331 Works

Additional file 29 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 29: Table S7. Characterization of Immune Infiltration in PDAC. Table S7A Matrix of xCell signatures significantly altered in 5 immune subgroups. Table S7B Matrix describing the expression of proteins in 5 immune subgroups. Table S7C Matrix of GSVA scores of pathways significantly altered in 5 immune subgroups, transcriptome level. Table S7D Matrix of amplification/deletion events of genes in 5 immune subgroups. Table S7E Matrix describing the expression of proteins involved in TCA cycle.

Additional file 30 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 30: Table S8. HOGA1 inactivation promotes pancreatic cancer growth through activating LARP7-CDK1 pathway. Table S8A Quantified western blot results of 12 pairs of samples. Table S8B Proliferation of PANC-1 and BxPC-3 cells associated with HOGA1 knocked down. Table S8C Proliferation of PANC-1 and BxPC-3 cells associated with HOGA1 overexpressed. Table S8D Proliferation of PANC-1 and BxPC-3 cells associated with metabolic enzyme treatment. Table S8E A list of 773 different proteins detected in PANC-1...

Additional file 30 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 30: Table S8. HOGA1 inactivation promotes pancreatic cancer growth through activating LARP7-CDK1 pathway. Table S8A Quantified western blot results of 12 pairs of samples. Table S8B Proliferation of PANC-1 and BxPC-3 cells associated with HOGA1 knocked down. Table S8C Proliferation of PANC-1 and BxPC-3 cells associated with HOGA1 overexpressed. Table S8D Proliferation of PANC-1 and BxPC-3 cells associated with metabolic enzyme treatment. Table S8E A list of 773 different proteins detected in PANC-1...

Angular rate results.xlsx

Ming Yang, Hanglei An, Sifan Mo, Huinan Gong, Bingbing Dong & Guanggui Chen
The measured angular rates by the SM and MV method.

Non-specific binding of compounds in in vitro metabolism assays: a comparison of microsomal and hepatocyte binding in different species and an assessment of the accuracy of prediction models

Iain Gardner, Mandy Xu, Chunyan Han, Yi Wang, Xingjin Jiao, Masoud Jamei, Hiba Khalidi, Peter Kilford, Sibylle Neuhoff, Roz Southall, David B. Turner, Helen Musther, Barry Jones & Simon Taylor
Non-specific binding in in vitro metabolism systems leads to an underestimation of the true intrinsic metabolic clearance of compounds being studied. Therefore in vitro binding needs to be accounted for when extrapolating in vitro data to predict the in vivo metabolic clearance of a compound. While techniques exist for experimentally determining the fraction of a compound unbound in in vitro metabolism systems, early in drug discovery programmes computational approaches are often used to estimate the...

Knockdown of lncRNA PCAT6 suppresses the growth of non-small cell lung cancer cells by inhibiting macrophages M2 polarization via miR-326/KLF1 axis

Yun Chen, Chaojin Hong, Jing Qu, Junjun Chen & Zhiquan Qin
Non-small cell lung cancer (NSCLC) is the most common malignant tumor of lung, which seriously threatens the life of people. It has been reported that lncRNA prostate cancer-associated transcript 6 (PCAT6) could facilitate the metastasis of NSCLC cells. However, whether lncRNA PCAT6 in NSCLC cells could affect the tumor microenvironment (TME) remains unclear. In the present study, the level of PCAT6 in NSCLC cells was detected using RT-qPCR. The effects of PCAT6 knockdown on the...

Additional file 2 of The long non-coding RNA lncMYOZ2 mediates an AHCY/MYOZ2 axis to promote adipogenic differentiation in porcine preadipocytes

Yang Yang, Yiqi Wu, Mengting Ji, Xiaoyin Rong, Yanwei Zhang, Shuai Yang, Chang Lu, Chunbo Cai, Pengfei Gao, Xiaohong Guo, Bugao Li & Guoqing Cao
Additional file 2.

Additional file 3 of The long non-coding RNA lncMYOZ2 mediates an AHCY/MYOZ2 axis to promote adipogenic differentiation in porcine preadipocytes

Yang Yang, Yiqi Wu, Mengting Ji, Xiaoyin Rong, Yanwei Zhang, Shuai Yang, Chang Lu, Chunbo Cai, Pengfei Gao, Xiaohong Guo, Bugao Li & Guoqing Cao
Additional file 3.

Additional file 3 of The long non-coding RNA lncMYOZ2 mediates an AHCY/MYOZ2 axis to promote adipogenic differentiation in porcine preadipocytes

Yang Yang, Yiqi Wu, Mengting Ji, Xiaoyin Rong, Yanwei Zhang, Shuai Yang, Chang Lu, Chunbo Cai, Pengfei Gao, Xiaohong Guo, Bugao Li & Guoqing Cao
Additional file 3.

Additional file 7 of Epitope vaccine design for Toxoplasma gondii based on a genome-wide database of membrane proteins

Xuan-Wu Li, Ni Zhang, Zhuo-Lin Li, Nouhoum Dibo, Zhen-Rong Ma, Bin Lu, Ye-Hong Huang, Yun-Feng Chang, Hong-Zhi Chen & Xiang Wu
Additional file 7. Initial predicted mouse MHC-II binding epitopes.

Additional file 7 of Epitope vaccine design for Toxoplasma gondii based on a genome-wide database of membrane proteins

Xuan-Wu Li, Ni Zhang, Zhuo-Lin Li, Nouhoum Dibo, Zhen-Rong Ma, Bin Lu, Ye-Hong Huang, Yun-Feng Chang, Hong-Zhi Chen & Xiang Wu
Additional file 7. Initial predicted mouse MHC-II binding epitopes.

Additional file 11 of Transcriptomic analysis of paternal behaviors in prairie voles

Florian Duclot, Yan Liu, Samantha K. Saland, Zuoxin Wang & Mohamed Kabbaj
Additional file 11. Summary statistics for the differential expression analysis. DE: differentially expressed. LS: lateral septum, MPOA: medial preoptic area, NAc: nucleus accumbens.

Additional file 1 of Morphological changes of TMJ disc in surgically treated ADDwoR patients: a retrospective study

Ruiyu Wang, Ruiye Bi, Yao Liu, Pinyin Cao, Bassam Abotaleb & Songsong Zhu
Additional file 1. Raw data of TMJ discs of ADDwoR patients.

Additional file 2 of Morphological changes of TMJ disc in surgically treated ADDwoR patients: a retrospective study

Ruiyu Wang, Ruiye Bi, Yao Liu, Pinyin Cao, Bassam Abotaleb & Songsong Zhu
Additional file 2. Raw data of TMJ discs following disc repositioning surgery.

Additional file 3 of Morphological changes of TMJ disc in surgically treated ADDwoR patients: a retrospective study

Ruiyu Wang, Ruiye Bi, Yao Liu, Pinyin Cao, Bassam Abotaleb & Songsong Zhu
Additional file 3. Stl files of TMJ discs in all patients.

Additional file 3 of Small molecule modulation of microbiota: a systems pharmacology perspective

Qiao Liu, Bohyun Lee & Lei Xie
Additional file 3. Table S2. Microbes with commensal effects on human health by manually literature review.

Additional file 4 of Small molecule modulation of microbiota: a systems pharmacology perspective

Qiao Liu, Bohyun Lee & Lei Xie
Additional file 4. Table S3. The Microbes with unknown effects in literature reviews and their SRWR inferred microbe effects.

Additional file 5 of Exosomal DNAJB11 promotes the development of pancreatic cancer by modulating the EGFR/MAPK pathway

Peng Liu, Fuqiang Zu, Hui Chen, Xiaoli Yin & Xiaodong Tan
Additional file 5: Table S5. The results of the Seahorse assay.

Additional file 6 of Exosomal DNAJB11 promotes the development of pancreatic cancer by modulating the EGFR/MAPK pathway

Peng Liu, Fuqiang Zu, Hui Chen, Xiaoli Yin & Xiaodong Tan
Additional file 6: Table S6. List of proteins identified in CoIP-based LC–MS/MS.

From Black Box to Shining Spotlight: Using Random Forest Prediction Intervals to Illuminate the Impact of Assumptions in Linear Regression

Andrew J. Sage, Yang Liu & Joe Sato
We introduce a pair of Shiny web applications that allow users to visualize random forest prediction intervals alongside those produced by linear regression models. The apps are designed to help undergraduate students deepen their understanding of the role that assumptions play in statistical modeling by comparing and contrasting intervals produced by regression models with those produced by more flexible algorithmic techniques. We describe the mechanics of each approach, illustrate the features of the apps, provide...

Additional file 2 of Proteomic alterations associated with residual disease in neoadjuvant chemotherapy treated ovarian cancer tissues

Emily R. Penick, Nicholas W. Bateman, Christine Rojas, Cuauhtemoc Magana, Kelly Conrads, Ming Zhou, Brian L. Hood, Guisong Wang, Niyati Parikh, Ying Huang, Kathleen M. Darcy, Yovanni Casablanca, Paulette Mhawech-Fauceglia, Thomas P. Conrads & G. Larry Maxwell
Additional file 2: Table S1. Proteins significantly altered between post versus pre-NACT tissues (LIMMA p-value<0.01). Table S2. Proteins significantly altered between R1 versus R0 patients in pre-NACT tissues (LIMMA p-value<0.05). Table S3. Significantly (LIMMA p<0.05) co-altered proteins between pre-NACT tumors from patients with any level of residual disease vs R0 patients from an independent ovarian cancer cohort (CPTAC 2016) that exhibit highly correlated abundance trends with the present ovarian cancer cohort. Table S4. Diseases and...

Additional file 2 of Circulating tumor DNA integrating tissue clonality detects minimal residual disease in resectable non-small-cell lung cancer

Siwei Wang, Ming Li, Jingyuan Zhang, Peng Xing, Min Wu, Fancheng Meng, Feng Jiang, Jie Wang, Hua Bao, Jianfeng Huang, Binhui Ren, Mingfeng Yu, Ninglei Qiu, Houhuai Li, Fangliang Yuan, Zhi Zhang, Hui Jia, Xinxin Lu, Shuai Zhang, Xiaojun Wang, Youtao Xu, Wenjia Xia, Tongyan Liu, Weizhang Xu, Xinyu Xu … & Rong Yin
Additional file 2. Table S2: Adjuvant treatment information.

Additional file 1 of Transcriptome analysis of MYB transcription factors family and PgMYB genes involved in salt stress resistance in Panax ginseng

Mingming Liu, Ke Li, Shichao Sheng, Mingyu Wang, Panpan Hua, Yanfang Wang, Ping Chen, Kangyu Wang, Mingzhu Zhao, Yi Wang & Meiping Zhang
Additional file 1: Table S1. Basic information of PgMYB gene family.

Additional file 1 of Transcriptome analysis of MYB transcription factors family and PgMYB genes involved in salt stress resistance in Panax ginseng

Mingming Liu, Ke Li, Shichao Sheng, Mingyu Wang, Panpan Hua, Yanfang Wang, Ping Chen, Kangyu Wang, Mingzhu Zhao, Yi Wang & Meiping Zhang
Additional file 1: Table S1. Basic information of PgMYB gene family.

Additional file 4 of Transcriptome analysis of MYB transcription factors family and PgMYB genes involved in salt stress resistance in Panax ginseng

Mingming Liu, Ke Li, Shichao Sheng, Mingyu Wang, Panpan Hua, Yanfang Wang, Ping Chen, Kangyu Wang, Mingzhu Zhao, Yi Wang & Meiping Zhang
Additional file 4: Table S4. The expressions of the PgMYB gene transcripts in 14 tissues, 42 cultivars’ roots and 4 aged roots (TPM).

Registration Year

  • 2022
    331

Resource Types

  • Dataset
    331

Affiliations

  • Second Xiangya Hospital of Central South University
    331
  • Chinese Academy of Sciences
    190
  • Capital Medical University
    182
  • Zhejiang University
    181
  • Peking University
    168
  • Chinese Academy of Medical Sciences & Peking Union Medical College
    167
  • Central South University
    163
  • Shanghai Jiao Tong University
    156
  • Huazhong University of Science and Technology
    136
  • Shandong University
    129