bluuebunny/crossref_metadata_2025 huggingface dataset:
Table S2 from Glutamate Decarboxylase 65 Signals through the Androgen Receptor to Promote Castration Resistance in Prostate Cancer
Authors: Gao Yi , Chen Lu , Du ZunGuo , Gao WenChao , Wu ZhengMing , Liu XiuJuan , Huang Hai , Xu DanFeng , Li QingQuan
Published: April 2023

Table S2 shows the AR interacting proteins in PC-CR4 cells
Table S1 from Glutamate Decarboxylase 65 Signals through the Androgen Receptor to Promote Castration Resistance in Prostate Cancer
Authors: Gao Yi , Chen Lu , Du ZunGuo , Gao WenChao , Wu ZhengMing , Liu XiuJuan , Huang Hai , Xu DanFeng , Li QingQuan
Published: April 2023

Table S1 shows the detailed information of PDX lines used in this study
Supplementary Materials and Methods from Glutamate Decarboxylase 65 Signals through the Androgen Receptor to Promote Castration Resistance in Prostate Cancer
Authors: Gao Yi , Chen Lu , Du ZunGuo , Gao WenChao , Wu ZhengMing , Liu XiuJuan , Huang Hai , Xu DanFeng , Li QingQuan
Published: April 2023

Supplementary Materials and Methods shows the Extended materials and methods used in this study
Table S3 from MDM4 Is Targeted by 1q Gain and Drives Disease in Burkitt Lymphoma
Authors: Hüllein Jennifer , Słabicki Mikołaj , Rosolowski Maciej , Jethwa Alexander , Habringer Stefan , Tomska Katarzyna , Kurilov Roma , Lu Junyan , Scheinost Sebastian , Wagener Rabea , Huang Zhiqin , Lukas Marina , Yavorska Olena , Helfrich Hanne , Scholtysik René , Bonneau Kyle , Tedesco Donato , Küppers Ralf , Klapper Wolfram , Pott Christiane , Stilgenbauer Stephan , Burkhardt Birgit , Löffler Markus , Trümper Lorenz H. , Hummel Michael , Brors Benedikt , Zapatka Marc , Siebert Reiner , Kreuz Markus , Keller Ulrich , Huber Wolfgang , Zenz Thorsten
Published: April 2023

Gene expression fold-changes from microarray analysis
Figure S1 from Glutamate Decarboxylase 65 Signals through the Androgen Receptor to Promote Castration Resistance in Prostate Cancer
Authors: Gao Yi , Chen Lu , Du ZunGuo , Gao WenChao , Wu ZhengMing , Liu XiuJuan , Huang Hai , Xu DanFeng , Li QingQuan
Published: April 2023

Figure S1 shows increased GABA shunt activity in CRPC
Table S1 from Genetic Variants of VEGFA and FLT4 Are Determinants of Survival in Renal Cell Carcinoma Patients Treated with Sorafenib
Authors: Crona Daniel J. , Skol Andrew D. , Leppänen Veli-Matti , Glubb Dylan M. , Etheridge Amy S. , Hilliard Eleanor , Peña Carol E. , Peterson Yuri K. , Klauber-DeMore Nancy , Alitalo Kari K. , Innocenti Federico
Published: April 2023

Genotyped genes.
Table S1 from Gaussian Mixture Models for Probabilistic Classification of Breast Cancer
Authors: Prabakaran Indira , Wu Zhengdong , Lee Changgun , Tong Brian , Steeman Samantha , Koo Gabriel , Zhang Paul J. , Guvakova Marina A.
Published: April 2023

Table S1. Patient and tumor characteristics of the study population.
Figure S4 from Genetic Variants of VEGFA and FLT4 Are Determinants of Survival in Renal Cell Carcinoma Patients Treated with Sorafenib
Authors: Crona Daniel J. , Skol Andrew D. , Leppänen Veli-Matti , Glubb Dylan M. , Etheridge Amy S. , Hilliard Eleanor , Peña Carol E. , Peterson Yuri K. , Klauber-DeMore Nancy , Alitalo Kari K. , Innocenti Federico
Published: April 2023

T494A is located in the 5th Ig-like domain of VEGFR-3.
Supplementary Data from Gaussian Mixture Models for Probabilistic Classification of Breast Cancer
Authors: Prabakaran Indira , Wu Zhengdong , Lee Changgun , Tong Brian , Steeman Samantha , Koo Gabriel , Zhang Paul J. , Guvakova Marina A.
Published: April 2023

Figure S1. Bland-Altman plot. It shows the acceptable average of the differences (bias = -0.049; SD = 0.1038) between two image-based methods of measuring the IGF-IR expression levels in IHC stained tissue: ImageJ and COMPAi.
Figure S3 from Genetic Variants of VEGFA and FLT4 Are Determinants of Survival in Renal Cell Carcinoma Patients Treated with Sorafenib
Authors: Crona Daniel J. , Skol Andrew D. , Leppänen Veli-Matti , Glubb Dylan M. , Etheridge Amy S. , Hilliard Eleanor , Peña Carol E. , Peterson Yuri K. , Klauber-DeMore Nancy , Alitalo Kari K. , Innocenti Federico
Published: April 2023

Expression of WT and T494A VEGFR-3 in HUVECs (A) and replication of phosphorylation experiments testing the effect of FLT4 rs307826 (A>G, T494A) on VEGFR-3 phosphorylation (B).
Supplementary Data from Gaussian Mixture Models for Probabilistic Classification of Breast Cancer
Authors: Prabakaran Indira , Wu Zhengdong , Lee Changgun , Tong Brian , Steeman Samantha , Koo Gabriel , Zhang Paul J. , Guvakova Marina A.
Published: April 2023

Figure S2. The optimization of GMM curve fitting in to histogram of ERBB2 data assuming that cancer unchanged and normal group distributions are similar. (A) Modeling two Gaussians, bin width = 10, the adjusted R2 = 70.49%. (B) Modeling three Gaussians, bin width = 15, the adjusted R2 = 88.95%. Note, modeling "downregulated" group does not allow the cutoff with "unchanged" group. (C) Final modeling two Gaussians, bin width = 15, the adjusted R2 = 97.69%. Boxplot shows control levels of ERBB2 in healthy breast tissue.
Figure S2 from Genetic Variants of VEGFA and FLT4 Are Determinants of Survival in Renal Cell Carcinoma Patients Treated with Sorafenib
Authors: Crona Daniel J. , Skol Andrew D. , Leppänen Veli-Matti , Glubb Dylan M. , Etheridge Amy S. , Hilliard Eleanor , Peña Carol E. , Peterson Yuri K. , Klauber-DeMore Nancy , Alitalo Kari K. , Innocenti Federico
Published: April 2023

Kaplan-Meier plots of genetic variants versus PFS.
Figure S1 from Genetic Variants of VEGFA and FLT4 Are Determinants of Survival in Renal Cell Carcinoma Patients Treated with Sorafenib
Authors: Crona Daniel J. , Skol Andrew D. , Leppänen Veli-Matti , Glubb Dylan M. , Etheridge Amy S. , Hilliard Eleanor , Peña Carol E. , Peterson Yuri K. , Klauber-DeMore Nancy , Alitalo Kari K. , Innocenti Federico
Published: April 2023

Study schematic for patients genotyped in this study.
Supplementary Materials and Methods from PIN1 Maintains Redox Balance via the c-Myc/NRF2 Axis to Counteract Kras-Induced Mitochondrial Respiratory Injury in Pancreatic Cancer Cells
Authors: Liang Chen , Shi Si , Liu Mingyang , Qin Yi , Meng Qingcai , Hua Jie , Ji Shunrong , Zhang Yuqing , Yang Jingxuan , Xu Jin , Ni Quanxing , Li Min , Yu Xianjun
Published: April 2023

The Supplementary Data includes Supplementary Materials and Methods.
Supplementary Data from Stathmin Is Required for Normal Mouse Mammary Gland Development and Δ16HER2-Driven Tumorigenesis
Authors: Segatto Ilenia , Zompit Mara De Marco , Citron Francesca , D'Andrea Sara , Vinciguerra Gian Luca Rampioni , Perin Tiziana , Berton Stefania , Mungo Giorgia , Schiappacassi Monica , Marchini Cristina , Amici Augusto , Vecchione Andrea , Baldassarre Gustavo , Belletti Barbara
Published: April 2023

Supplementary Information includes Supplementary Materials and Methods, Supplementary Figures 1-7, with Legends and Supplementary References. Supplementary Figure S1: Loss of stathmin impairs mouse mammary gland development. Supplementary Figure S2: Loss of stathmin decreases the growth of mammary epithelial cells. Supplementary Figure S3: Loss of stathmin alters the mammary gland organization. Supplementary Figure S4: mRNA levels of STAT5 target genes are differently modulated when stathmin is silenced. Supplementary Figure S5: Stathmin expression correlates with poor prognosis in breast cancer patients. Supplementary Figure S6: Î"16HER2-driven mammary neoplastic lesions display luminal features. Supplementary Figure S7: Absence of stathmin in pre-neoplastic mouse mammary glands (13 weeks of age) weakens the activation of Î"16HER2 transformation-related pathways
Supplementary Figure Legends from Inhibition of ATM Increases Interferon Signaling and Sensitizes Pancreatic Cancer to Immune Checkpoint Blockade Therapy
Authors: Zhang Qiang , Green Michael D. , Lang Xueting , Lazarus Jenny , Parsels Joshua D. , Wei Shuang , Parsels Leslie A. , Shi Jiaqi , Ramnath Nithya , Wahl Daniel R. , Pasca di Magliano Marina , Frankel Timothy L. , Kryczek Ilona , Lei Yu L. , Lawrence Theodore S. , Zou Weiping , Morgan Meredith A.
Published: April 2023

SF1 Legend: ATM regulates type I interferon signaling in pancreatic cancer. SF2 Legend: ATM regulation of the type I interferon pathway is cGAS/STING independent but SRC dependent. SF3 Legend: ATM inhibition cooperates with radiation to activate type I interferon signaling. SF4 Legend: ATM regulates pancreatic tumor immunity and ICB efficacy in vivo.
Supplementary Data from Asporin Restricts Mesenchymal Stromal Cell Differentiation, Alters the Tumor Microenvironment, and Drives Metastatic Progression
Authors: Hughes Robert M. , Simons Brian W. , Khan Hamda , Miller Rebecca , Kugler Valentina , Torquato Samantha , Theodros Debebe , Haffner Michael C. , Lotan Tamara , Huang Jessie , Davicioni Elai , An Steven S. , Riddle Ryan C. , Thorek Daniel L.J. , Garraway Isla P. , Fertig Elana J. , Isaacs John T. , Brennen W. Nathaniel , Park Ben H. , Hurley Paula J.
Published: April 2023

Figure S1: Comparison of Aspn+/+ and Aspn-/- mice. Figure S2: Representative gating of murine MSCs. Figure S3: ASPN restricts MSC differentiation. Figure S4: ASPN expression in cancer cell lines. Figure S5: ASPN increases cancer cell migration. Figure S6: ASPN expression in B6CaP allografts and organoids.
Supplementary Data from Cell-Cycle–Dependent Phosphorylation of PRPS1 Fuels Nucleotide Synthesis and Promotes Tumorigenesis
Authors: Jing Xiaoqian , Wang Xiong-jun , Zhang Tao , Zhu Wencheng , Fang Yi , Wu Haoxuan , Liu Xinyu , Ma Ding , Ji Xiaopin , Jiang Yimei , Liu Kun , Chen Xianze , Shi Yi , Zhang Yaqi , Shi Minmin , Qiu Weihua , Zhao Ren
Published: April 2023

Roles of PRPS1 and PRPS1 in cell cycle progression and some of experimental verifications are included in this file.
Tables S1-S9 and Figures S1-S5 from Analysis of the CDKN2A Gene in FAMMM Syndrome Families Reveals Early Age of Onset for Additional Syndromic Cancers
Authors: Middlebrooks Candace D. , Stacey Mark L. , Li Qing , Snyder Carrie , Shaw Trudy G. , Richardson-Nelson Tami , Rendell Marc , Ferguson Claire , Silberstein Peter , Casey Murray J. , Bailey-Wilson Joan E. , Lynch Henry T.
Published: April 2023

Table S1: CDKN2A mutations found in each family; Table S2: Cancers found in each family; Table S2b: Full cancer names and abbreviations; Table S3: Order of cancer occurrence for individuals with multiple primaries; Table S4: Summary statistics for various covariates; Table S5: Sample missingness by cancer and carrier status; Table S6: Sample counts and proportions by cancer and carrier status; Table S7: Hazard ratios for replication analysis and replication cancers combined with other cancers; Table S8: Sample counts by family relationship and carrier status; Table S9: Cancer counts by cancer type Figure S1: Representative FAMMM pedigree; Figure S2: Survival plot for replication cancers; Figure S3: Survival plot for replication and other cancers; Figure S4: Survival plot stratified by family relationship and carrier status Figure S5: CDKN2A mutation locations within protein;
Supplementary Figures from The Cdk2–c-Myc–miR-571 Axis Regulates DNA Replication and Genomic Stability by Targeting Geminin
Authors: Zhang Yi , Li Zhuqing , Hao Qiang , Tan Wei , Sun Jing , Li Jing , Chen Chi-wei , Li Zongzhu , Meng Yunxiao , Zhou Yuan , Han Zhiyong , Pei Huadong , DePamphilis Melvin L. , Zhu Wenge
Published: April 2023

Supplementary Figure 1. miR-571 regulates DNA re-replication Supplementary Figure 2. Geminin is the major target by miR-571 to regulate DNA re-replication. Supplementary Figure 3. miR-571 regulates DNA replication and S phase cell cycle progression Supplementary Figure 4. c-Myc negatively regulates miR-571 and its host gene Supplementary Figure 5. c-Myc regulates miR-571 expression Supplementary Figure 6. Cdk2 regulates DNA replication through c-Myc Supplementary Figure 7. Phosphorylation of c-Myc at Ser62 by Cdk2 regulates miR-571 expression Supplementary Figure 8. miR-571 induced DNA re-replication is independent of mitotic failure
Supplementary Data from Antifibrotic Therapy Disrupts Stromal Barriers and Modulates the Immune Landscape in Pancreatic Ductal Adenocarcinoma
Authors: Elahi-Gedwillo Kianna Y. , Carlson Marjorie , Zettervall Jon , Provenzano Paolo P.
Published: April 2023

Supplementary figures showing 1) strong correlations between TGF-beta and ECM transcripts, 2) validation of isolated primary PSCs showing high purity for cells isolated and used in this study, 3) increased therapeutic perfusion following antifibrotic therapy in PDA, 4) image analysis of our novel algorithm to capture features histologically evaluated immune infiltration, 5) increased immune infiltration, and particularly anti-tumor immune cell infiltration, in PDA following antifibrotic therapy, and 6) no apparent whole animal or normal-adjacent pancreas toxicity following HF treatment.
Supplementary Figure 3 from SUMO-Specific Protease 1 Is Critical for Myeloid-Derived Suppressor Cell Development and Function
Authors: Huang Xian , Zuo Yong , Wang Xiuzhi , Wu Xuefeng , Tan Hongsheng , Fan Qiuju , Dong Baijun , Xue Wei , Chen Guo-Qiang , Cheng Jinke
Published: April 2023

SENP1 deficiency promotes tumor-associated MDSC expansion
Microfluidics chip based exosome proteomic profiling from A Microfluidic Chip Enables Isolation of Exosomes and Establishment of Their Protein Profiles and Associated Signaling Pathways in Ovarian Cancer
Authors: Dorayappan Kalpana Deepa Priya , Gardner Miranda L. , Hisey Colin L. , Zingarelli Roman A. , Smith Brentley Q. , Lightfoot Michelle D.S. , Gogna Rajan , Flannery Meghan M. , Hays John , Hansford Derek J. , Freitas Michael A. , Yu Lianbo , Cohn David E. , Selvendiran Karuppaiyah
Published: April 2023

Supplementary Figures: S1 is a work flow for exosome isolation in cancer cells. S2-S5 is protomic profiling in cancer cells Vs normal cells using different techniques. S6-S8 is The top Canonical pathways identified in the exosome protein
Supplementary Materials and Method from CXCR7 Reactivates ERK Signaling to Promote Resistance to EGFR Kinase Inhibitors in NSCLC
Authors: Becker Jeffrey H. , Gao Yandi , Soucheray Margaret , Pulido Ines , Kikuchi Eiki , Rodríguez María L. , Gandhi Rutu , Lafuente-Sanchis Aranzazu , Aupí Miguel , Alcácer Fernández-Coronado Javier , Martín-Martorell Paloma , Cremades Antonio , Galbis-Caravajal José M. , Alcácer Javier , Christensen Camilla L. , Simms Patricia , Hess Ashley , Asahina Hajime , Kahle Michael P. , Al-Shahrour Fatima , Borgia Jeffrey A. , Lahoz Agustín , Insa Amelia , Juan Oscar , Jänne Pasi A. , Wong Kwok-Kin , Carretero Julian , Shimamura Takeshi
Published: April 2023

Supplementary Materials and Methods
Supplementary Figures S1-S6 from CXCR7 Reactivates ERK Signaling to Promote Resistance to EGFR Kinase Inhibitors in NSCLC
Authors: Becker Jeffrey H. , Gao Yandi , Soucheray Margaret , Pulido Ines , Kikuchi Eiki , Rodríguez María L. , Gandhi Rutu , Lafuente-Sanchis Aranzazu , Aupí Miguel , Alcácer Fernández-Coronado Javier , Martín-Martorell Paloma , Cremades Antonio , Galbis-Caravajal José M. , Alcácer Javier , Christensen Camilla L. , Simms Patricia , Hess Ashley , Asahina Hajime , Kahle Michael P. , Al-Shahrour Fatima , Borgia Jeffrey A. , Lahoz Agustín , Insa Amelia , Juan Oscar , Jänne Pasi A. , Wong Kwok-Kin , Carretero Julian , Shimamura Takeshi
Published: April 2023

Supplementary Figures
Table S2 from Arming Tumor-Associated Macrophages to Reverse Epithelial Cancer Progression
Authors: Wettersten Hiromi I. , Weis Sara M. , Pathria Paulina , Von Schalscha Tami , Minami Toshiyuki , Varner Judith A. , Cheresh David A.
Published: April 2023

Gene expression marker sets, including immune cell markers used for Figure 1
Supplementary Table S2 from Multiparametric MRI and Coregistered Histology Identify Tumor Habitats in Breast Cancer Mouse Models
Authors: Jardim-Perassi Bruna V. , Huang Suning , Dominguez-Viqueira William , Poleszczuk Jan , Budzevich Mikalai M. , Abdalah Mahmoud A. , Pillai Smitha R. , Ruiz Epifanio , Bui Marilyn M. , Zuccari Debora A.P.C. , Gillies Robert J. , Martinez Gary V.
Published: April 2023

Similarity index based on the weighted moving/sliding window was used to quantify the agreement for all incorrect classifications between the habitat-maps derived from MRI (6-parameters) and histology. The correct habitats from histological maps were compared with incorrect habitats from MRI maps. Thus, there were 9 incorrect classifications for maps containing V, H1, H2 and N, and 2 incorrect classifications for maps containing V, combined H1 + H2 and N to compare. The total average score for all wrong classifications for each sample is also shown in Supplementary Table S1.
Supplementary Table S1 from Multiparametric MRI and Coregistered Histology Identify Tumor Habitats in Breast Cancer Mouse Models
Authors: Jardim-Perassi Bruna V. , Huang Suning , Dominguez-Viqueira William , Poleszczuk Jan , Budzevich Mikalai M. , Abdalah Mahmoud A. , Pillai Smitha R. , Ruiz Epifanio , Bui Marilyn M. , Zuccari Debora A.P.C. , Gillies Robert J. , Martinez Gary V.
Published: April 2023

Similarity index based on the weighted moving/sliding window was used to quantify the agreement between the habitat-maps derived from MRI and histology. MRI habitat maps were generated by clustering six MRI-parameters (T2-map, T2*-map, Apparent diffusion coefficient (ADC), Slope, Area under the curve (AUC) and time to max (TTM)).
Supplementary Figures from Pathogenic Epigenetic Consequences of Genetic Alterations in IDH-Wild-Type Diffuse Astrocytic Gliomas
Authors: Ohka Fumiharu , Shinjo Keiko , Deguchi Shoichi , Matsui Yusuke , Okuno Yusuke , Katsushima Keisuke , Suzuki Miho , Kato Akira , Ogiso Noboru , Yamamichi Akane , Aoki Kosuke , Suzuki Hiromichi , Sato Shinya , Arul Rayan Nirmala , Prabhakar Shyam , Göke Jonathan , Shimamura Teppei , Maruyama Reo , Takahashi Satoru , Suzumura Akio , Kimura Hiroshi , Wakabayashi Toshihiko , Zong Hui , Natsume Atsushi , Kondo Yutaka
Published: April 2023

SF1: Loss of p53 and NF1 expression in MADM GFP-positive precancerous cells and tumor cells; SF2: Clustering analysis of gene expression status in human gliomas; SF3: Expression levels of epigenetic genes in MADM tumors, human IDH-wild-type DAGs-MF and DAGs-nonMF; SF4: Histone modifications and expression status in Ezh2 wild-type MADM tumors; SF5: Copy number analysis of genes located on chromosomes 7 and 10 in the TM31 cell line; SF6: Relationship between Ezh2 expression and RAS signaling pathway; SF7: Inhibition of EZH2/PRC2 as a specific treatment strategy for IDH-wild-type DAGs-nonMF.
Supplementary Data from Cys34 Adductomics Links Colorectal Cancer with the Gut Microbiota and Redox Biology
Authors: Grigoryan Hasmik , Schiffman Courtney , Gunter Marc J. , Naccarati Alessio , Polidoro Silvia , Dagnino Sonia , Dudoit Sandrine , Vineis Paolo , Rappaport Stephen M.
Published: April 2023

Supplemental information
Figure S4 from Deoxycytidine Release from Pancreatic Stellate Cells Promotes Gemcitabine Resistance
Authors: Dalin Simona , Sullivan Mark R. , Lau Allison N. , Grauman-Boss Beatrice , Mueller Helen S. , Kreidl Emanuel , Fenoglio Silvia , Luengo Alba , Lees Jacqueline A. , Vander Heiden Matthew G. , Lauffenburger Douglas A. , Hemann Michael T.
Published: April 2023

Fig. S4. Boiling does not inactivate ENT inhibitors 8-MDP and dipyridamole. Dose response curves with gemcitabine supplemented with boiled or untreated media containing 6.67 uM of ENT inhibitors 8-MDP or dipyridamole. Data represent the mean of three biological replicates +/- SEM. *, ns, not significant, **, P {less than or equal to} 0.01 (one-way ANOVA with Bonferroni post-tests).
Figure S1 from miR-221 Targets QKI to Enhance the Tumorigenic Capacity of Human Colorectal Cancer Stem Cells
Authors: Mukohyama Junko , Isobe Taichi , Hu Qingjiang , Hayashi Takanori , Watanabe Takashi , Maeda Masao , Yanagi Hisano , Qian Xin , Yamashita Kimihiro , Minami Hironobu , Mimori Koshi , Sahoo Debashis , Kakeji Yoshihiro , Suzuki Akira , Dalerba Piero , Shimono Yohei
Published: April 2023

Gating strategy for the purification of distinct subtypes of epithelial cells in the mouse colon.
Supplemental Methods from Targeting Glycolysis through Inhibition of Lactate Dehydrogenase Impairs Tumor Growth in Preclinical Models of Ewing Sarcoma
Authors: Yeung Choh , Gibson Anna E. , Issaq Sameer H. , Oshima Nobu , Baumgart Joshua T. , Edessa Leah D. , Rai Ganesha , Urban Daniel J. , Johnson Michelle S. , Benavides Gloria A. , Squadrito Giuseppe L. , Yohe Marielle E. , Lei Haiyan , Eldridge Sandy , Hamre John , Dowdy Tyrone , Ruiz-Rodado Victor , Lita Adrian , Mendoza Arnulfo , Shern Jack F. , Larion Mioara , Helman Lee J. , Stott Gordon M. , Krishna Murali C. , Hall Matthew D. , Darley-Usmar Victor , Neckers Leonard M. , Heske Christine M.
Published: April 2023

A description of additional supplemental methods
Supplementary Data from Pleiotropic Effects of PPARD Accelerate Colorectal Tumorigenesis, Progression, and Invasion
Authors: Liu Yi , Deguchi Yasunori , Tian Rui , Wei Daoyan , Wu Ling , Chen Weidong , Xu Weiguo , Xu Min , Liu Fuyao , Gao Shen , Jaoude Jonathan C. , Chrieki Sarah P. , Moussalli Micheline J. , Gagea Mihai , Morris Jeffrey , Broaddus Russell R. , Zuo Xiangsheng , Shureiqi Imad
Published: April 2023

This file includes 2 supplementary tables. Table S1. Comparisons of IHC scores for PPARD, total active Î²-catenin, nuclear active Î²-catenin, EIF4G1 and nuclear CDK1 expression levels among colorectal adenomas, CRC tumor centers and CRC invasive fronts in 41 human paired samples. Table S2. Comparisons of IHC scores for PPARD, EIF4G1 and nuclear CDK1 expression levels between CRC invasive fronts and paired CRC tumor centers in relation to nuclear Î²-catenin localization.
Figure S2 from Epidemiologic and Clinical Analysis of Cervical Cancer Using Data from the Population-Based Osaka Cancer Registry
Authors: Yagi Asami , Ueda Yutaka , Kakuda Mamoru , Tanaka Yusuke , Ikeda Sayaka , Matsuzaki Shinya , Kobayashi Eiji , Morishima Toshitaka , Miyashiro Isao , Fukui Keisuke , Ito Yuri , Nakayama Tomio , Kimura Tadashi
Published: April 2023

5-years relative survival rate, by stage and age group (1976-2010, SCC and adenocarcinoma of the cervix)
Supplementary Data from SET Domain–Containing Protein 4 Epigenetically Controls Breast Cancer Stem Cell Quiescence
Authors: Ye Sen , Ding Yan-Fu , Jia Wen-Huan , Liu Xiao-Li , Feng Jing-Yi , Zhu Qian , Cai Sun-Li , Yang Yao-Shun , Lu Qian-Yun , Huang Xue-Ting , Yang Jin-Shu , Jia Sheng-Nan , Ding Guo-Ping , Wang Yue-Hong , Zhou Jiao-Jiao , Chen Yi-Ding , Yang Wei-Jun
Published: April 2023

Supplementary Table S1 and Supplementary Figure S1 to S11
Supplementary Data from Banding Together: A Systematic Comparison of The Cancer Genome Atlas and the Mitelman Databases
Authors: Denomy Connor , Germain Samuel , Haave Bjorn , Vizeacoumar Frederick S. , Freywald Andrew , Weaver Beth A. , Vizeacoumar Franco J.
Published: April 2023

This file contains two figures and five tables which enhance the reader's comprehension by providing a pictorial representation of common cytogenetic aberrations mentioned in the text, as well as additional data such as statistics regarding the frequency of specific cytogenetic events. Supplementary table 5 also provides key information needed to interpret figure 5 of the main text.
Table S5J-part2 from Integrated Pan-Cancer Map of EBV-Associated Neoplasms Reveals Functional Host–Virus Interactions
Authors: Chakravorty Srishti , Yan Bingyu , Wang Chong , Wang Luopin , Quaid Joseph Taylor , Lin Chin Fang , Briggs Scott D. , Majumder Joydeb , Canaria D. Alejandro , Chauss Daniel , Chopra Gaurav , Olson Matthew R. , Zhao Bo , Afzali Behdad , Kazemian Majid
Published: April 2023

Table S5J-part2, expression values (transcripts per million; T.P.M.) of all genes (rows) in each sample (columns).
Table S5 from Integrated Pan-Cancer Map of EBV-Associated Neoplasms Reveals Functional Host–Virus Interactions
Authors: Chakravorty Srishti , Yan Bingyu , Wang Chong , Wang Luopin , Quaid Joseph Taylor , Lin Chin Fang , Briggs Scott D. , Majumder Joydeb , Canaria D. Alejandro , Chauss Daniel , Chopra Gaurav , Olson Matthew R. , Zhao Bo , Afzali Behdad , Kazemian Majid
Published: April 2023

list of DEGs (fold change >1.5, FDR<0.05) between EBV+ and EBV- samples in each cancer (A-G). For each gene, shown are the mean expression value across EBV- and EBV+ cancer samples. The log-fold change, p-value and FDR values were obtained using differential expression analysis in edgeR. H, genes involved in Type I and Type II interferon activity (see methods). I, interferon activity of EBV+ tumor types. Shown in columns are cancer types, classification into IFN+ or IFN- groups for EBV+ samples or control group for EBV- samples, EBV status, Type I and Type II interferon signature score, and z-scores of genes related to Type I and Type II interferon signatures, for each sample (rows). J, expression values (transcripts per million; T.P.M.) of all genes (rows) in each sample (columns).
Supplementary methods from Integrated Pan-Cancer Map of EBV-Associated Neoplasms Reveals Functional Host–Virus Interactions
Authors: Chakravorty Srishti , Yan Bingyu , Wang Chong , Wang Luopin , Quaid Joseph Taylor , Lin Chin Fang , Briggs Scott D. , Majumder Joydeb , Canaria D. Alejandro , Chauss Daniel , Chopra Gaurav , Olson Matthew R. , Zhao Bo , Afzali Behdad , Kazemian Majid
Published: April 2023

Detailed information on different computational analysis performed in this study. This file additionally includes supplementary table legends and Table S2.
Figure S2 from Anti–PD-L1 Treatment Results in Functional Remodeling of the Macrophage Compartment
Authors: Xiong Huizhong , Mittman Stephanie , Rodriguez Ryan , Moskalenko Marina , Pacheco-Sanchez Patricia , Yang Yagai , Nickles Dorothee , Cubas Rafael
Published: April 2023

Anti-PDL1 treatment leads to genome-wide TAM and monocyte re-programming
Figure S1 from Anti–PD-L1 Treatment Results in Functional Remodeling of the Macrophage Compartment
Authors: Xiong Huizhong , Mittman Stephanie , Rodriguez Ryan , Moskalenko Marina , Pacheco-Sanchez Patricia , Yang Yagai , Nickles Dorothee , Cubas Rafael
Published: April 2023

Tumor macrophages have a suppressive phenotype
Supplementary Table S1 from Collagen Remodeling in the Hypoxic Tumor-Mesothelial Niche Promotes Ovarian Cancer Metastasis
Authors: Natarajan Suchitra , Foreman Kaitlyn M. , Soriano Michaela I. , Rossen Ninna S. , Shehade Hussein , Fregoso Daniel R. , Eggold Joshua T. , Krishnan Venkatesh , Dorigo Oliver , Krieg Adam J. , Heilshorn Sarah C. , Sinha Subarna , Fuh Katherine C. , Rankin Erinn B.
Published: April 2023

Supplementary Table S1 shows the list of genes upregulated in metastasis verus matched primary HGSOC. Suppl. to Fig 1.
Figure S5 from Oncogenic Properties of the Antisense lncRNA COMET in BRAF- and RET-Driven Papillary Thyroid Carcinomas
Authors: Esposito Roberta , Esposito Daniela , Pallante Pierlorenzo , Fusco Alfredo , Ciccodicola Alfredo , Costa Valerio
Published: April 2023

COMET silencing specificity
Supplementary Figure 3 from Targeting Hippo-Dependent and Hippo-Independent YAP1 Signaling for the Treatment of Childhood Rhabdomyosarcoma
Authors: Slemmons Katherine K. , Yeung Choh , Baumgart Joshua T. , Juarez Jhazeel O. Martinez , McCalla Amy , Helman Lee J.
Published: April 2023

YEST348I expression rescues Dasatinib treatment in aRMS cells.
Supplementary Figure 2 from Targeting Hippo-Dependent and Hippo-Independent YAP1 Signaling for the Treatment of Childhood Rhabdomyosarcoma
Authors: Slemmons Katherine K. , Yeung Choh , Baumgart Joshua T. , Juarez Jhazeel O. Martinez , McCalla Amy , Helman Lee J.
Published: April 2023

RASSF family expression in additional RMS cell lines.
Supplemental Table and Figure Legends from Targeting Hippo-Dependent and Hippo-Independent YAP1 Signaling for the Treatment of Childhood Rhabdomyosarcoma
Authors: Slemmons Katherine K. , Yeung Choh , Baumgart Joshua T. , Juarez Jhazeel O. Martinez , McCalla Amy , Helman Lee J.
Published: April 2023

Supplemental Table and Figure Legends for Tables 1-2 and Figures 1-5
Figure S1 from Oncogenic Properties of the Antisense lncRNA COMET in BRAF- and RET-Driven Papillary Thyroid Carcinomas
Authors: Esposito Roberta , Esposito Daniela , Pallante Pierlorenzo , Fusco Alfredo , Ciccodicola Alfredo , Costa Valerio
Published: April 2023

Summary of the computational framework
Supplemental Table 1,2 and figure 1,2,3 from Eomes+T-betlow CD8+ T Cells Are Functionally Impaired and Are Associated with Poor Clinical Outcome in Patients with Acute Myeloid Leukemia
Authors: Jia Bei , Zhao Chenchen , Rakszawski Kevin L. , Claxton David F. , Ehmann W. Christopher , Rybka Witold B. , Mineishi Shin , Wang Ming , Shike Hiroko , Bayerl Michael G. , Sivik Jeffrey M. , Schell Todd D. , Drabick Joseph J. , Hohl Raymond J. , Zheng Hong
Published: April 2023

Supplemental Table 1: Analysis of potential confounding factors; Supplemental Table 2: Multivariate Cox proportional hazard analysis; Supplemental Figure 1: The expression of CXCR5 and TCF1; Supplemental Figure 2: Comparing Fraction III CD8 T cells vs. overall survival; Supplemental Figure 3: The expression of CD39.
Supplementary Table 3 from A Single-Step, High-Dose Selection Scheme Reveals Distinct Mechanisms of Acquired Resistance to Oncogenic Kinase Inhibition in Cancer Cells
Authors: Finn Kenneth J. , Martin Scott E. , Settleman Jeff
Published: April 2023

Sampling from the literature, highlighting methodology used for resistance modeling.
Supplementary Table 2 from A Single-Step, High-Dose Selection Scheme Reveals Distinct Mechanisms of Acquired Resistance to Oncogenic Kinase Inhibition in Cancer Cells
Authors: Finn Kenneth J. , Martin Scott E. , Settleman Jeff
Published: April 2023

Summary of sequencing results from BRAF transgene knock-in clones.
Supplementary Data from A Genome-Wide Association Study Identifies Two Novel Susceptible Regions for Squamous Cell Carcinoma of the Head and Neck
Authors: Shete Sanjay , Liu Hongliang , Wang Jian , Yu Robert , Sturgis Erich M. , Li Guojun , Dahlstrom Kristina R. , Liu Zhensheng , Amos Christopher I. , Wei Qingyi
Published: April 2023

Supp Figures 1-7. Supplementary Figure 1: Workflow of the two-phase study (discovery and replication). Supplementary Figure 2: Proportion of ancestry inference using first and second principal component (PC) score in the discovery study (including 2,171 cases and 4,507 controls). Supplementary Figure 3: Histogram of imputation quality info (R-squared) of SNPs in the discovery GWAS study. Supplementary Figure 4: Quantile-quantile (Q-Q) plots of observed and expected P-values for discovery results. Supplementary Figure 5: eQTL results of representative SNPs in four identified regions in GTEx (https://gtexportal.org/home/). Supplementary Figure 6: Significant eQTL results of representative SNPs or their high LD SNPs. Supplementary Figure 7: Differential expression analysis of five genes in the identified regions by using the mRNA expression data in 520 SCCHN tumor tissues and 44 adjacent normal tissue in TCGA (http://ualcan.path.uab.edu/cgi-bin/ualcan-res.pl).
Supplementary Table 1 from A Single-Step, High-Dose Selection Scheme Reveals Distinct Mechanisms of Acquired Resistance to Oncogenic Kinase Inhibition in Cancer Cells
Authors: Finn Kenneth J. , Martin Scott E. , Settleman Jeff
Published: April 2023

Mean viability data from small molecule screen.
Supplementary Figures and Legends from A Single-Step, High-Dose Selection Scheme Reveals Distinct Mechanisms of Acquired Resistance to Oncogenic Kinase Inhibition in Cancer Cells
Authors: Finn Kenneth J. , Martin Scott E. , Settleman Jeff
Published: April 2023

Supplementary Figures 1-8, with corresponding legends.
Supplementary Table 1 and 2 from 4E-BP1 Is a Tumor Suppressor Protein Reactivated by mTOR Inhibition in Head and Neck Cancer
Authors: Wang Zhiyong , Feng Xiaodong , Molinolo Alfredo A. , Martin Daniel , Vitale-Cross Lynn , Nohata Nijiro , Ando Mizuo , Wahba Amy , Amornphimoltham Panomwat , Wu Xingyu , Gilardi Mara , Allevato Michael , Wu Victoria , Steffen Dana J. , Tofilon Philip , Sonenberg Nahum , Califano Joseph , Chen Qianming , Lippman Scott M. , Gutkind J. Silvio
Published: April 2023

Supplementary Table 1 shows the list of oligonucleotides used for qPCR. Supplementary Table 2 shows the complete list of genes whose polysome association was significantly altered by mTOR inhibition.
Supplementary Figure S1-S7 from Targeted Metabolomics Identifies the Cytochrome P450 Monooxygenase Eicosanoid Pathway as a Novel Therapeutic Target of Colon Tumorigenesis
Authors: Wang Weicang , Yang Jun , Edin Matthew L. , Wang Yuxin , Luo Ying , Wan Debin , Yang Haixia , Song Chun-Qing , Xue Wen , Sanidad Katherine Z. , Song Mingyue , Bisbee Heather A. , Bradbury Jennifer A. , Nan Guanjun , Zhang Jianan , Shih Pei-an Betty , Lee Kin Sing Stephen , Minter Lisa M. , Kim Daeyoung , Xiao Hang , Liu Jun-Yan , Hammock Bruce D. , Zeldin Darryl C. , Zhang Guodong
Published: April 2023

SF1: CYP monooxygenase expression in human colon cancer cells; SF2: gene expression of Cyp2e1 in the liver of Cyp2c+/+, Cyp2c+/-, and Cyp2c-/- mice; SF3: liver inflammation in Cyp2c+/+, Cyp2c+/-, and Cyp2c-/- mice; SF4: survival curve of the AOM/DSS-stimulated Cyp2c+/+, Cyp2c+/-, and Cyp2c-/- mice; SF5: pharmacological inhibition of CYP monooxygenases suppresses AOM/DSS-induced colon tumorigenesis in mice; SF6: effects of 12,13-EpOME on MC38 tumor growth in C57BL/6 mice; SF7: mRNA expression levels of CYP monooxygenases in control subjects and colon cancer patients
Supplementary Figure S4 from 4E-BP1 Is a Tumor Suppressor Protein Reactivated by mTOR Inhibition in Head and Neck Cancer
Authors: Wang Zhiyong , Feng Xiaodong , Molinolo Alfredo A. , Martin Daniel , Vitale-Cross Lynn , Nohata Nijiro , Ando Mizuo , Wahba Amy , Amornphimoltham Panomwat , Wu Xingyu , Gilardi Mara , Allevato Michael , Wu Victoria , Steffen Dana J. , Tofilon Philip , Sonenberg Nahum , Califano Joseph , Chen Qianming , Lippman Scott M. , Gutkind J. Silvio
Published: April 2023

Supplementary Figure S4 shows (A) Western blot analysis, (B) m7GTP pull down, (C) eIF4G co-IP analyzing the regulation of the translation initiation complex formation by 4E-BP1; D, densitometry analysis of western blots in Figure S4B; E, tumor growth curve and F, representative histological tissue sections of HN12 cells expressing empty vector (iG) or 4EBP1 M (iG 4E-BP1).
Supplementary Figure S2 from 4E-BP1 Is a Tumor Suppressor Protein Reactivated by mTOR Inhibition in Head and Neck Cancer
Authors: Wang Zhiyong , Feng Xiaodong , Molinolo Alfredo A. , Martin Daniel , Vitale-Cross Lynn , Nohata Nijiro , Ando Mizuo , Wahba Amy , Amornphimoltham Panomwat , Wu Xingyu , Gilardi Mara , Allevato Michael , Wu Victoria , Steffen Dana J. , Tofilon Philip , Sonenberg Nahum , Califano Joseph , Chen Qianming , Lippman Scott M. , Gutkind J. Silvio
Published: April 2023

Supplementary Figure S2 shows A, the first intron of EIF4E-BP1 as an active target for epigenetic regulation of transcription; and B, 4NQO-induced tumors in eif4e-bp1/2 KO mice.
Table S1 from Tumor-Derived Prostaglandin E2 Promotes p50 NF-κB-Dependent Differentiation of Monocytic MDSCs
Authors: Porta Chiara , Consonni Francesca Maria , Morlacchi Sara , Sangaletti Sabina , Bleve Augusto , Totaro Maria Grazia , Larghi Paola , Rimoldi Monica , Tripodo Claudio , Strauss Laura , Banfi Stefania , Storto Mariangela , Pressiani Tiziana , Rimassa Lorenza , Tartari Silvia , Ippolito Alessandro , Doni Andrea , Soldà Giulia , Duga Stefano , Piccolo Viviana , Ostuni Renato , Natoli Gioacchino , Bronte Vincenzo , Balzac Fiorella , Turco Emilia , Hirsch Emilio , Colombo Mario P. , Sica Antonio
Published: April 2023

selective gene expression alterations in p50-/- M-MDSC stimulated with IFNγ for 4 hours as compared to WT M-MDSC
Supplementary Figure S1 from 4E-BP1 Is a Tumor Suppressor Protein Reactivated by mTOR Inhibition in Head and Neck Cancer
Authors: Wang Zhiyong , Feng Xiaodong , Molinolo Alfredo A. , Martin Daniel , Vitale-Cross Lynn , Nohata Nijiro , Ando Mizuo , Wahba Amy , Amornphimoltham Panomwat , Wu Xingyu , Gilardi Mara , Allevato Michael , Wu Victoria , Steffen Dana J. , Tofilon Philip , Sonenberg Nahum , Califano Joseph , Chen Qianming , Lippman Scott M. , Gutkind J. Silvio
Published: April 2023

Supplementary Figure S1 shows A, EIF4E-BP1 alterations in HNSCC; B, EIF4E-BP1 expression and HNSCC survival; C, 4E-BP1 re-expression analysis; and D, Spearman rank correlation coefficient analysis of EIF4E-BP1.
Figure S5 from The Lymphatic Cell Environment Promotes Kaposi Sarcoma Development by Prox1-Enhanced Productive Lytic Replication of Kaposi Sarcoma Herpes Virus
Authors: Choi Dongwon , Park Eunkyung , Kim Kyu Eui , Jung Eunson , Seong Young Jin , Zhao Luping , Madhavan Shrimika , Daghlian George , Lee Hansuh H. , Daghlian Patill T. , Daghlian Saren , Bui Khoa , Koh Chester J. , Wong Alex K. , Cho Il-Taeg , Hong Young-Kwon
Published: April 2023

Lytic DNA replication is essential for persistent KSHV infection in LECs
Figure S4 from The Lymphatic Cell Environment Promotes Kaposi Sarcoma Development by Prox1-Enhanced Productive Lytic Replication of Kaposi Sarcoma Herpes Virus
Authors: Choi Dongwon , Park Eunkyung , Kim Kyu Eui , Jung Eunson , Seong Young Jin , Zhao Luping , Madhavan Shrimika , Daghlian George , Lee Hansuh H. , Daghlian Patill T. , Daghlian Saren , Bui Khoa , Koh Chester J. , Wong Alex K. , Cho Il-Taeg , Hong Young-Kwon
Published: April 2023

RTA gene is required for KSHV viral maintenance in LECs
Figure S3 from The Lymphatic Cell Environment Promotes Kaposi Sarcoma Development by Prox1-Enhanced Productive Lytic Replication of Kaposi Sarcoma Herpes Virus
Authors: Choi Dongwon , Park Eunkyung , Kim Kyu Eui , Jung Eunson , Seong Young Jin , Zhao Luping , Madhavan Shrimika , Daghlian George , Lee Hansuh H. , Daghlian Patill T. , Daghlian Saren , Bui Khoa , Koh Chester J. , Wong Alex K. , Cho Il-Taeg , Hong Young-Kwon
Published: April 2023

Productive Lytic Replication in LECs, but not in BECs
Figure S2 from The Lymphatic Cell Environment Promotes Kaposi Sarcoma Development by Prox1-Enhanced Productive Lytic Replication of Kaposi Sarcoma Herpes Virus
Authors: Choi Dongwon , Park Eunkyung , Kim Kyu Eui , Jung Eunson , Seong Young Jin , Zhao Luping , Madhavan Shrimika , Daghlian George , Lee Hansuh H. , Daghlian Patill T. , Daghlian Saren , Bui Khoa , Koh Chester J. , Wong Alex K. , Cho Il-Taeg , Hong Young-Kwon
Published: April 2023

Different infection pattern between LECs and BECs.
Supplementary Methods from A Protease-Activated Fluorescent Probe Allows Rapid Visualization of Keratinocyte Carcinoma during Excision
Authors: Walker Ethan , Liu Yiqiao , Kim InYoung , Biro Mark , Iyer Sukanya Raj , Ezaldein Harib , Scott Jeffrey , Merati Miesha , Mistur Rachel , Zhou Bo , Straight Brian , Yim Joshua J. , Bogyo Matthew , Mann Margaret , Wilson David L. , Basilion James P. , Popkin Daniel L.
Published: April 2023

Supplementary Methods include description of: 1) "Puzzle"-fit" analysis, 2) Intensity-based objective sensitivity and specificity analysis, 3) Blinded physician "Reader Study" analysis, and 4) Evaluation of reader responses regarding intensity.
Supplementary Data from Acetylation of CCAR2 Establishes a BET/BRD9 Acetyl Switch in Response to Combined Deacetylase and Bromodomain Inhibition
Authors: Rajendran Praveen , Johnson Gavin , Li Li , Chen Ying-Shiuan , Dashwood Mohaiza , Nguyen Nhung , Ulusan Ahmet , Ertem Furkan , Zhang Mutian , Li Jia , Sun Deqiang , Huang Yun , Wang Shan , Leung Hon-Chiu , Lieberman David , Beaver Laura , Ho Emily , Bedford Mark , Chang Kyle , Vilar Eduardo , Dashwood Roderick
Published: April 2023

Fig S1 shows HDAC3 knockdown, Fig S2 shows CCAR2 acetylation in SW480 colon cancer cells. Fig S3 shows mass spectrometry data, Fig S4 shows acetylation mutant data, Fig S5 shows a Working model, Fig S6 shows genetically encoded acetylation data, Fig S7 shows in silico docking, Fig S8 shows apoptosis by SFN+JQ1, Fig S9 shows CCAR2/β-catenin interaction in human polyps, and Fig S10 shows ChIP data in cells.
Figure S2 from A Protease-Activated Fluorescent Probe Allows Rapid Visualization of Keratinocyte Carcinoma during Excision
Authors: Walker Ethan , Liu Yiqiao , Kim InYoung , Biro Mark , Iyer Sukanya Raj , Ezaldein Harib , Scott Jeffrey , Merati Miesha , Mistur Rachel , Zhou Bo , Straight Brian , Yim Joshua J. , Bogyo Matthew , Mann Margaret , Wilson David L. , Basilion James P. , Popkin Daniel L.
Published: April 2023

Figure S2 shows histology of all false negative (FN) skin cancer samples.
Supplementary Table from EIF3H Orchestrates Hippo Pathway–Mediated Oncogenesis via Catalytic Control of YAP Stability
Authors: Zhou Zhuan , Zhou Honghong , Ponzoni Luca , Luo Aiping , Zhu Rui , He Mingjing , Huang Yi , Guan Kun-Liang , Bahar Ivet , Liu Zhihua , Wan Yong
Published: April 2023

Tab S1 Mass spectry proteins report of F/H-EIF3H purification. Tab S2 Characteristics of breast invasive ductal carcinoma patients
Supplemental Figures 1-11 from EIF3H Orchestrates Hippo Pathway–Mediated Oncogenesis via Catalytic Control of YAP Stability
Authors: Zhou Zhuan , Zhou Honghong , Ponzoni Luca , Luo Aiping , Zhu Rui , He Mingjing , Huang Yi , Guan Kun-Liang , Bahar Ivet , Liu Zhihua , Wan Yong
Published: April 2023

Fig.S1 EIF3H promotes EMT and tumor invasion. Fig.S2 Clinico-pathological correlations of EIF3H. Fig.S3 Lys63-linked tetra-ubiquitin in-vitro cleavage assay. Fig.S4 GST Pull-down assay. Fig.S5 EIF3H binds to YAP1 and stabilizes YAP1. Fig.S6 EIF3H acts as a deubiquitinase that stabilizes YAP from ubiquitin-dependent degradation. Fig. S7 Molecular docking analysis. Fig. S8 EIF3H acts as a deubiquitinase that stabilizes YAP and promotes epithelial-mesenchymal transition. Fig. S9 Stabilization of YAP by EIF3H promotes breast cancer invasion and metastasis. Fig. S10 Blockade of EIF3H phosphorylation and YAP expression inhibit tumor cells invasion. Fig. S11 Stabilization of YAP by EIF3H promotes breast cancer invasion and metastasis.
Supplementary Fig 7 from Myc and Loss of p53 Cooperate to Drive Formation of Choroid Plexus Carcinoma
Authors: Wang Jun , Merino Diana M. , Light Nicholas , Murphy Brian L. , Wang Yong-Dong , Guo Xiaohui , Hodges Andrew P. , Chau Lianne Q. , Liu Kun-Wei , Dhall Girish , Asgharzadeh Shahab , Kiehna Erin N. , Shirey Ryan J. , Janda Kim D. , Taylor Michael D. , Malkin David , Ellison David W. , VandenBerg Scott R. , Eberhart Charles G. , Sears Rosalie C. , Roussel Martine F. , Gilbertson Richard J. , Wechsler-Reya Robert J.
Published: April 2023

Figure S7 shows effects of CDK4/6 inhibitors on viability of mouse CPC cells and drug synergy between Triptolide and Dinaciclib.
Supplementary Table 1-7 from Whole Genome–Derived Tiled Peptide Arrays Detect Prediagnostic Autoantibody Signatures in Non–Small-Cell Lung Cancer
Authors: Yan Yuanqing , Sun Nan , Wang Hong , Kobayashi Makoto , Ladd Jon J. , Long James P. , Lo Ken C. , Patel Jigar , Sullivan Eric , Albert Thomas , Goodman Gary E. , Do Kim-Anh , Hanash Samir M.
Published: April 2023

Supplementary Table 1. Subject characteristics, Supplementary. Table 2 Proteins with three or more hotspots higher in control. Supplementary Table 3. Empirical distribution of reactive hot spot differences between cases and controls based on 500 permutation tests for the set of 35 and 9 proteins with case/control reactivity differences. Supplementary Table 4 Gene set enrichment of canonical pathways. Supplementary Table 5 AUCs of proteins with three or more hotspots in squamous lung cancer and their occurrence in the Ig bound and Ig free fractions by mass spectrometry. Supplementary Table 6 AUCs of proteins with three or more hotspots in adenocarcinoma and their occurrence in the Ig bound and Ig free fractions by mass spectrometry. Supplementary Table 7: Proteins with two hot spots among all cases.
Supplementary Fig 6 from Myc and Loss of p53 Cooperate to Drive Formation of Choroid Plexus Carcinoma
Authors: Wang Jun , Merino Diana M. , Light Nicholas , Murphy Brian L. , Wang Yong-Dong , Guo Xiaohui , Hodges Andrew P. , Chau Lianne Q. , Liu Kun-Wei , Dhall Girish , Asgharzadeh Shahab , Kiehna Erin N. , Shirey Ryan J. , Janda Kim D. , Taylor Michael D. , Malkin David , Ellison David W. , VandenBerg Scott R. , Eberhart Charles G. , Sears Rosalie C. , Roussel Martine F. , Gilbertson Richard J. , Wechsler-Reya Robert J.
Published: April 2023

Figure S6 shows Monte Carlo simulation to test the probability of significantly underexpressed human and murine genes overlapping by chance.
Supplementary Fig 1 from Myc and Loss of p53 Cooperate to Drive Formation of Choroid Plexus Carcinoma
Authors: Wang Jun , Merino Diana M. , Light Nicholas , Murphy Brian L. , Wang Yong-Dong , Guo Xiaohui , Hodges Andrew P. , Chau Lianne Q. , Liu Kun-Wei , Dhall Girish , Asgharzadeh Shahab , Kiehna Erin N. , Shirey Ryan J. , Janda Kim D. , Taylor Michael D. , Malkin David , Ellison David W. , VandenBerg Scott R. , Eberhart Charles G. , Sears Rosalie C. , Roussel Martine F. , Gilbertson Richard J. , Wechsler-Reya Robert J.
Published: April 2023

Figure S1 shows other models of choroid plexus tumors generated from different Cre lines and their corresponding Kaplan-Meier survival curve.
Supplementary Figure. S4 from Disruption of Endolysosomal RAB5/7 Efficiently Eliminates Colorectal Cancer Stem Cells
Authors: Takeda Mitsunobu , Koseki Jun , Takahashi Hidekazu , Miyoshi Norikatsu , Nishida Naohiro , Nishimura Junichi , Hata Taishi , Matsuda Chu , Mizushima Tsunekazu , Yamamoto Hirofumi , Ishii Hideshi , Doki Yuichiro , Mori Masaki , Haraguchi Naotsugu
Published: April 2023

Double knockdown of RAB5/7.
Supplementary Figure. S3 from Disruption of Endolysosomal RAB5/7 Efficiently Eliminates Colorectal Cancer Stem Cells
Authors: Takeda Mitsunobu , Koseki Jun , Takahashi Hidekazu , Miyoshi Norikatsu , Nishida Naohiro , Nishimura Junichi , Hata Taishi , Matsuda Chu , Mizushima Tsunekazu , Yamamoto Hirofumi , Ishii Hideshi , Doki Yuichiro , Mori Masaki , Haraguchi Naotsugu
Published: April 2023

Only the mice treated by MQ+SN-38 revealed no apparent signs of tumor regrowth.
Table S1 from A Custom Genotyping Array Reveals Population-Level Heterogeneity for the Genetic Risks of Prostate Cancer and Other Cancers in Africa
Authors: Harlemon Maxine , Ajayi Olabode , Kachambwa Paidamoyo , Kim Michelle S. , Simonti Corinne N. , Quiver Melanie H. , Petersen Desiree C. , Mittal Anuradha , Fernandez Pedro W. , Hsing Ann W. , Baichoo Shakuntala , Agalliu Ilir , Jalloh Mohamed , Gueye Serigne M. , Snyper Nana Yaa F. , Adusei Ben , Mensah James E. , Abrahams Afua O.D. , Adebiyi Akindele O. , Orunmuyi Akin T. , Aisuodionoe-Shadrach Oseremen I. , Nwegbu Maxwell M. , Joffe Maureen , Chen Wenlong C. , Irusen Hayley , Neugut Alfred I. , Quintana Yuri , Seutloali Moleboheng , Fadipe Mayowa B. , Warren Christopher , Woehrmann Marcos H. , Zhang Peng , Ongaco Chrissie M. , Mawhinney Michelle , McBride Jo , Andrews Caroline V. , Adams Marcia , Pugh Elizabeth , Rebbeck Timothy R. , Petersen Lindsay N. , Lachance Joseph
Published: April 2023

Successfully called markers on the MADCaP Array. This tab-delimited file includes genomic positions, inclusion criteria, and overlap with other arrays.
Figure S1 from A Custom Genotyping Array Reveals Population-Level Heterogeneity for the Genetic Risks of Prostate Cancer and Other Cancers in Africa
Authors: Harlemon Maxine , Ajayi Olabode , Kachambwa Paidamoyo , Kim Michelle S. , Simonti Corinne N. , Quiver Melanie H. , Petersen Desiree C. , Mittal Anuradha , Fernandez Pedro W. , Hsing Ann W. , Baichoo Shakuntala , Agalliu Ilir , Jalloh Mohamed , Gueye Serigne M. , Snyper Nana Yaa F. , Adusei Ben , Mensah James E. , Abrahams Afua O.D. , Adebiyi Akindele O. , Orunmuyi Akin T. , Aisuodionoe-Shadrach Oseremen I. , Nwegbu Maxwell M. , Joffe Maureen , Chen Wenlong C. , Irusen Hayley , Neugut Alfred I. , Quintana Yuri , Seutloali Moleboheng , Fadipe Mayowa B. , Warren Christopher , Woehrmann Marcos H. , Zhang Peng , Ongaco Chrissie M. , Mawhinney Michelle , McBride Jo , Andrews Caroline V. , Adams Marcia , Pugh Elizabeth , Rebbeck Timothy R. , Petersen Lindsay N. , Lachance Joseph
Published: April 2023

Figure S1. Cross-validation error in ADMIXTURE analyses. The best fit to data occurs at K = 3.