with histone modification-related genes and identification of potential drugs in pancreatic cancer

Author

Chen, Yuan, Xu, Ruiyuan, Ruze, Rexiati, Yang, Jinshou, Wang, Huanyu, Song, Jianlu, You, Lei, Wang, Chengcheng, and Zhao, Yupei

Abstract

Additional file 5: Figure S1. Further validation of the risk signature for the survival prediction in testing set, the entire TCGA set and the GSE57495 set. (A–C) Heatmap of the four genes expression, the risk scores distribution and survival status of the patients in the testing set, entire TCGA set and GSE57495 set.

Published
2021
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36. Additional file 9 of Construction of a prognostic model with histone modification-related genes and identification of potential drugs in pancreatic cancer

Author

Chen, Yuan, Xu, Ruiyuan, Ruze, Rexiati, Yang, Jinshou, Wang, Huanyu, Song, Jianlu, You, Lei, Wang, Chengcheng, and Zhao, Yupei

Abstract

Additional file 9: Figure S5. The mutations status and mechanisms of function of DPY30, CBX8, CENPT and PADI1. (A) Mutation information of DPY30, CBX8, CENPT and PADI1 from the cBioPortal database. (B–E) Interaction of DPY30, CBX8, CENPT and PADI1 with other proteins obtained from STRING database and validation in the TCGA entire set.

Published
2021
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40. [Expression of c-FLIP in peripheral blood mononuclear cells of patients with rheumatoid arthritis and its relation with extrinsic apoptotic pathway].

Author

Lin M, Xu R, Zhang T, Zhang L, and Mei X

Subjects
Apoptosis genetics, Gene Expression Profiling, Humans, Arthritis, Rheumatoid blood, CASP8 and FADD-Like Apoptosis Regulating Protein genetics, Gene Expression Regulation, Leukocytes, Mononuclear metabolism
Abstract

Objective: To investigate the expression of apoptosis related protein cellular Fas associated death domain like interleukin 1 converting enzyme inhibitory protein (c-FLIP) in peripheral blood mononuclear cells (PBMCs) of patients with rheumatoid arthritis and its relation with extrinsic apoptotic pathway., Methods: Sixty patients with rheumatoid arthritis were collected from Zhangzhou Affiliated Hospital of Fujian Medical University during January 2014 and June 2015, including 22 patients with low activities (DAS28<3.2), 20 patients with middle activities (3.2 ≤ DAS28 ≤ 5.1), and 18 patients with high activities (DAS28>5.1). And 25 healthy controls were also collected. The mRNA and protein expression levels of c-FLIP and the extrinsic apoptotic pathway related proteins Fas-associated protein with death domain (FADD), caspase-8 in PBMCs were detected by real-time RT-PCR and Western blot, respectively. Correlations between c-FLIP and FADD, caspase-8 in PBMCs were analyzed by pearson test., Results: mRNA expression levels of c-FLIP, FADD and caspase-8 in PBMCs of patients with rheumatoid arthritis were all higher than those of healthy controls (all P <0.05). mRNA expression levels of FADD and caspase-8 in patients with middle activities were significantly higher than those in patients with low activities (all P <0.05), but the mRNA expression level of c-FLIP was not significantly higher than that in patients with low activities. mRNA expression level of c-FLIP in patients with high activities was higher than those in patients with middle or low activities (all P <0.05), while the mRNA expression level of caspase-8 was lower than those in patients with middle or low activities (all P <0.05). mRNA expression level of FADD in patients with high activities was higher than those in patients with low activities ( P <0.05). Pearson analysis showed that there was a positive correlation between c-FLIP and FADD mRNA expression ( r =0.323, P <0.05), and negative correlation between c-FLIP and caspase-8 mRNA expression ( r= -1.104, P <0.05). The protein expression levels of c-FLIP and FADD in patients with middle activities were significantly higher than those in control group and patients with low or high activities ( P <0.05 or 0.01). The protein expression levels of caspase-8 in patients with middle and high activities were significantly higher than those in control group and patients with low activities ( P <0.05 or P <0.01), and the protein expression level of caspase-8 in patients with high activities was higher than that in patients with middle activities ( P <0.05)., Conclusions: c-FLIP may be involved in the extrinsic apoptotic pathway in rheumatoid arthritis, and can provide reference for the evaluation of disease activities.

Published
2018
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