DRPPM: Data Wrangler
DRPPM is a library collection of scripts for analyzing DNA/RNA/Proteome/Post-translational Modifications. The program is capable of performing data wrangling of genomics, transcriptomics, and proteomics data. See https://github.com/gatechatl/DRPPM_Example_Input_Output for examples.
Projects that utilized the pipeline include:
Timothy I. Shaw*, Li Dong*, Liqing Tian, Chenxi Qian, Yu Liu, Bensheng Ju, Anthony High, Kanisha Kavdia, Vishwajeeth R. Pagala, Bridget Shaner, Deqing Pei, John Easton, Laura J. Janke, Shaina N. Porter, Xiaotu Ma, Cheng Cheng, Shondra M Pruett-Miller, John Choi, Jiyang Yu, Junmin Peng, Wei Gu, A. Thomas Look, James R Downing & Jinghui Zhang. Integrative Network Analysis Reveals USP7 Haploinsufficiency Inhibits E-protein Activity in Pediatric T-lineage Acute Lymphoblastic Leukemia (T-ALL). Scientific Reports. Accepted.
Joung Hyuck Joo*, Bo Wang*, Elisa Frankel, Liang Ge, Lu Xu, Rekha Iyengar, XiuJie Li-Harms, Christopher Wright, Timothy I. Shaw,Tullia Lindsten, Douglas R. Green, Junmin Peng, Linda M. Hendershot, Fusun Kilic, Ji Ying Sze, Anjon Audhya, Mondira Kundu#. The Noncanonical Role of ULK/ATG1 in ER-to-Golgi Trafficking Is Essential for Cellular Homeostasis. Mol Cell.2016 May 19;62(4):491-506. doi: 10.1016/j.molcel.2016.04.020.
Kyung-Ha Lee*, Peipei Zhang*, Hong Joo Kim*, Mohona Sarkar, Diana Mitrea, Brian Freibaum, Jaclyn Cika, MauraCoughlin, James Messing, Amandine Molliex, Brian Maxwell, Nam Chul Kim, Jamshid Temirov,Jennifer Moore, Timothy I. Shaw, Bing Bai, Junmin Peng, Richard Kriwacki, Paul J.Taylor#. C9orf72 dipeptide repeats impair the assembly, dynamics and function of membrane-lessorganelles. Cell. 2016 Oct 20;167(3):774-788.e17. doi: 10.1016/j.cell.2016.10.002
DRPPM: Immuno-Oncology Pipelines
To build on top of DRPPM, we have developed a series of pipelines for immune-oncology. These include 1) the analysis of immune signatures. 2) the analysis of TCR and BCRs. 3) identification of CAR targets. 4) identify immune modulators. Many functions were repurposed from the DRPPM package.
Example publications include:
Haiyan Tan*, Kai Yang*, Yuxin Li*, Timothy I. Shaw*, Yanyan Wang, Daniel Bastardo Blanco, Xusheng Wang, Ji-Hoon Cho, Hong Wang, Sherri Rankin, Cliff Guy, Junmin Peng#, Hongbo Chi#. Integrative Proteomics and Phosphoproteomics Profiling Reveals Dynamic Signaling Networks and Bioenergetics Pathways Underlying T Cell Activation. Immunity. 2017 Mar 21;46(3):488-503. doi: 10.1016/j.immuni.2017.02.010. https://www.sciencedirect.com/science/article/pii/S1074761317300729
Jessica Wagner, Elizabeth Wickman, Timothy I Shaw, Alejandro Allo Anido, Deanna Langfitt, Jinghui Zhang, Shaina N Porter, Shondra M Pruett-Miller, Heather Tillman, Giedre Krenciute, Stephen Gottschalk. Antitumor effects of CAR T cells redirected to the EDB splice variant of fibronectin.Cancer Immunol Res. 2020 Dec 22;. doi: 10.1158/2326-6066.CIR-20-0280.
Dalia Haydar, Haley Houke, Jason Chiang, Zhongzhen, Zelda Odé, Kenneth Caldwell, Xiaoyun Zhu, Kimberley S Mercer, Jennifer L Stripay, Timothy I Shaw, Peter Vogel, Christopher DeRenzo, Suzanne J Baker, Martine F Roussel, Stephen Gottschalk, Giedre Krenciute.Cell surface antigen profiling of pediatric brain tumors: B7-H3 is consistently expressed and can be targeted via local or systemic CAR T-cell delivery. Neuro-Oncol. 2020 Dec 15;. doi: 10.1093/neuonc/noaa278.
Shaw et al. Immune Signature of pediatric tumors. In Prep.
Shaw et al. CSI-Miner. In Prep.
DRPPM: Splicing Analysis
We have developed a number of algorithms to perform alternative splicing analysis. These analysis include 1) annotate novel exons and alternative start sites. 2) exon quantification. 3) quantifying splicing deficiency. In the future we plan to incorporate spliceQTL analysis.
Projects that utilized the pipeline include:
Gang Wu*, Liying Fan*, Michael N Edmondson, Timothy Shaw, Kristy Boggs, John Easton, Michael C Rusch, Thomas R Webb, Jinghui Zhang, Philip M Potter#. Inhibition of SF3B1 by molecules targeting the spliceosome results in massive aberrant exon skipping. RNA. 2018 May 29. pii: rna.065383.117. doi: 10.1261/rna.065383.117.
Yuxin Li, Xusheng Wang, Zhiping Wu, Bing Bai, Ji-Hoon Cho, Timothy I. Shaw, Hong Wang, Suiping Zhou, Thomas Beach, Gang Wu, Jinghui Zhang, Junmin Peng#. JUMPg: An Integrative Proteogenomics Pipeline Identifying Unannotated Proteins in Human Brain and Cancer Cells. J Proteome Res. 2016 Jul 1;15(7):2309-20. doi: 10.1021/acs.jproteome.6b00344.
Young Don Kwak, Timothy I. Shaw, Susanna M. Downing, Ambika Tewari, Aditi, Yang Li, Hongjian Jin, Sachin Katyal, Kamran Khodakhah, Helen R. Russell and Peter J. McKinnon. In revision.
Ping-Chung Chen*, Xian Han*, Timothy I. Shaw, Yun Jiao, Brett J. W. Teubner, DonnieEddins, Mingming Niu, Bing Bai, Joseph Mertz, Yuxin Li, Ji-Hoon Cho, XushengWang, Zhiping Wu, Ariana Mancieri, Laurie R. Earls, Elizabeth Stewart, Peter Vogel, Thomas G. Beach, Michael A. Dyer, Richard J. Smeyne, Stanislav S. Zakharenko, Gang Yu, and Junmin Peng. Under submission.
IKAP: Kinase Activity
We have adapted a machine learning algorithm to calculate gene activity. https://github.com/gatechatl/KinaseActivity
Examples of applying the algorithm:
Haiyan Tan*, Kai Yang*, Yuxin Li*, Timothy I. Shaw*, Yanyan Wang, Daniel Bastardo Blanco, Xusheng Wang, Ji-Hoon Cho, Hong Wang, Sherri Rankin, Cliff Guy, Junmin Peng#, Hongbo Chi#. Integrative Proteomics and Phosphoproteomics Profiling Reveals Dynamic Signaling Networks and Bioenergetics Pathways Underlying T Cell Activation. Immunity. 2017 Mar 21;46(3):488-503. doi: 10.1016/j.immuni.2017.02.010.
Hong Wang, Alexander K. Diaz, Timothy I. Shaw,Yuxin Li, Mingming Niu, Ji-Hoon Cho, Barbara S. Paugh, Yang Zhang, Jeffrey Sifford, Bing Bai, Zhiping Wu, Haiyan Tan, Suiping Zhou, Laura D. Hover, Heather S. Tillman, Abbas Shirinifard, Suresh Thiagarajan, Andras Sablauer, Vishwajeeth Pagala, Anthony A. High, Xusheng Wang, Chunliang Li, Suzanne J. Baker, Junmin Peng. Deep multiomics profiling of brain tumors identifies signaling networks downstream of cancer driver genes. Nature Communications. 2019 Aug 16. 10 (1), 3718. doi.org/10.1038/s41467-019-11661-4
Bing Bai, Xusheng Wang, Yuxin Li, Ping-Chung Chen, Kaiwen Yu, Kaushik Kumar Dey, Jay M. Yarbro, Xian Han, Brianna M. Lutz, Shuquan Rao, Yun Jiao, Jeffrey M. Sifford, Jonghee Han, Minghui Wang, Haiyan Tan, Timothy I. Shaw, Ji-Hoon Cho, Suiping Zhou, Hong Wang, Mingming Niu, Ariana Mancieri, Kaitlynn Messler, Xiaojun Sun, Zhiping Wu, Vishwajeeth Pagala, Anthony A. High, Wenjian Bi, Hui Zhang, Hongbo Chi, Vahram Haroutunian, Bin Zhang, Thomas G. Beach, Gang Yu and Junmin Peng. Deep Multilayer Brain Proteomics Identifies Molecular Networks in Alzheimer’s Disease Progression. Neuron. 2020 May 20;106(4):700. doi: 10.1016/j.neuron.2020.04.031
MASPECTOR: Metabolomics Library
We have developed a package for certain metabolomics associated analyses.
https://github.com/gatechatl/MaSpecTOR
Projects that utilized the pipeline include:
Xusheng Wang, Ji-Hoon Cho, Suresh Poudel, Yuxin Li, Drew R Jones, Timothy I Shaw, Haiyan Tan, Boer Xie, Junmin Peng. JUMPm: A Tool for Large-Scale Identification of Metabolites in Untargeted Metabolomics. Metabolites. 2020 May 12;10(5):190. doi: 10.3390/metabo10050190.
Boer Xie*, Yuanyuan Wang*, Drew R. Jones*, Kaushik Kumar Dey, Xusheng Wang, Yuxin Li, Ji-Hoon Cho, Timothy I Shaw, Haiyan Tan, and Junmin Peng#. Isotope Labeling-assisted Evaluation of Hydrophilic and Hydrophobic Liquid Chromatograph-Mass Spectrometry for Metabolomics Profiling. Anal Chem. 2018 Jun 8. doi: 10.1021/acs.analchem.8b01591
Xusheng Wang*, Drew R Jones*, Timothy I Shaw, Ji-Hoon Cho, Yuanyuan Wang, Haiyan Tan, Boer Xie, Suiping Zhou, Yuxin Li, Junmin Peng#. Target-decoy Based False Discovery Rate Estimation for Large-scale Metabolite Identification. Journal of proteome research.2018 May 23. 10.1021/acs.jproteome.8b00019.