bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Data from The Cytochrome P450 Slow Metabolizers CYP2C9*2 and CYP2C9*3 Directly Regulate Tumorigenesis via Reduced Epoxyeicosatrienoic Acid Production
Authors: Sausville Lindsay N. , Gangadhariah Mahesha H. , Chiusa Manuel , Mei Shaojun , Wei Shouzuo , Zent Roy , Luther James M. , Shuey Megan M. , Capdevila Jorge H. , Falck John R. , Guengerich F. Peter , Williams Scott M. , Pozzi Ambra
Published: April 2023

This file contains the primer sequence of CYP2C9* variants (Supplementary Table S1); the SNPs genotyped in the BioVU NSCLC study (Supplementary Table S2); quality control measures of SNPs in the BioVU NSCLC study (Supplementary Table S3); clinical and demographic description of NSCLC cases (Supplementary Table S4); the association of clinical and demographic variables with survival (Supplementary Table S5); the genotypes in the NSCLC cases (Supplementary Table S6); the spectra of CYP2C9* variants and the effect of arachidonic acid on CYP2C9* variant (Supplementary Figure S1); the association between CYP2C9* variants and platinum chemotherapy (Supplementary Figure S2).
Supplementary Fig 3 from FGFR1 Is Critical for RBL2 Loss–Driven Tumor Development and Requires PLCG1 Activation for Continued Growth of Small Cell Lung Cancer
Authors: Kim Kee-Beom , Kim Youngchul , Rivard Christopher J. , Kim Dong-Wook , Park Kwon-Sik
Published: April 2023

H&E staining and immunostaining for pHH3 (phospho-histone H3) on sections of subcutaneous tumors generated from control or Ad-Cre-infected Fgfr1D/lox Rb1/Trp53/Rbl2 SCLC cells. DAPI (blue) stains nuclei. Scale bars: 50 µm.
Supplementary Data Tables S1-S15 from State-Transition Analysis of Time-Sequential Gene Expression Identifies Critical Points That Predict Development of Acute Myeloid Leukemia
Authors: Rockne Russell C. , Branciamore Sergio , Qi Jing , Frankhouser David E. , O'Meally Denis , Hua Wei-Kai , Cook Guerry , Carnahan Emily , Zhang Lianjun , Marom Ayelet , Wu Herman , Maestrini Davide , Wu Xiwei , Yuan Yate-Ching , Liu Zheng , Wang Leo D. , Forman Stephen , Carlesso Nadia , Kuo Ya-Huei , Marcucci Guido
Published: April 2023

Table S1. Differentially expressed genes for c_1 vs c_1^* Table S2. Differentially expressed genes for c_2 vs c_1^* Table S3. Differentially expressed genes for c_3 vs c_1^* Table S4. Differentially expressed genes for c_2 vs c_1 Table S5. Differentially expressed genes for c_3 vs c_1 Table S6. Differentially expressed genes for c_3 vs c_2 Tables S7-S10. Differentially expressed genes for early, transition, persistent, and leukemia events. Tables S11-S14. GO terms enriched for early, transition, persistent, and leukemia events. Table S15. Top 1% of eigengenes.
Supplementary Data 2 from FGFR1 Is Critical for RBL2 Loss–Driven Tumor Development and Requires PLCG1 Activation for Continued Growth of Small Cell Lung Cancer
Authors: Kim Kee-Beom , Kim Youngchul , Rivard Christopher J. , Kim Dong-Wook , Park Kwon-Sik
Published: April 2023

Result of GO-term analysis for differentially expressed genes between control and FGFR1-expressing preSC
Supplementary Figure S4 from Replication Stress Drives Constitutive Activation of the DNA Damage Response and Radioresistance in Glioblastoma Stem-like Cells
Authors: Carruthers Ross D. , Ahmed Shafiq U. , Ramachandran Shaliny , Strathdee Karen , Kurian Kathreena M. , Hedley Ann , Gomez-Roman Natividad , Kalna Gabriela , Neilson Mathew , Gilmour Lesley , Stevenson Katrina H. , Hammond Ester M. , Chalmers Anthony J.
Published: April 2023

Supplementary Figure S4 shows additional images of immunofluorescent staining in GBM intracranial xenografts.
Supplementary Data and Tables from Cell Adhesiveness Serves as a Biophysical Marker for Metastatic Potential
Authors: Beri Pranjali , Popravko Anna , Yeoman Benjamin , Kumar Aditya , Chen Kevin , Hodzic Enio , Chiang Alyssa , Banisadr Afsheen , Placone Jesse K. , Carter Hannah , Fraley Stephanie I. , Katira Parag , Engler Adam J.
Published: April 2023

Complete Supplemental Figures 1-8 and Supplemental Tables 1-2 are embedded in this file. Each item contains its respective legend.
Supplementary Figure S2 from Replication Stress Drives Constitutive Activation of the DNA Damage Response and Radioresistance in Glioblastoma Stem-like Cells
Authors: Carruthers Ross D. , Ahmed Shafiq U. , Ramachandran Shaliny , Strathdee Karen , Kurian Kathreena M. , Hedley Ann , Gomez-Roman Natividad , Kalna Gabriela , Neilson Mathew , Gilmour Lesley , Stevenson Katrina H. , Hammond Ester M. , Chalmers Anthony J.
Published: April 2023

Supplementary Figure S2 shows additional data obtained during aphidicolin studies detailed in Fig 1 and additional data detailing expression of genes associated with ongoing and stalled replication forks from figure 3.
Supplementary Figure S1 from Replication Stress Drives Constitutive Activation of the DNA Damage Response and Radioresistance in Glioblastoma Stem-like Cells
Authors: Carruthers Ross D. , Ahmed Shafiq U. , Ramachandran Shaliny , Strathdee Karen , Kurian Kathreena M. , Hedley Ann , Gomez-Roman Natividad , Kalna Gabriela , Neilson Mathew , Gilmour Lesley , Stevenson Katrina H. , Hammond Ester M. , Chalmers Anthony J.
Published: April 2023

Supplementary figure S1 displays examples of flow cytometry gating for FACS sorted cell populations, abrogation of Chk1 phosphorylation by VE-821 in GSC and patterns of γ-H2AX staining produced by replication stress.
Supplemental tables 1, 2 and 3 from Replication Stress Drives Constitutive Activation of the DNA Damage Response and Radioresistance in Glioblastoma Stem-like Cells
Authors: Carruthers Ross D. , Ahmed Shafiq U. , Ramachandran Shaliny , Strathdee Karen , Kurian Kathreena M. , Hedley Ann , Gomez-Roman Natividad , Kalna Gabriela , Neilson Mathew , Gilmour Lesley , Stevenson Katrina H. , Hammond Ester M. , Chalmers Anthony J.
Published: April 2023

Supplemental Table 1 Summary table of in vivo growth characteristics of E2, G7, R10, R15, R24, R9 and S2 GSC primary GBM cultures after intracranial injection in CD1 nude mice. Supplemental Table 2 List of primary antibodies utilised Supplemental Table 3 List of secondary antibodies utilised
Supplementary Table 1 from Oncogenic ERG Represses PI3K Signaling through Downregulation of IRS2
Authors: Mao Ninghui , Gao Dong , Hu Wenhuo , Gadal Sunyana , Hieronymus Haley , Wang Shangqian , Lee Young Sun , Sullivan Patrick , Zhang Zeda , Choi Danielle , Rosen Neal , Sawyers Charles L. , Gopalan Anuradha , Chen Yu , Carver Brett S.
Published: April 2023

List of most significantly differentially expressed genes following ERG knock-out.
Supplementary Figures from Oncogenic ERG Represses PI3K Signaling through Downregulation of IRS2
Authors: Mao Ninghui , Gao Dong , Hu Wenhuo , Gadal Sunyana , Hieronymus Haley , Wang Shangqian , Lee Young Sun , Sullivan Patrick , Zhang Zeda , Choi Danielle , Rosen Neal , Sawyers Charles L. , Gopalan Anuradha , Chen Yu , Carver Brett S.
Published: April 2023

The supplementary figures provide additional data demonstrating that ERG represses RTK-PI3K signaling through direct transcriptional repression of IRS2 across multiple model systems. Additional data is provided showing the biologic role of ERG and PI3K signaling in promoting cell proliferation and migration.
Supplementary Data from ERINA Is an Estrogen-Responsive LncRNA That Drives Breast Cancer through the E2F1/RB1 Pathway
Authors: Fang Zihui , Wang Yue , Wang Zehua , Xu Meishu , Ren Songrong , Yang Da , Hong Mei , Xie Wen
Published: April 2023

Supplemental Methods
Supplementary Tables from Comprehensive Analysis of Radiomic Datasets by RadAR
Authors: Benelli Matteo , Barucci Andrea , Zoppetti Nicola , Calusi Silvia , Redapi Laura , Della Gala Giuseppe , Piffer Stefano , Bernardi Luca , Fusi Franco , Pallotta Stefania
Published: April 2023

Supplementary Tables 1-2. STable 1: Table of the results of differential radiomic analysis between dead and alive patients from the Lung1 dataset (Aerts et al., 2014). STable 2: Table of the results of differential radiomic analysis across different disease stages for patients from the Lung1 dataset (Aerts et al., 2014).
Quick guide to model assumptions from Pharmacokinetic Profiles Determine Optimal Combination Treatment Schedules in Computational Models of Drug Resistance
Authors: Irurzun-Arana Itziar , McDonald Thomas O. , Trocóniz Iñaki F. , Michor Franziska
Published: April 2023

Quick guide to model assumptions
Supplementary Table S2 from Genetic Variants Implicate Dual Oxidase-2 in Familial and Sporadic Nonmedullary Thyroid Cancer
Authors: Bann Darrin V. , Jin Qunyan , Sheldon Kathryn E. , Houser Kenneth R. , Nguyen Lan , Warrick Joshua I. , Baker Maria J. , Broach James R. , Gerhard Glenn S. , Goldenberg David
Published: April 2023

Supplemental Table 2. Hereditary cancer syndromes associated with increased non-medullary thyroid cancer risk
Supplementary Table S1 from Genetic Variants Implicate Dual Oxidase-2 in Familial and Sporadic Nonmedullary Thyroid Cancer
Authors: Bann Darrin V. , Jin Qunyan , Sheldon Kathryn E. , Houser Kenneth R. , Nguyen Lan , Warrick Joshua I. , Baker Maria J. , Broach James R. , Gerhard Glenn S. , Goldenberg David
Published: April 2023

Supplemental Table 1. PCR and sequencing primers
Figure S2 from Microenvironmental Cues Determine Tumor Cell Susceptibility to Neutrophil Cytotoxicity
Authors: Gershkovitz Maya , Fainsod-Levi Tanya , Khawaled Saleh , Shaul Merav E. , Sionov Ronit V. , Cohen-Daniel Leonor , Aqeilan Rami I. , Shaul Yoav D. , Fridlender Zvi G. , Granot Zvi
Published: April 2023

Supplemental Figure S2. Circulating tumor cells express higher levels of TRPM2 compared with primary tumor cells in pancreatic cancer patients. A. Transcriptome analysis of mesenchymal genes, epithelial genes and TRPM2 on primary 4T1 tumor cells and circulating 4T1 tumor cells. The analysis was performed on dataset (GSE37244) published by LeBlue et al. (28). B. Microarray study for gene expression (GSE18670) changes in 6 samples from pancreatic cancer primary tumor (Primary) and circulating tumor cells (CTC) was described previously by Sergeant at al. (29). Here the same dataset was reanalyzed for the log2 expression ratio of TRMP2 in these samples. Data show TRPM2 expression in primary tumor cells (blue) and CTC (Red). *p<0.05 (2-tailed paired t-test).
Figure S1 from Microenvironmental Cues Determine Tumor Cell Susceptibility to Neutrophil Cytotoxicity
Authors: Gershkovitz Maya , Fainsod-Levi Tanya , Khawaled Saleh , Shaul Merav E. , Sionov Ronit V. , Cohen-Daniel Leonor , Aqeilan Rami I. , Shaul Yoav D. , Fridlender Zvi G. , Granot Zvi
Published: April 2023

Supplemental Figure S1. Neutrophils in the premetastatic lung outnumber and interact with disseminated tumor cells. Ly6G immunohistochemistry of metastases-laden lungs from 28 day 4T1 tumor-bearing mouse. Insets are high power magnification.
Video S6 from ΔNp63-Regulated Epithelial-to-Mesenchymal Transition State Heterogeneity Confers a Leader–Follower Relationship That Drives Collective Invasion
Authors: Westcott Jill M. , Camacho Sharon , Nasir Apsra , Huysman Molly E. , Rahhal Raneen , Dang Tuyen T. , Riegel Anna T. , Brekken Rolf A. , Pearson Gray W.
Published: April 2023

Live imaging of the inset region of clustered spheroids containing SUM159O cells expressing control or a p63 shRNA (H2B:mCherry, red, nuclei) showing cell motility.
Supplementary Data from Genomic Predictors of Good Outcome, Recurrence, or Progression in High-Grade T1 Non–Muscle-Invasive Bladder Cancer
Authors: Bellmunt Joaquim , Kim Jaegil , Reardon Brendan , Perera-Bel Júlia , Orsola Anna , Rodriguez-Vida Alejo , Wankowicz Stephanie A. , Bowden Michaela , Barletta Justine A. , Morote Juan , de Torres Inés , Juanpere Nuria , Lloreta-Trull Josep , Hernandez Silvia , Mouw Kent W. , Taplin Mary-Ellen , Cejas Paloma , Long Henry W. , Van Allen Eliezer M. , Getz Gad , Kwiatkowski David J.
Published: April 2023

Supplementary figures, tables, material & methods and results
Video S5 from ΔNp63-Regulated Epithelial-to-Mesenchymal Transition State Heterogeneity Confers a Leader–Follower Relationship That Drives Collective Invasion
Authors: Westcott Jill M. , Camacho Sharon , Nasir Apsra , Huysman Molly E. , Rahhal Raneen , Dang Tuyen T. , Riegel Anna T. , Brekken Rolf A. , Pearson Gray W.
Published: April 2023

Live imaging of clustered spheroids containing SUM159O cells expressing control or a p63 shRNA (H2B:mCherry, red, nuclei) showing cell motility.
Supplementary Figures from Gain of HIF1 Activity and Loss of miRNA let-7d Promote Breast Cancer Metastasis to the Brain via the PDGF/PDGFR Axis
Authors: Wyss Christof B. , Duffey Nathalie , Peyvandi Sanam , Barras David , Martinez Usatorre Amaïa , Coquoz Oriana , Romero Pedro , Delorenzi Mauro , Lorusso Girieca , Rüegg Curzio
Published: April 2023

This file contains 6 supplementary figures and figure legends.
Video S2 from ΔNp63-Regulated Epithelial-to-Mesenchymal Transition State Heterogeneity Confers a Leader–Follower Relationship That Drives Collective Invasion
Authors: Westcott Jill M. , Camacho Sharon , Nasir Apsra , Huysman Molly E. , Rahhal Raneen , Dang Tuyen T. , Riegel Anna T. , Brekken Rolf A. , Pearson Gray W.
Published: April 2023

Live imaging of the inset region of clustered spheroids containing SUM159T-dox:Î"Np63 cells {plus minus} doxycycline (H2B:GFP, green, nuclei) showing cell motility.
Supplementary Data from ΔNp63-Regulated Epithelial-to-Mesenchymal Transition State Heterogeneity Confers a Leader–Follower Relationship That Drives Collective Invasion
Authors: Westcott Jill M. , Camacho Sharon , Nasir Apsra , Huysman Molly E. , Rahhal Raneen , Dang Tuyen T. , Riegel Anna T. , Brekken Rolf A. , Pearson Gray W.
Published: April 2023

Supplemental Figures S1-S5 and Supplemental Legends
Supplementary Data from The Alternative Splicing Factor, MBNL1, Inhibits Glioblastoma Tumor Initiation and Progression by Reducing Hypoxia-Induced Stemness
Authors: Voss Dillon M. , Sloan Anthony , Spina Raffaella , Ames Heather M. , Bar Eli E.
Published: April 2023

Supplementary Figures 1-8 S1. MBNL1 expression in Glioblastoma by subtype S2. MBNL1 target gene splicing S3. MBNL1 expression in cultured GSCs S4. MBNL1 activity is monitored with RG6 splicing reporter minigene S5. Effect of induced MBNL1 expression on GSC proliferation S6. Self-renewal assays in 622 and 08-387 neurospheres S7. Self-renewal assays in 913-luciferase neurospheres S8. Survival analysis for RTTA control cells
Supplemental Table ST5 from Linking Transcriptomic and Imaging Data Defines Features of a Favorable Tumor Immune Microenvironment and Identifies a Combination Biomarker for Primary Melanoma
Authors: Gartrell-Corrado Robyn D. , Chen Andrew X. , Rizk Emanuelle M. , Marks Douglas K. , Bogardus Margaret H. , Hart Thomas D. , Silverman Andrew M. , Bayan Claire-Audrey Y. , Finkel Grace G. , Barker Luke W. , Komatsubara Kimberly M. , Carvajal Richard D. , Horst Basil A. , Chang Rui , Monod Anthea , Rabadan Raul , Saenger Yvonne M.
Published: April 2023

Univariable Cox regression analysis.
Supplemental Table ST4 from Linking Transcriptomic and Imaging Data Defines Features of a Favorable Tumor Immune Microenvironment and Identifies a Combination Biomarker for Primary Melanoma
Authors: Gartrell-Corrado Robyn D. , Chen Andrew X. , Rizk Emanuelle M. , Marks Douglas K. , Bogardus Margaret H. , Hart Thomas D. , Silverman Andrew M. , Bayan Claire-Audrey Y. , Finkel Grace G. , Barker Luke W. , Komatsubara Kimberly M. , Carvajal Richard D. , Horst Basil A. , Chang Rui , Monod Anthea , Rabadan Raul , Saenger Yvonne M.
Published: April 2023

Survival statistics for MIP, CD8/CD68, and Combination biomarkers in 53-patient Combination cohort.
Supplemental Table ST3 from Linking Transcriptomic and Imaging Data Defines Features of a Favorable Tumor Immune Microenvironment and Identifies a Combination Biomarker for Primary Melanoma
Authors: Gartrell-Corrado Robyn D. , Chen Andrew X. , Rizk Emanuelle M. , Marks Douglas K. , Bogardus Margaret H. , Hart Thomas D. , Silverman Andrew M. , Bayan Claire-Audrey Y. , Finkel Grace G. , Barker Luke W. , Komatsubara Kimberly M. , Carvajal Richard D. , Horst Basil A. , Chang Rui , Monod Anthea , Rabadan Raul , Saenger Yvonne M.
Published: April 2023

Patient characteristics of the DSP cohort.
Supplementary Figures and Legends from Functional Precision Medicine Identifies New Therapeutic Candidates for Medulloblastoma
Authors: Rusert Jessica M. , Juarez Edwin F. , Brabetz Sebastian , Jensen James , Garancher Alexandra , Chau Lianne Q. , Tacheva-Grigorova Silvia K. , Wahab Sameerah , Udaka Yoko T. , Finlay Darren , Seker-Cin Huriye , Reardon Brendan , Gröbner Susanne , Serrano Jonathan , Ecker Jonas , Qi Lin , Kogiso Mari , Du Yuchen , Baxter Patricia A. , Henderson Jacob J. , Berens Michael E. , Vuori Kristiina , Milde Till , Cho Yoon-Jae , Li Xiao-Nan , Olson James M. , Reyes Iris , Snuderl Matija , Wong Terence C. , Dimmock David P. , Nahas Shareef A. , Malicki Denise , Crawford John R. , Levy Michael L. , Van Allen Eliezer M. , Pfister Stefan M. , Tamayo Pablo , Kool Marcel , Mesirov Jill P. , Wechsler-Reya Robert J.
Published: April 2023

Supplementary Figures 1-5
Figure S2 from Normal Breast-Derived Epithelial Cells with Luminal and Intrinsic Subtype-Enriched Gene Expression Document Interindividual Differences in Their Differentiation Cascade
Authors: Kumar Brijesh , Prasad Mayuri , Bhat-Nakshatri Poornima , Anjanappa Manjushree , Kalra Maitri , Marino Natascia , Storniolo Anna Maria , Rao Xi , Liu Sheng , Wan Jun , Liu Yunlong , Nakshatri Harikrishna
Published: April 2023

CD201/EpCAM and CD271/EpCAM staining pattern of KTB cell lines
Supplementary Data from A Genetic Vaccine Encoding Shared Cancer Neoantigens to Treat Tumors with Microsatellite Instability
Authors: Leoni Guido , D'Alise Anna Morena , Cotugno Gabriella , Langone Francesca , Garzia Irene , De Lucia Maria , Fichera Imma , Vitale Rosa , Bignone Veronica , Tucci Fabio Giovanni , Mori Federica , Leuzzi Adriano , Di Matteo Elena , Troise Fulvia , Abbate Adele , Merone Rossella , Ruzza Valentino , Diodoro Maria Grazia , Yadav Mahesh , Gordon-Alonso Monica , Vanhaver Cristophe , Panigada Maddalena , Soprana Elisa , Siccardi Antonio , Folgori Antonella , Colloca Stefano , van der Bruggen Pierre , Nicosia Alfredo , Lahm Armin , Catanese Maria Teresa , Scarselli Elisa
Published: April 2023

Fig. S1: Number of immunogenic epitopes in healthy donors vaccinated with viral antigens. Fig. S2: Size distribution of FSPs in Nous-209. Fig. S3: Detection of Nous-209 FSMs in early and late stage MSI tumors. Fig.S4: Mutation allele frequency of Nous-209 FSMs detected in tumor and healthy mucosa of 20 CRC MSI patients. Fig. S5: Schematic of Nous-209 vaccine. Fig. S6: Overview of the procedure to isolate T cells recognizing peptide Ly4_24.
Supplementary Data from The Synthetic Small Molecule FL3 Combats Intestinal Tumorigenesis via Axin1-Mediated Inhibition of Wnt/β-Catenin Signaling
Authors: Jackson Dakota N. , Alula Kibrom M. , Delgado-Deida Yaritza , Tabti Redouane , Turner Kevin , Wang Xuan , Venuprasad K. , Souza Rhonda F. , Désaubry Laurent , Theiss Arianne L.
Published: April 2023

FL3 induces death of established colonic tumoroids derived from mice.
Figure S7 from Chemotherapy-Induced Upregulation of Small Extracellular Vesicle-Associated PTX3 Accelerates Breast Cancer Metastasis
Authors: Wills Carson A. , Liu Xiaoming , Chen Longgui , Zhao Yuanjun , Dower Christopher M. , Sundstrom Jeffrey , Wang Hong-Gang
Published: April 2023

Inhibition of small extracellular vesicle uptake and secretion does not affect breast cancer migration in vitro or primary tumor growth in vivo.
Figure S5 from Chemotherapy-Induced Upregulation of Small Extracellular Vesicle-Associated PTX3 Accelerates Breast Cancer Metastasis
Authors: Wills Carson A. , Liu Xiaoming , Chen Longgui , Zhao Yuanjun , Dower Christopher M. , Sundstrom Jeffrey , Wang Hong-Gang
Published: April 2023

Small extracellular vesicles derived from MDA-MB-468 DXR-treated cells prime the pre-metastatic niche.
Figure S4 from Chemotherapy-Induced Upregulation of Small Extracellular Vesicle-Associated PTX3 Accelerates Breast Cancer Metastasis
Authors: Wills Carson A. , Liu Xiaoming , Chen Longgui , Zhao Yuanjun , Dower Christopher M. , Sundstrom Jeffrey , Wang Hong-Gang
Published: April 2023

Breast cancer-derived small extracellular vesicles primarily localize to the lungs and liver in vivo.
Table S4 from 3D Functional Genomics Screens Identify CREBBP as a Targetable Driver in Aggressive Triple-Negative Breast Cancer
Authors: Peck Barrie , Bland Philip , Mavrommati Ioanna , Muirhead Gareth , Cottom Hannah , Wai Patty T. , Maguire Sarah L. , Barker Holly E. , Morrison Eamonn , Kriplani Divya , Yu Lu , Gibson Amy , Falgari Giulia , Brennan Keith , Farnie Gillian , Buus Richard , Marlow Rebecca , Novo Daniela , Knight Eleanor , Guppy Naomi , Kolarevic Daniela , Susnjar Snezana , Milijic Natasa Medic , Naidoo Kalnisha , Gazinska Patrycja , Roxanis Ioannis , Pancholi Sunil , Martin Lesley-Ann , Holgersen Erle M. , Cheang Maggie C.U. , Noor Farzana , Postel-Vinay Sophie , Quinn Gerard , McDade Simon , Krasny Lukas , Huang Paul , Daley Frances , Wallberg Fredrik , Choudhary Jyoti S. , Haider Syed , Tutt Andrew N. , Natrajan Rachael
Published: April 2023

Phosphorylated, acetylated peptides and total proteins identified in HAP1 CREBBP WT and mutant spheroids.
Table S1 from 3D Functional Genomics Screens Identify CREBBP as a Targetable Driver in Aggressive Triple-Negative Breast Cancer
Authors: Peck Barrie , Bland Philip , Mavrommati Ioanna , Muirhead Gareth , Cottom Hannah , Wai Patty T. , Maguire Sarah L. , Barker Holly E. , Morrison Eamonn , Kriplani Divya , Yu Lu , Gibson Amy , Falgari Giulia , Brennan Keith , Farnie Gillian , Buus Richard , Marlow Rebecca , Novo Daniela , Knight Eleanor , Guppy Naomi , Kolarevic Daniela , Susnjar Snezana , Milijic Natasa Medic , Naidoo Kalnisha , Gazinska Patrycja , Roxanis Ioannis , Pancholi Sunil , Martin Lesley-Ann , Holgersen Erle M. , Cheang Maggie C.U. , Noor Farzana , Postel-Vinay Sophie , Quinn Gerard , McDade Simon , Krasny Lukas , Huang Paul , Daley Frances , Wallberg Fredrik , Choudhary Jyoti S. , Haider Syed , Tutt Andrew N. , Natrajan Rachael
Published: April 2023

Gene list for the spheroid screen
Supplementary Data from Radiomic Detection of EGFR Mutations in NSCLC
Authors: Rossi Giovanni , Barabino Emanuele , Fedeli Alessandro , Ficarra Gianluca , Coco Simona , Russo Alessandro , Adamo Vincenzo , Buemi Francesco , Zullo Lodovica , Dono Mariella , De Luca Giuseppa , Longo Luca , Dal Bello Maria Giovanna , Tagliamento Marco , Alama Angela , Cittadini Giuseppe , Pronzato Paolo , Genova Carlo
Published: April 2023

Matlab Algorhitm plus raw data
Supplementary Table 1 from Hormonal Regulation of Semaphorin 7a in ER+ Breast Cancer Drives Therapeutic Resistance
Authors: Crump Lyndsey S. , Wyatt Garhett L. , Rutherford Taylor R. , Richer Jennifer K. , Porter Weston W. , Lyons Traci R.
Published: April 2023

Antibodies used for Western blots and IHC
Supplementary Figure 5 from Hormonal Regulation of Semaphorin 7a in ER+ Breast Cancer Drives Therapeutic Resistance
Authors: Crump Lyndsey S. , Wyatt Garhett L. , Rutherford Taylor R. , Richer Jennifer K. , Porter Weston W. , Lyons Traci R.
Published: April 2023

Generation of fulvestrant resistant cells and gating strategy for flow cytometry analysis
Table S8 from SCIRT lncRNA Restrains Tumorigenesis by Opposing Transcriptional Programs of Tumor-Initiating Cells
Authors: Zagorac Sladjana , de Giorgio Alex , Dabrowska Aleksandra , Kalisz Mark , Casas-Vila Nuria , Cathcart Paul , Yiu Angela , Ottaviani Silvia , Degani Neta , Lombardo Ylenia , Tweedie Alistair , Nissan Tracy , Vance Keith W. , Ulitsky Igor , Stebbing Justin , Castellano Leandro
Published: April 2023

Sequence of primers used in the study
Supplementary Figure 4 from Hormonal Regulation of Semaphorin 7a in ER+ Breast Cancer Drives Therapeutic Resistance
Authors: Crump Lyndsey S. , Wyatt Garhett L. , Rutherford Taylor R. , Richer Jennifer K. , Porter Weston W. , Lyons Traci R.
Published: April 2023

Response of SEMA7A OE cells/tumors to targeted therapies
Supplementary Figure 2 from Hormonal Regulation of Semaphorin 7a in ER+ Breast Cancer Drives Therapeutic Resistance
Authors: Crump Lyndsey S. , Wyatt Garhett L. , Rutherford Taylor R. , Richer Jennifer K. , Porter Weston W. , Lyons Traci R.
Published: April 2023

Identification of drug concentrations for in vitro analyses
Table S4 from SCIRT lncRNA Restrains Tumorigenesis by Opposing Transcriptional Programs of Tumor-Initiating Cells
Authors: Zagorac Sladjana , de Giorgio Alex , Dabrowska Aleksandra , Kalisz Mark , Casas-Vila Nuria , Cathcart Paul , Yiu Angela , Ottaviani Silvia , Degani Neta , Lombardo Ylenia , Tweedie Alistair , Nissan Tracy , Vance Keith W. , Ulitsky Igor , Stebbing Justin , Castellano Leandro
Published: April 2023

Significant CHART-seq SCIRT peaks identified using HOMER
Supplementary Figure 1 from Unraveling the Mysteries of PAX8 in Reproductive Tract Cancers
Authors: Chaves-Moreira Daniele , Morin Patrice J. , Drapkin Ronny
Published: April 2023

Supplementary Figure 1 from Unraveling the Mysteries of PAX8 in Reproductive Tract Cancers
Supplementary Tables from “3G” Trial: An RNA Editing Signature to Guide Gastric Cancer Chemotherapy
Authors: An Omer , Song Yangyang , Ke Xinyu , So Jimmy Bok-Yan , Sundar Raghav , Yang Henry , Rha Sun Young , Lee Ming Hui , Tay Su Ting , Ong Xuewen , Tan Angie Lay Keng , Ng Matthew Chau Hsien , Tantoso Erwin , Chen Leilei , Tan Patrick , Yong Wei Peng
Published: April 2023

Supplementary Tables S1-S5
Supplementary Online Methods from Altered Mitochondria Functionality Defines a Metastatic Cell State in Lung Cancer and Creates an Exploitable Vulnerability
Authors: Chuang Chen-Hua , Dorsch Madeleine , Dujardin Philip , Silas Sukrit , Ueffing Kristina , Hölken Johanna M. , Yang Dian , Winslow Monte M. , Grüner Barbara M.
Published: April 2023

Extended online methods
Supplementary Information from “3G” Trial: An RNA Editing Signature to Guide Gastric Cancer Chemotherapy
Authors: An Omer , Song Yangyang , Ke Xinyu , So Jimmy Bok-Yan , Sundar Raghav , Yang Henry , Rha Sun Young , Lee Ming Hui , Tay Su Ting , Ong Xuewen , Tan Angie Lay Keng , Ng Matthew Chau Hsien , Tantoso Erwin , Chen Leilei , Tan Patrick , Yong Wei Peng
Published: April 2023

Legends for Supplementary Figures and Tables
Supplementary Figure 6 from “3G” Trial: An RNA Editing Signature to Guide Gastric Cancer Chemotherapy
Authors: An Omer , Song Yangyang , Ke Xinyu , So Jimmy Bok-Yan , Sundar Raghav , Yang Henry , Rha Sun Young , Lee Ming Hui , Tay Su Ting , Ong Xuewen , Tan Angie Lay Keng , Ng Matthew Chau Hsien , Tantoso Erwin , Chen Leilei , Tan Patrick , Yong Wei Peng
Published: April 2023

Supplementary Figure 6
Supplementary Data Tables S3,S4,S5,S6 from Altered Mitochondria Functionality Defines a Metastatic Cell State in Lung Cancer and Creates an Exploitable Vulnerability
Authors: Chuang Chen-Hua , Dorsch Madeleine , Dujardin Philip , Silas Sukrit , Ueffing Kristina , Hölken Johanna M. , Yang Dian , Winslow Monte M. , Grüner Barbara M.
Published: April 2023

Supplementary Data Tables S3,S4,S5,S6
Supplementary Data Table S9 from Altered Mitochondria Functionality Defines a Metastatic Cell State in Lung Cancer and Creates an Exploitable Vulnerability
Authors: Chuang Chen-Hua , Dorsch Madeleine , Dujardin Philip , Silas Sukrit , Ueffing Kristina , Hölken Johanna M. , Yang Dian , Winslow Monte M. , Grüner Barbara M.
Published: April 2023

Supplementary Data Table S9
Supplementary Figure 2 from “3G” Trial: An RNA Editing Signature to Guide Gastric Cancer Chemotherapy
Authors: An Omer , Song Yangyang , Ke Xinyu , So Jimmy Bok-Yan , Sundar Raghav , Yang Henry , Rha Sun Young , Lee Ming Hui , Tay Su Ting , Ong Xuewen , Tan Angie Lay Keng , Ng Matthew Chau Hsien , Tantoso Erwin , Chen Leilei , Tan Patrick , Yong Wei Peng
Published: April 2023

Supplementary Figure 2
Supplementary Data Table S1 from Altered Mitochondria Functionality Defines a Metastatic Cell State in Lung Cancer and Creates an Exploitable Vulnerability
Authors: Chuang Chen-Hua , Dorsch Madeleine , Dujardin Philip , Silas Sukrit , Ueffing Kristina , Hölken Johanna M. , Yang Dian , Winslow Monte M. , Grüner Barbara M.
Published: April 2023

Supplementary Data Table S1
Supplementary Data from Axl and Mertk Receptors Cooperate to Promote Breast Cancer Progression by Combined Oncogenic Signaling and Evasion of Host Antitumor Immunity
Authors: Davra Viralkumar , Kumar Sushil , Geng Ke , Calianese David , Mehta Dhriti , Gadiyar Varsha , Kasikara Canan , Lahey Kevin C. , Chang Yun-juan , Wichroski Michael , Gao Chan , De Lorenzo Mariana S. , Kotenko Sergei V. , Bergsbaken Tessa , Mishra Pankaj K. , Gause William C. , Quigley Michael , Spires Thomas E. , Birge Raymond B.
Published: April 2023

Figure S1-S6
Supplementary Tables from Dual Inhibition of MEK and AXL Targets Tumor Cell Heterogeneity and Prevents Resistant Outgrowth Mediated by the Epithelial-to-Mesenchymal Transition in NSCLC
Authors: Konen Jessica M. , Rodriguez B. Leticia , Padhye Aparna , Ochieng Joshua K. , Gibson Laura , Diao Lixia , Fowlkes Natalie W. , Fradette Jared J. , Peng David H. , Cardnell Robert J. , Kovacs Jeffrey J. , Wang Jing , Byers Lauren A. , Gibbons Don L.
Published: April 2023

Supplementary Tables 1-8
Supplementary Data from PKCϵ Is Required for KRAS-Driven Lung Tumorigenesis
Authors: Garg Rachana , Cooke Mariana , Benavides Fernando , Abba Martín C. , Cicchini Michelle , Feldser David M. , Kazanietz Marcelo G.
Published: April 2023

Table S1. PKCe- and KRAS-regulated genes.
Supplement Figures from Dual Inhibition of MEK and AXL Targets Tumor Cell Heterogeneity and Prevents Resistant Outgrowth Mediated by the Epithelial-to-Mesenchymal Transition in NSCLC
Authors: Konen Jessica M. , Rodriguez B. Leticia , Padhye Aparna , Ochieng Joshua K. , Gibson Laura , Diao Lixia , Fowlkes Natalie W. , Fradette Jared J. , Peng David H. , Cardnell Robert J. , Kovacs Jeffrey J. , Wang Jing , Byers Lauren A. , Gibbons Don L.
Published: April 2023

Supplement Figures 1-9 with legends
Supplementary Data from PKCϵ Is Required for KRAS-Driven Lung Tumorigenesis
Authors: Garg Rachana , Cooke Mariana , Benavides Fernando , Abba Martín C. , Cicchini Michelle , Feldser David M. , Kazanietz Marcelo G.
Published: April 2023

Table S2. Bioprocess enriched in the PKCe and KRAS gene expression signatures.
Supplementary Materials from The Landscape of the Heritable Cancer Genome
Authors: Fanfani Viola , Citi Luca , Harris Adrian L. , Pezzella Francesco , Stracquadanio Giovanni
Published: April 2023

Supplementary Methods, Figures, Tables
Supplementary Data from DMDRMR-Mediated Regulation of m6A-Modified CDK4 by m6A Reader IGF2BP3 Drives ccRCC Progression
Authors: Gu Yinmin , Niu Shaoxi , Wang Yang , Duan Liqiang , Pan Yongbo , Tong Zhou , Zhang Xu , Yang Zhenyu , Peng Bo , Wang Xiaodong , Han Xiaoqi , Li Yuxin , Cheng Tianyou , Liu Yajuan , Shang Lina , Liu Tongfeng , Yang Xiwang , Sun Minxuan , Jiang Siyuan , Zhang Chang , Zhang Ning , Ye Qinong , Gao Shan
Published: April 2023

Dataset S2
Fig S1 from Cisplatin-Mediated Upregulation of APE2 Binding to MYH9 Provokes Mitochondrial Fragmentation and Acute Kidney Injury
Authors: Hu Yi , Yang Chun , Amorim Tania , Maqbool Mohsin , Lin Jenny , Li Chen , Fang Chuanfeng , Xue Li , Kwart Ariel , Fang Hua , Yin Mei , Janocha Allison J. , Tsuchimoto Daisuke , Nakabeppu Yusaku , Jiang Xiaofeng , Mejia-Garcia Alex , Anwer Faiz , Khouri Jack , Qi Xin , Zheng Qing Y. , Yu Jennifer S. , Yan Shan , LaFramboise Thomas , Anderson Kenneth C. , Herlitz Leal C. , Munshi Nikhil C. , Lin Jianhong , Zhao Jianjun
Published: April 2023

Slight increase of APE2 expression in mouse PTCs after carboplatin and oxaliplatin treatment.
Table S5 from A GRN Autocrine-Dependent FAM135B/AKT/mTOR Feedforward Loop Promotes Esophageal Squamous Cell Carcinoma Progression
Authors: Dong Dezuo , Zhang Weimin , Xiao Wenchang , Wu Qingnan , Cao Yiren , Gao Xiaohan , Huang Lijie , Wang Yan , Chen Jie , Wang Weihu , Zhan Qimin
Published: April 2023

4-NQO induced tumorigenesis in FAM135B-Tg and wild-type mice
Table S4 from A GRN Autocrine-Dependent FAM135B/AKT/mTOR Feedforward Loop Promotes Esophageal Squamous Cell Carcinoma Progression
Authors: Dong Dezuo , Zhang Weimin , Xiao Wenchang , Wu Qingnan , Cao Yiren , Gao Xiaohan , Huang Lijie , Wang Yan , Chen Jie , Wang Weihu , Zhan Qimin
Published: April 2023

Univariate and multivariable Cox regression analysis of overall survival(n=87)
Supplementary Data from DMDRMR-Mediated Regulation of m6A-Modified CDK4 by m6A Reader IGF2BP3 Drives ccRCC Progression
Authors: Gu Yinmin , Niu Shaoxi , Wang Yang , Duan Liqiang , Pan Yongbo , Tong Zhou , Zhang Xu , Yang Zhenyu , Peng Bo , Wang Xiaodong , Han Xiaoqi , Li Yuxin , Cheng Tianyou , Liu Yajuan , Shang Lina , Liu Tongfeng , Yang Xiwang , Sun Minxuan , Jiang Siyuan , Zhang Chang , Zhang Ning , Ye Qinong , Gao Shan
Published: April 2023

Dataset S1
Supplementary Data from DMDRMR-Mediated Regulation of m6A-Modified CDK4 by m6A Reader IGF2BP3 Drives ccRCC Progression
Authors: Gu Yinmin , Niu Shaoxi , Wang Yang , Duan Liqiang , Pan Yongbo , Tong Zhou , Zhang Xu , Yang Zhenyu , Peng Bo , Wang Xiaodong , Han Xiaoqi , Li Yuxin , Cheng Tianyou , Liu Yajuan , Shang Lina , Liu Tongfeng , Yang Xiwang , Sun Minxuan , Jiang Siyuan , Zhang Chang , Zhang Ning , Ye Qinong , Gao Shan
Published: April 2023

Supplementary Information
Figure S3 from A GRN Autocrine-Dependent FAM135B/AKT/mTOR Feedforward Loop Promotes Esophageal Squamous Cell Carcinoma Progression
Authors: Dong Dezuo , Zhang Weimin , Xiao Wenchang , Wu Qingnan , Cao Yiren , Gao Xiaohan , Huang Lijie , Wang Yan , Chen Jie , Wang Weihu , Zhan Qimin
Published: April 2023

Establishment of the FAM135B transgenic mouse model
Figure S4 from Folate Receptor Beta Designates Immunosuppressive Tumor-Associated Myeloid Cells That Can Be Reprogrammed with Folate-Targeted Drugs
Authors: Cresswell Gregory M. , Wang Bingbing , Kischuk Erin M. , Broman Meaghan M. , Alfar Rami A. , Vickman Renee E. , Dimitrov Dimiter S. , Kularatne Sumith A. , Sundaram Chandru P. , Singhal Sunil , Eruslanov Evgeniy B. , Crist Scott A. , Elzey Bennett D. , Ratliff Timothy L. , Low Philip S.
Published: April 2023

supplemental figure 4
Figure S3 from Folate Receptor Beta Designates Immunosuppressive Tumor-Associated Myeloid Cells That Can Be Reprogrammed with Folate-Targeted Drugs
Authors: Cresswell Gregory M. , Wang Bingbing , Kischuk Erin M. , Broman Meaghan M. , Alfar Rami A. , Vickman Renee E. , Dimitrov Dimiter S. , Kularatne Sumith A. , Sundaram Chandru P. , Singhal Sunil , Eruslanov Evgeniy B. , Crist Scott A. , Elzey Bennett D. , Ratliff Timothy L. , Low Philip S.
Published: April 2023

supplemental figure 3
Supplementary Figures from Protein Arginine Methyltransferase 5 Promotes pICln-Dependent Androgen Receptor Transcription in Castration-Resistant Prostate Cancer
Authors: Beketova Elena , Fang Shuyi , Owens Jake L. , Liu Sheng , Chen Xufeng , Zhang Qingfu , Asberry Andrew M. , Deng Xuehong , Malola Jonathan , Huang Jiaoti , Li Chenglong , Pili Roberto , Elzey Bennett D. , Ratliff Timothy L. , Wan Jun , Hu Chang-Deng
Published: April 2023

Supplementary Figure S1 - S8
Figure S4 from Enhanced Antitumor Immunity via Endocrine Therapy Prevents Mammary Tumor Relapse and Increases Immune Checkpoint Blockade Sensitivity
Authors: Sequeira Gonzalo R. , Sahores Ana , Dalotto-Moreno Tomás , Perrotta Ramiro M. , Pataccini Gabriela , Vanzulli Silvia I. , Polo María L. , Radisky Derek C. , Sartorius Carol A. , Novaro Virginia , Lamb Caroline A. , Rabinovich Gabriel A. , Salatino Mariana , Lanari Claudia
Published: April 2023

Supplementary Figure 4. 59-2-HI tumors express PD-L1 and MFP treatment upregulates PD-L1 expression in CD45neg cells and F4/80+ macrophages in vivo
Figure S3 from ATG5-Dependent Autophagy Uncouples T-cell Proliferative and Effector Functions and Separates Graft-versus-Host Disease from Graft-versus-Leukemia
Authors: Oravecz-Wilson Katherine , Rossi Corinne , Zajac Cynthia , Sun Yaping , Li Lu , Decoville Thomas , Fujiwara Hideaki , Kim Stephanie , Peltier Daniel , Reddy Pavan
Published: April 2023

Fig S3 has ELISA data for CD3/CD28 stimulation as well as serum data from BMT animals
Figure S3 from Enhanced Antitumor Immunity via Endocrine Therapy Prevents Mammary Tumor Relapse and Increases Immune Checkpoint Blockade Sensitivity
Authors: Sequeira Gonzalo R. , Sahores Ana , Dalotto-Moreno Tomás , Perrotta Ramiro M. , Pataccini Gabriela , Vanzulli Silvia I. , Polo María L. , Radisky Derek C. , Sartorius Carol A. , Novaro Virginia , Lamb Caroline A. , Rabinovich Gabriel A. , Salatino Mariana , Lanari Claudia
Published: April 2023

Supplementary Figure 3: MFP treatment reduced MDSCs frequency in the TME and spleen
Figure S2 from Enhanced Antitumor Immunity via Endocrine Therapy Prevents Mammary Tumor Relapse and Increases Immune Checkpoint Blockade Sensitivity
Authors: Sequeira Gonzalo R. , Sahores Ana , Dalotto-Moreno Tomás , Perrotta Ramiro M. , Pataccini Gabriela , Vanzulli Silvia I. , Polo María L. , Radisky Derek C. , Sartorius Carol A. , Novaro Virginia , Lamb Caroline A. , Rabinovich Gabriel A. , Salatino Mariana , Lanari Claudia
Published: April 2023

Supplementary Figure 2. MFP induces tissue remodeling in tumors growing in NSG-R mice.
Supplementary Tables from USP24 Is a Cancer-Associated Ubiquitin Hydrolase, Novel Tumor Suppressor, and Chromosome Instability Gene Deleted in Neuroblastoma
Authors: Bedekovics Tibor , Hussain Sajjad , Zhang Ying , Ali Asma , Jeon Young J. , Galardy Paul J.
Published: April 2023

Supplementary tables 1-9
Supplementary Figure S1 from Holding on to Junk Bonds: Intron Retention in Cancer and Therapy
Authors: Monteuuis Geoffray , Schmitz Ulf , Petrova Veronika , Kearney Padraic S. , Rasko John E.J.
Published: April 2023

IR in CAR-T cell treatment and a possible approach to therapy. Development of antisense oligonucleotides-based therapies to correct pathological IR events.
Video 2 from Glutamine-Directed Migration of Cancer-Activated Fibroblasts Facilitates Epithelial Tumor Invasion
Authors: Mestre-Farrera Aida , Bruch-Oms Marina , Peña Raúl , Rodríguez-Morató José , Alba-Castellón Lorena , Comerma Laura , Quintela-Fandino Miguel , Duñach Mireia , Baulida Josep , Pozo Óscar J. , García de Herreros Antonio
Published: April 2023

Video showing migration of activated CAFs toward the Gln-rich compartment when cultured in Gln-high conditions (2 mM)
Supplementary Data from Glutamine-Directed Migration of Cancer-Activated Fibroblasts Facilitates Epithelial Tumor Invasion
Authors: Mestre-Farrera Aida , Bruch-Oms Marina , Peña Raúl , Rodríguez-Morató José , Alba-Castellón Lorena , Comerma Laura , Quintela-Fandino Miguel , Duñach Mireia , Baulida Josep , Pozo Óscar J. , García de Herreros Antonio
Published: April 2023

Supplementary Information containing supplementary methods, eight supplementary figures with legends and one supplementary table.
Table S4 from 2-Hydroxylation of Fatty Acids Represses Colorectal Tumorigenesis and Metastasis via the YAP Transcriptional Axis
Authors: Sun Liang , Yang Xiaoqin , Huang Xiaoheng , Yao Yizhou , Wei Xiangyu , Yang Shugao , Zhou Diyuan , Zhang Wei , Long Zhimin , Xu Xiaoyan , Zhu Xinguo , He Songbing , Su Xiong
Published: April 2023

Supplementary Table S4. Lipid species with significantly different levels (P < 0.05, fold change > 2) in SW480 cells with or without FA2H overexpression.
Supplementary Experimental Materials and Methods, Figure S1-4, Table S1-3 from 2-Hydroxylation of Fatty Acids Represses Colorectal Tumorigenesis and Metastasis via the YAP Transcriptional Axis
Authors: Sun Liang , Yang Xiaoqin , Huang Xiaoheng , Yao Yizhou , Wei Xiangyu , Yang Shugao , Zhou Diyuan , Zhang Wei , Long Zhimin , Xu Xiaoyan , Zhu Xinguo , He Songbing , Su Xiong
Published: April 2023

Supplementary Experimental Materials and Methods. Supplementary Figure S1. Expression of FA2H in human colorectal cancer cells. Supplementary Figure S2. siRNA-mediated FA2H knockdown promotes HCT116 cell proliferation and migration. Supplementary Figure S3. Regulation of Gli1 and phosphorylation of ERK1/2, p38, and JNK by FA2H. Supplementary Figure S4. FA2H promotes AMPK phosphorylation in CRC cells. Supplementary Table S1. Association between FA2H and clinic-pathological factors in 141 patients with colorectal cancer. Supplementary Table S2. Antibody information. Supplementary Table S3. Primers used for qRT-PCR analysis.
Supplementary Tables from Identifying Clear Cell Renal Cell Carcinoma Coexpression Networks Associated with Opioid Signaling and Survival
Authors: Scarpa Joseph R. , DiNatale Renzo G. , Mano Roy , Silagy Andrew W. , Kuo Fengshen , Irie Takeshi , McCormick Patrick J. , Fischer Gregory W. , Hakimi A. Ari , Mincer Joshua S.
Published: April 2023

Supplementary Tables 1-8. Table S1. Mutations of the Reactome opioid signaling pathway in ccRCC. Table S2. Module membership for each module. Table S3. Gene ontology coexpression network enrichment. Table S4. Cox survival analysis for association of the 15 networks and survival endpoints. Table S5. Clinical and demographic overrepresentation in sample subgroups with high module eigengene expression. Table S6. List of hub genes for the eight cancer-specific survival-associated networks. Table S7. Master regulators of the transition from normal to disease state. Table S8. Gene expression correlation statistics between immune signature genes and four ccRCC master regulator genes involved in opioid immunomodulation (CREB5, IL4R, CLEC2D, PLXNB1).
Supplementary Table S2 from Activation of Receptor Tyrosine Kinases Mediates Acquired Resistance to MEK Inhibition in Malignant Peripheral Nerve Sheath Tumors
Authors: Wang Jiawan , Pollard Kai , Calizo Ana , Pratilas Christine A.
Published: April 2023

Supplementary Table S2 shows a summary report for targeted gene sequencing.
Figure S9 from Identifying Clear Cell Renal Cell Carcinoma Coexpression Networks Associated with Opioid Signaling and Survival
Authors: Scarpa Joseph R. , DiNatale Renzo G. , Mano Roy , Silagy Andrew W. , Kuo Fengshen , Irie Takeshi , McCormick Patrick J. , Fischer Gregory W. , Hakimi A. Ari , Mincer Joshua S.
Published: April 2023

Figure S9. Gene expression correlation between immune signature genes (y axis) and four ccRCC master regulator genes (x axis): (A) PLXNB1, (B) CREB5, (C) IL4R, (D) CLEC2D.
Supplementary Table S1 from Activation of Receptor Tyrosine Kinases Mediates Acquired Resistance to MEK Inhibition in Malignant Peripheral Nerve Sheath Tumors
Authors: Wang Jiawan , Pollard Kai , Calizo Ana , Pratilas Christine A.
Published: April 2023

Supplementary Table S1 shows recurrent genomic alterations in MPNST cell lines.
Figure S7 from Identifying Clear Cell Renal Cell Carcinoma Coexpression Networks Associated with Opioid Signaling and Survival
Authors: Scarpa Joseph R. , DiNatale Renzo G. , Mano Roy , Silagy Andrew W. , Kuo Fengshen , Irie Takeshi , McCormick Patrick J. , Fischer Gregory W. , Hakimi A. Ari , Mincer Joshua S.
Published: April 2023

Figure S7. Gene network enrichment for microenvironment cell-type specific gene signatures.
Figure S6 from Identifying Clear Cell Renal Cell Carcinoma Coexpression Networks Associated with Opioid Signaling and Survival
Authors: Scarpa Joseph R. , DiNatale Renzo G. , Mano Roy , Silagy Andrew W. , Kuo Fengshen , Irie Takeshi , McCormick Patrick J. , Fischer Gregory W. , Hakimi A. Ari , Mincer Joshua S.
Published: April 2023

Figure S6. Correlation between TCGA and MSKCC gene expression for eight survival-associated networks.
Supplementary Data from MEK Inhibition Reverses Aberrant Signaling in Melanoma Cells through Reorganization of NRas and BRAF in Self Nanoclusters
Authors: Yakovian Oren , Sajman Julia , Arafeh Rand , Neve-Oz Yair , Alon Michal , Samuels Yardena , Sherman Eilon
Published: April 2023

Supplementary tables
Figure S4 from Identifying Clear Cell Renal Cell Carcinoma Coexpression Networks Associated with Opioid Signaling and Survival
Authors: Scarpa Joseph R. , DiNatale Renzo G. , Mano Roy , Silagy Andrew W. , Kuo Fengshen , Irie Takeshi , McCormick Patrick J. , Fischer Gregory W. , Hakimi A. Ari , Mincer Joshua S.
Published: April 2023

Figure S4. Individual sample expression across module eigengenes.
Supplementary Data from Transcriptional Activation of MYC-Induced Genes by GCN5 Promotes B-cell Lymphomagenesis
Authors: Farria Aimee T. , Plummer Joshua B. , Salinger Andrew P. , Shen Jianjun , Lin Kevin , Lu Yue , McBride Kevin M. , Koutelou Evangelia , Dent Sharon Y.R.
Published: April 2023

Suppl figs 1-4: Suppl fig 1 Flow cytometry data, B cells Suppl Fig 2 qRT PCR plasmabalst genes Suppl Fig 3 Flow Cytometry Prelymphomic B cells Suppl Fig 4 RNA seq analyses
Supplementary Data Tables from Transcriptional Activation of MYC-Induced Genes by GCN5 Promotes B-cell Lymphomagenesis
Authors: Farria Aimee T. , Plummer Joshua B. , Salinger Andrew P. , Shen Jianjun , Lin Kevin , Lu Yue , McBride Kevin M. , Koutelou Evangelia , Dent Sharon Y.R.
Published: April 2023

Supple Table 1 DAVID GO pathways Suppl Table 2 EGFR Down regulated genes Suppl Table 3 Hgf Down regulated genes Suppl Tab 4 VEGF down regulated genes Suppl Table 5 Antibodies used Suppl Table 6 Primers used
Supplementary Table 5 from Enhanced Efficacy of Simultaneous PD-1 and PD-L1 Immune Checkpoint Blockade in High-Grade Serous Ovarian Cancer
Authors: Wan Changxin , Keany Matthew P. , Dong Han , Al-Alem Linah F. , Pandya Unnati M. , Lazo Suzan , Boehnke Karsten , Lynch Katherine N. , Xu Rui , Zarrella Dominique T. , Gu Shengqing , Cejas Paloma , Lim Klothilda , Long Henry W. , Elias Kevin M. , Horowitz Neil S. , Feltmate Colleen M. , Muto Michael G. , Worley Michael J. , Berkowitz Ross S. , Matulonis Ursula A. , Nucci Marisa R. , Crum Christopher P. , Rueda Bo R. , Brown Myles , Liu Xiaole Shirley , Hill Sarah J.
Published: April 2023

Table S5. List of Genes Used to Generate NK Cell Activation Scores.
Supplementary Table S2 from Estrogen Receptor Alpha Mutations in Breast Cancer Cells Cause Gene Expression Changes through Constant Activity and Secondary Effects
Authors: Arnesen Spencer , Blanchard Zannel , Williams Michelle M. , Berrett Kristofer C. , Li Zheqi , Oesterreich Steffi , Richer Jennifer K. , Gertz Jason
Published: April 2023

Table S2. Mutant-specific up- and down-regulated genes.
Supplementary Table 2 from Enhanced Efficacy of Simultaneous PD-1 and PD-L1 Immune Checkpoint Blockade in High-Grade Serous Ovarian Cancer
Authors: Wan Changxin , Keany Matthew P. , Dong Han , Al-Alem Linah F. , Pandya Unnati M. , Lazo Suzan , Boehnke Karsten , Lynch Katherine N. , Xu Rui , Zarrella Dominique T. , Gu Shengqing , Cejas Paloma , Lim Klothilda , Long Henry W. , Elias Kevin M. , Horowitz Neil S. , Feltmate Colleen M. , Muto Michael G. , Worley Michael J. , Berkowitz Ross S. , Matulonis Ursula A. , Nucci Marisa R. , Crum Christopher P. , Rueda Bo R. , Brown Myles , Liu Xiaole Shirley , Hill Sarah J.
Published: April 2023

Table S2. Differential expression analysis for Treg CD4 T cells.
Supplementary Table 1 from Enhanced Efficacy of Simultaneous PD-1 and PD-L1 Immune Checkpoint Blockade in High-Grade Serous Ovarian Cancer
Authors: Wan Changxin , Keany Matthew P. , Dong Han , Al-Alem Linah F. , Pandya Unnati M. , Lazo Suzan , Boehnke Karsten , Lynch Katherine N. , Xu Rui , Zarrella Dominique T. , Gu Shengqing , Cejas Paloma , Lim Klothilda , Long Henry W. , Elias Kevin M. , Horowitz Neil S. , Feltmate Colleen M. , Muto Michael G. , Worley Michael J. , Berkowitz Ross S. , Matulonis Ursula A. , Nucci Marisa R. , Crum Christopher P. , Rueda Bo R. , Brown Myles , Liu Xiaole Shirley , Hill Sarah J.
Published: April 2023

Table S1. Differential expression analysis for CD8 T cells.
Supplementary Materials from Enhanced Efficacy of Simultaneous PD-1 and PD-L1 Immune Checkpoint Blockade in High-Grade Serous Ovarian Cancer
Authors: Wan Changxin , Keany Matthew P. , Dong Han , Al-Alem Linah F. , Pandya Unnati M. , Lazo Suzan , Boehnke Karsten , Lynch Katherine N. , Xu Rui , Zarrella Dominique T. , Gu Shengqing , Cejas Paloma , Lim Klothilda , Long Henry W. , Elias Kevin M. , Horowitz Neil S. , Feltmate Colleen M. , Muto Michael G. , Worley Michael J. , Berkowitz Ross S. , Matulonis Ursula A. , Nucci Marisa R. , Crum Christopher P. , Rueda Bo R. , Brown Myles , Liu Xiaole Shirley , Hill Sarah J.
Published: April 2023

Supplementary Materials and Methods, Figures, and Figure and Table legends