bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Data from MVisAGe Identifies Concordant and Discordant Genomic Alterations of Driver Genes in Squamous Tumors
Authors: Walter Vonn , Du Ying , Danilova Ludmila , Hayward Michele C. , Hayes D. Neil
Published: March 2023

This file contains summary data tables and MVisAGe output described in the manuscript.
Supplementary Data from MVisAGe Identifies Concordant and Discordant Genomic Alterations of Driver Genes in Squamous Tumors
Authors: Walter Vonn , Du Ying , Danilova Ludmila , Hayward Michele C. , Hayes D. Neil
Published: March 2023

Description of the use of the mixtools R package to fit mixture models of two normal distributions to gene-level Pearson correlation coefficients.
Table S3 from Licofelone Enhances the Efficacy of Paclitaxel in Ovarian Cancer by Reversing Drug Resistance and Tumor Stem-like Properties
Authors: Hirst Jeff , Pathak Harsh B. , Hyter Stephen , Pessetto Ziyan Y. , Ly Thuc , Graw Stefan , Koestler Devin C. , Krieg Adam J. , Roby Katherine F. , Godwin Andrew K.
Published: March 2023

Supplemental Table 3. Mante-Haenszel hazard ratio shows licofelone combination increases the efficacy of paclitaxel.
Figures S1-S2 from Expression of Adipocyte/Macrophage Fatty Acid–Binding Protein in Tumor-Associated Macrophages Promotes Breast Cancer Progression
Authors: Hao Jiaqing , Yan Fei , Zhang Yuwen , Triplett Ashley , Zhang Ying , Schultz Debra A. , Sun Yanwen , Zeng Jun , Silverstein Kevin A.T. , Zheng Qi , Bernlohr David A. , Cleary Margot P. , Egilmez Nejat K. , Sauter Edward , Liu Shujun , Suttles Jill , Li Bing
Published: March 2023

Figure S1 shows PROGgene anaysis of FABP/breast cancer survival associations in TCGA dataset. Figure S2 shows immunopheotype of naive WT and A-FABP-/- mice.
Suppl Figure Legends and Tables from FSTL1 Promotes Metastasis and Chemoresistance in Esophageal Squamous Cell Carcinoma through NFκB–BMP Signaling Cross-talk
Authors: Lau Marco Chi-Chung , Ng Kai Yu , Wong Tin Lok , Tong Man , Lee Terence K. , Ming Xiao-Yan , Law Simon , Lee Nikki P. , Cheung Annie L. , Qin Yan-Ru , Chan Kwok Wah , Ning Wen , Guan Xin-Yuan , Ma Stephanie
Published: March 2023

Suppl Figure Legends 1-5 and Tables showing clinico-pathological correlation of endogenous and secretory FSTL1 as well as pathway analysis of ESCC cells with or without FSTL1 overexpressed.
Suppl Figure 4 from FSTL1 Promotes Metastasis and Chemoresistance in Esophageal Squamous Cell Carcinoma through NFκB–BMP Signaling Cross-talk
Authors: Lau Marco Chi-Chung , Ng Kai Yu , Wong Tin Lok , Tong Man , Lee Terence K. , Ming Xiao-Yan , Law Simon , Lee Nikki P. , Cheung Annie L. , Qin Yan-Ru , Chan Kwok Wah , Ning Wen , Guan Xin-Yuan , Ma Stephanie
Published: March 2023

Quantification of number of cells that migrated through a membrane, invaded through a Matrigel-coated membrane, formed spheroids or formed colonies in (A) KYSE150-Luc cells co-cultured with conditioned medium collected from EV or FSTL1 OE cells; or (B) KYSE150-Luc cells treated with control or recombinant FSTL1, in the presence or absence of IMD-0354.
Suppl Figure 3 from FSTL1 Promotes Metastasis and Chemoresistance in Esophageal Squamous Cell Carcinoma through NFκB–BMP Signaling Cross-talk
Authors: Lau Marco Chi-Chung , Ng Kai Yu , Wong Tin Lok , Tong Man , Lee Terence K. , Ming Xiao-Yan , Law Simon , Lee Nikki P. , Cheung Annie L. , Qin Yan-Ru , Chan Kwok Wah , Ning Wen , Guan Xin-Yuan , Ma Stephanie
Published: March 2023

FSTL1(+) cells in ESCC clinical samples that received (with treatment, n = 22) or did not receive (without treatment, n = 15) chemotherapy treatment prior to resection, as detected by IHC analyses.
Table S2 from Discovery of Human-Similar Gene Fusions in Canine Cancers
Authors: Ulvé Ronan , Rault Mélanie , Bahin Mathieu , Lagoutte Laetitia , Abadie Jérôme , De Brito Clotilde , Coindre Jean-Michel , Botherel Nadine , Rousseau Audrey , Wucher Valentin , Cadieu Edouard , Thieblemont Catherine , Hitte Christophe , Cornevin Laurence , Cabillic Florian , Bachelot Laura , Gilot David , Hennuy Benoit , Guillaudeux Thierry , Le Goff Arnaud , Derrien Thomas , Hédan Benoît , André Catherine
Published: March 2023

Primers used for validation of the canine gene fusions.
Table S1 from NFAT1-Mediated Regulation of NDEL1 Promotes Growth and Invasion of Glioma Stem-like Cells
Authors: Jiang Yang , Song Yifu , Wang Run , Hu Tianhao , Zhang Di , Wang Zixun , Tie Xinxin , Wang Minghao , Han Sheng
Published: March 2023

Clinical information of G10 and G03
Figure S3 from Discovery of Human-Similar Gene Fusions in Canine Cancers
Authors: Ulvé Ronan , Rault Mélanie , Bahin Mathieu , Lagoutte Laetitia , Abadie Jérôme , De Brito Clotilde , Coindre Jean-Michel , Botherel Nadine , Rousseau Audrey , Wucher Valentin , Cadieu Edouard , Thieblemont Catherine , Hitte Christophe , Cornevin Laurence , Cabillic Florian , Bachelot Laura , Gilot David , Hennuy Benoit , Guillaudeux Thierry , Le Goff Arnaud , Derrien Thomas , Hédan Benoît , André Catherine
Published: March 2023

Characterization of the canine anaplastic oligodendroglioma.
Figure S4 from NFAT1-Mediated Regulation of NDEL1 Promotes Growth and Invasion of Glioma Stem-like Cells
Authors: Jiang Yang , Song Yifu , Wang Run , Hu Tianhao , Zhang Di , Wang Zixun , Tie Xinxin , Wang Minghao , Han Sheng
Published: March 2023

NFAT1-NDEL1 signaling affects Erk activation and stemness marker expression.
Figure S2 from NFAT1-Mediated Regulation of NDEL1 Promotes Growth and Invasion of Glioma Stem-like Cells
Authors: Jiang Yang , Song Yifu , Wang Run , Hu Tianhao , Zhang Di , Wang Zixun , Tie Xinxin , Wang Minghao , Han Sheng
Published: March 2023

Isolation of glioma stem-like cells.
Supplementary Data 8 from Inhibition of EphB4–Ephrin-B2 Signaling Reprograms the Tumor Immune Microenvironment in Head and Neck Cancers
Authors: Bhatia Shilpa , Oweida Ayman , Lennon Shelby , Darragh Laurel B. , Milner Dallin , Phan Andy V. , Mueller Adam C. , Van Court Benjamin , Raben David , Serkova Natalie J. , Wang Xiao-Jing , Jimeno Antonio , Clambey Eric T. , Pasquale Elena B. , Karam Sana D.
Published: March 2023

Mice implanted with PDX tumors show significantly reduced uptake of supra-paramagnetic iron oxide nanoparticles (SPIO) in the combined sEphB4-HSA and RT group compared to the groups treated with RT alone or with sEphB4-HSA alone in DCE-MRI imaging (A-B). Delta T2 represents magnitude of decrease in T2 signal. One-way ANOVA was used to calculate the significance of the differences between groups. CIBERSORT analysis of a HNSCC TCGA dataset shows that patients with low M2:M1 ratio have improved overall survival (C) and disease-free survival (D). Analysis of HNSCC TCGA showing correlation between M2-related marker-HRH1 and ephrin-B2 (EFNB2) (E), EphB4 (F).
Supplemental Table I from Cross-talk Signaling between HER3 and HPV16 E6 and E7 Mediates Resistance to PI3K Inhibitors in Head and Neck Cancer
Authors: Brand Toni M. , Hartmann Stefan , Bhola Neil E. , Li Hua , Zeng Yan , O'Keefe Rachel A. , Ranall Max V. , Bandyopadhyay Sourav , Soucheray Margaret , Krogan Nevan J. , Kemp Carolyn , Duvvuri Umamaheswar , LaVallee Theresa , Johnson Daniel E. , Ozbun Michelle A. , Bauman Julie E. , Grandis Jennifer R.
Published: March 2023

Clinical characteristics of patients prior to surgery and PDX establishment
Supplemental Figure 4 from Cross-talk Signaling between HER3 and HPV16 E6 and E7 Mediates Resistance to PI3K Inhibitors in Head and Neck Cancer
Authors: Brand Toni M. , Hartmann Stefan , Bhola Neil E. , Li Hua , Zeng Yan , O'Keefe Rachel A. , Ranall Max V. , Bandyopadhyay Sourav , Soucheray Margaret , Krogan Nevan J. , Kemp Carolyn , Duvvuri Umamaheswar , LaVallee Theresa , Johnson Daniel E. , Ozbun Michelle A. , Bauman Julie E. , Grandis Jennifer R.
Published: March 2023

HER3 blockade enhances the sensitivity of HPV(+) cell lines to BKM120
Supplemental Figure 3 from Cross-talk Signaling between HER3 and HPV16 E6 and E7 Mediates Resistance to PI3K Inhibitors in Head and Neck Cancer
Authors: Brand Toni M. , Hartmann Stefan , Bhola Neil E. , Li Hua , Zeng Yan , O'Keefe Rachel A. , Ranall Max V. , Bandyopadhyay Sourav , Soucheray Margaret , Krogan Nevan J. , Kemp Carolyn , Duvvuri Umamaheswar , LaVallee Theresa , Johnson Daniel E. , Ozbun Michelle A. , Bauman Julie E. , Grandis Jennifer R.
Published: March 2023

Blockade of the PI3K pathway with BKM120 or BEZ235 increases HER3/AKT signaling
Supplementary Data 1 from Inhibition of EphB4–Ephrin-B2 Signaling Reprograms the Tumor Immune Microenvironment in Head and Neck Cancers
Authors: Bhatia Shilpa , Oweida Ayman , Lennon Shelby , Darragh Laurel B. , Milner Dallin , Phan Andy V. , Mueller Adam C. , Van Court Benjamin , Raben David , Serkova Natalie J. , Wang Xiao-Jing , Jimeno Antonio , Clambey Eric T. , Pasquale Elena B. , Karam Sana D.
Published: March 2023

Immunofluorescence staining showing co-expression of EphB4 and pan-keratin in Ly2 tumors.
Video 2 from Computational Radiomics System to Decode the Radiographic Phenotype
Authors: van Griethuysen Joost J.M. , Fedorov Andriy , Parmar Chintan , Hosny Ahmed , Aucoin Nicole , Narayan Vivek , Beets-Tan Regina G.H. , Fillion-Robin Jean-Christophe , Pieper Steve , Aerts Hugo J.W.L.
Published: March 2023

Instruction Video with details about the Radiomics.io and the use of PyRadiomics, an engineered radiomic feature extraction platform.
Supplements from Computational Radiomics System to Decode the Radiographic Phenotype
Authors: van Griethuysen Joost J.M. , Fedorov Andriy , Parmar Chintan , Hosny Ahmed , Aucoin Nicole , Narayan Vivek , Beets-Tan Regina G.H. , Fillion-Robin Jean-Christophe , Pieper Steve , Aerts Hugo J.W.L.
Published: March 2023

Supplementary Material with detailed descriptions of: I) selected feature within analysis for lung lesion characterization, II) methods describing lung lesion datasets used in analysis, and radiomic feature extraction and data analysis details, III) feature definitions included in PyRadiomics, and IV) links to additional resources.
Supplementary Data: User guide from Hemap: An Interactive Online Resource for Characterizing Molecular Phenotypes across Hematologic Malignancies
Authors: Pölönen Petri , Mehtonen Juha , Lin Jake , Liuksiala Thomas , Häyrynen Sergei , Teppo Susanna , Mäkinen Artturi , Kumar Ashwini , Malani Disha , Pohjolainen Virva , Porkka Kimmo , Heckman Caroline A. , May Patrick , Hautamäki Ville , Granberg Kirsi J. , Lohi Olli , Nykter Matti , Heinäniemi Merja
Published: March 2023

User guide for hemap web application.
Supplementary Material 2 from Cross-Talk between Receptor Tyrosine Kinases AXL and ERBB3 Regulates Invadopodia Formation in Melanoma Cells
Authors: Revach Or-Yam , Sandler Oded , Samuels Yardena , Geiger Benjamin
Published: March 2023

In the Excel file, the raw data for the screens (3 in A375 cells, and 2 in 63T cells). Every tab contains one screen and all the genes that were tested. The data for each screen are quantified, and the results, summarized.
Table S1 from Enhancer Remodeling and MicroRNA Alterations Are Associated with Acquired Resistance to ALK Inhibitors
Authors: Yun Mi Ran , Lim Sun Min , Kim Seon-Kyu , Choi Hun Mi , Pyo Kyoung-Ho , Kim Seong Keun , Lee Ji Min , Lee You Won , Choi Jae Woo , Kim Hye Ryun , Hong Min Hee , Haam Keeok , Huh Nanhyung , Kim Jong-Hwan , Kim Yong Sung , Shim Hyo Sup , Soo Ross Andrew , Shih Jin-Yuan , Yang James Chih-Hsin , Kim Mirang , Cho Byoung Chul
Published: March 2023

qRT-PCR primers
Supplementary Table S1 from FGFR1-Activated Translation of WNT Pathway Components with Structured 5′ UTRs Is Vulnerable to Inhibition of EIF4A-Dependent Translation Initiation
Authors: Nguyen Tuan M. , Kabotyanski Elena B. , Dou Yongchao , Reineke Lucas C. , Zhang Peng , Zhang Xiang H.-F. , Malovannaya Anna , Jung Sung Yun , Mo Qianxing , Roarty Kevin P. , Chen Yiwen , Zhang Bing , Neilson Joel R. , Lloyd Richard E. , Perou Charles M. , Ellis Matthew J. , Rosen Jeffrey M.
Published: March 2023

Supplementary Table S1 provides expression data of RNA, ribosome occupancy and protein used for multi-omics correlation analysis as well as complete lists of TE UP, TE DOWN and background genes.
Supplementary Methods and Figure Legends from FGFR1-Activated Translation of WNT Pathway Components with Structured 5′ UTRs Is Vulnerable to Inhibition of EIF4A-Dependent Translation Initiation
Authors: Nguyen Tuan M. , Kabotyanski Elena B. , Dou Yongchao , Reineke Lucas C. , Zhang Peng , Zhang Xiang H.-F. , Malovannaya Anna , Jung Sung Yun , Mo Qianxing , Roarty Kevin P. , Chen Yiwen , Zhang Bing , Neilson Joel R. , Lloyd Richard E. , Perou Charles M. , Ellis Matthew J. , Rosen Jeffrey M.
Published: March 2023

Supplementary Methods and Figure Legends provide further details of the study methods and legends for supplementary figures and tables.
Supplementary Figure S5 from FGFR1-Activated Translation of WNT Pathway Components with Structured 5′ UTRs Is Vulnerable to Inhibition of EIF4A-Dependent Translation Initiation
Authors: Nguyen Tuan M. , Kabotyanski Elena B. , Dou Yongchao , Reineke Lucas C. , Zhang Peng , Zhang Xiang H.-F. , Malovannaya Anna , Jung Sung Yun , Mo Qianxing , Roarty Kevin P. , Chen Yiwen , Zhang Bing , Neilson Joel R. , Lloyd Richard E. , Perou Charles M. , Ellis Matthew J. , Rosen Jeffrey M.
Published: March 2023

Supplementary Figure S5 demonstrates that silvestrol treatment does not affect mouse body weight and proliferation rate of tumor cells, but selectively inhibits translation of WNT signaling components, and also shows that EIFA1 levels predominate EIF4A2 expression in the WNT/iR1 model, whose tumors are enriched with basal-like and Her2 signatures.
Supplementary Materials and Methods from Enhancer Remodeling and MicroRNA Alterations Are Associated with Acquired Resistance to ALK Inhibitors
Authors: Yun Mi Ran , Lim Sun Min , Kim Seon-Kyu , Choi Hun Mi , Pyo Kyoung-Ho , Kim Seong Keun , Lee Ji Min , Lee You Won , Choi Jae Woo , Kim Hye Ryun , Hong Min Hee , Haam Keeok , Huh Nanhyung , Kim Jong-Hwan , Kim Yong Sung , Shim Hyo Sup , Soo Ross Andrew , Shih Jin-Yuan , Yang James Chih-Hsin , Kim Mirang , Cho Byoung Chul
Published: March 2023

Supplementary Materials and Methods that contain detailed experimental procedures
Supplementary Figure S1 from FGFR1-Activated Translation of WNT Pathway Components with Structured 5′ UTRs Is Vulnerable to Inhibition of EIF4A-Dependent Translation Initiation
Authors: Nguyen Tuan M. , Kabotyanski Elena B. , Dou Yongchao , Reineke Lucas C. , Zhang Peng , Zhang Xiang H.-F. , Malovannaya Anna , Jung Sung Yun , Mo Qianxing , Roarty Kevin P. , Chen Yiwen , Zhang Bing , Neilson Joel R. , Lloyd Richard E. , Perou Charles M. , Ellis Matthew J. , Rosen Jeffrey M.
Published: March 2023

Supplementary Figure S1 describes the iFGFR1 system, mating scheme for generation of WNT/iR1 mice and alterations in the mammary glands induced by iFGFR1 activation.
Supplemental Table S1 from An HK2 Antisense Oligonucleotide Induces Synthetic Lethality in HK1−HK2+ Multiple Myeloma
Authors: Xu Shili , Zhou Tianyuan , Doh Hanna M. , Trinh K Ryan , Catapang Art , Lee Jason T. , Braas Daniel , Bayley Nicholas A. , Yamada Reiko E. , Vasuthasawat Alex , Sasine Joshua P. , Timmerman John M. , Larson Sarah M. , Kim Youngsoo , MacLeod A. Robert , Morrison Sherie L. , Herschman Harvey R.
Published: March 2023

Metabolite measurement in OPM2 cells treated with HK2-ASO1, DPI, MET, PER, and their combinations.
Supplementary Figure 3 from Pomalidomide Inhibits PD-L1 Induction to Promote Antitumor Immunity
Authors: Fujiwara Yuki , Sun Yi , Torphy Robert J. , He Jiadai , Yanaga Katsuhiko , Edil Barish H. , Schulick Richard D. , Zhu Yuwen
Published: March 2023

Figure S3
Supplemental Figures from An HK2 Antisense Oligonucleotide Induces Synthetic Lethality in HK1−HK2+ Multiple Myeloma
Authors: Xu Shili , Zhou Tianyuan , Doh Hanna M. , Trinh K Ryan , Catapang Art , Lee Jason T. , Braas Daniel , Bayley Nicholas A. , Yamada Reiko E. , Vasuthasawat Alex , Sasine Joshua P. , Timmerman John M. , Larson Sarah M. , Kim Youngsoo , MacLeod A. Robert , Morrison Sherie L. , Herschman Harvey R.
Published: March 2023

This file contains supplemental figures: Supplemental Figure S1. HK2 ASOs selectively inhibit the proliferation of HK1-HK2+ MM cells. Supplemental Figure S2. The HK2-ASO1/DPI/PER combination causes synthetic lethality in HK1-HK2+ cells. Supplemental Figure 3. In vivo effects of HK2-ASO1, DPI, PER on MM OPM2 xenograft models. Supplemental Figure 4. MET can replace DPI for mitochondrial oxidative phosphorylation inhibition. Supplemental Figure S5. Effects of 24 h treatments of HK1-HK2+ OPM2 cells with HK2-ASO1, DPI, MET and PER, alone and in combination, on relative amounts of amino acids, TCA cycle metabolites, fatty acid intermediates, purines and pyrimidines. Supplemental Figure S6. Effect of 24 h treatments of HK1-HK2+ OPM2 cells with HK2-ASO1, DPI, MET and PER, alone and in combination, on relative 13C-labeled portions of TCA cycle metabolites, amino acids, purines, and pyrimidines. Supplemental Figure S7. In vitro and in vivo effects of mouse HK2 (mHK2) ASOs, as single agents and in combination with DPI, MET, and PER in mouse P3 (HK1-HK2+) and P3 (HK1+HK2+) isogenic MM cells.
Supplemental Tables from Demethylation-Induced Overexpression of Shc3 Drives c-Raf–Independent Activation of MEK/ERK in HCC
Authors: Liu Yun , Zhang Xinran , Yang Baicai , Zhuang Hao , Guo Hua , Wei Wen , Li Yuan , Chen Ruibing , Li Yongmei , Zhang Ning
Published: March 2023

This file contains all Supplemental tables that including clinicopathological information of HCC tissue samples and sequences of DNA primer, siRNAs, and shRNAs.
Supplemental Material and Methods from Demethylation-Induced Overexpression of Shc3 Drives c-Raf–Independent Activation of MEK/ERK in HCC
Authors: Liu Yun , Zhang Xinran , Yang Baicai , Zhuang Hao , Guo Hua , Wei Wen , Li Yuan , Chen Ruibing , Li Yongmei , Zhang Ning
Published: March 2023

This file contains all detailed Supplemental Material and Methods from this research.
Supplementary Data from Cistrome Cancer: A Web Resource for Integrative Gene Regulation Modeling in Cancer
Authors: Mei Shenglin , Meyer Clifford A. , Zheng Rongbin , Qin Qian , Wu Qiu , Jiang Peng , Li Bo , Shi Xiaohui , Wang Binbin , Fan Jingyu , Shih Celina , Brown Myles , Zang Chongzhi , Liu X. Shirley
Published: March 2023

Supplementary Data include: 1, Supplementary Methods: a detailed description of data processing, computational analysis, and web interface functions; 2, Supplementary References; 3, Supplementary Figures 1-6: Fig. S1: Cancer sample reclustering; Fig. S2: Cancer type reannotation; Fig. S3: TF target prediction in cancer; Fig. S4: Snapshot of the Cistrome Cancer TF target prediction webpage; Fig. S5: FOXM1, a pan-cancer active TF; Fig. S6: Distinct patterns of immune cell infiltration in kidney and colorectal cancers; and 4, Supplementary Table 1: Cancer Type Abbreviations.
Supplementary information from Lysyl Oxidase–like Protein LOXL2 Promotes Lung Metastasis of Breast Cancer
Authors: Salvador Fernando , Martin Alberto , López-Menéndez Celia , Moreno-Bueno Gema , Santos Vanesa , Vázquez-Naharro Alberto , Santamaría Patricia G. , Morales Saleta , Dubus Pierre R. , Muinelo-Romay Laura , López-López Rafael , Tung Jason C. , Weaver Valerie M. , Portillo Francisco , Cano Amparo
Published: March 2023

Suppplementary Material and Methods and related references
Figures S1-S3 from Lysyl Oxidase–like Protein LOXL2 Promotes Lung Metastasis of Breast Cancer
Authors: Salvador Fernando , Martin Alberto , López-Menéndez Celia , Moreno-Bueno Gema , Santos Vanesa , Vázquez-Naharro Alberto , Santamaría Patricia G. , Morales Saleta , Dubus Pierre R. , Muinelo-Romay Laura , López-López Rafael , Tung Jason C. , Weaver Valerie M. , Portillo Francisco , Cano Amparo
Published: March 2023

Size (Fig. S1) and expression of Lox family members in PyMT tumors (Fig. S2) with deregulated Loxl2. Fig. S3: Loxl2 expression in PyMT tumors compared to normal mammary gland.
Figure S8 & S9 from Lysyl Oxidase–like Protein LOXL2 Promotes Lung Metastasis of Breast Cancer
Authors: Salvador Fernando , Martin Alberto , López-Menéndez Celia , Moreno-Bueno Gema , Santos Vanesa , Vázquez-Naharro Alberto , Santamaría Patricia G. , Morales Saleta , Dubus Pierre R. , Muinelo-Romay Laura , López-López Rafael , Tung Jason C. , Weaver Valerie M. , Portillo Francisco , Cano Amparo
Published: March 2023

Orthotopic injection of PyMT cells with Loxl2 overexpression (Fig. S8) and fibrillar collagen in xenografts from PyMT cells with deregulated Loxl2
Supplementary Material and Methods from O-GlcNAcylation of the Tumor Suppressor FOXO3 Triggers Aberrant Cancer Cell Growth
Authors: Shin Heon , Cha Hyun-Jeong , Na Keun , Lee Min Jung , Cho Jin-Young , Kim Chae-Yeon , Kim Eun Kyung , Kang Chang Moo , Kim Hoguen , Paik Young-Ki
Published: March 2023

This file contains all detailed Supplementary Material and Methods from this research.
Figure S4 from Transplantation of iPS-Derived Tumor Cells with a Homozygous MHC Haplotype Induces GRP94 Antibody Production in MHC-Matched Macaques
Authors: Ishigaki Hirohito , Maeda Toshinaga , Inoue Hirokazu , Akagi Tsuyoshi , Sasamura Takako , Ishida Hideaki , Inubushi Toshiro , Okahara Junko , Shiina Takashi , Nakayama Misako , Itoh Yasushi , Ogasawara Kazumasa
Published: March 2023

IgG against GRP94 in plasma is autoantibody.
Supplementary Information from Integrative Modeling Identifies Key Determinants of Inhibitor Sensitivity in Breast Cancer Cell Lines
Authors: Jastrzebski Katarzyna , Thijssen Bram , Kluin Roelof J.C. , de Lint Klaas , Majewski Ian J. , Beijersbergen Roderick L. , Wessels Lodewyk F.A.
Published: March 2023

This document contains Supplementary Materials & Methods including a mathematical specification of the model, as well as Supplementary Note 1 (Inferred signaling estimates agree with on-treatment phosphorylation measurements), Supplementary Note 2 (A simplified model can describe the response to seven drugs simultaneously), Supplementary Note 3 (Inclusion of feedback signaling from MTORC1 to PI3K does not improve the fit for drug response to AZD8055 and lapatinib), Supplementary Tables 1 (cell line panel), 9-10 (literature references for model nodes and interactions) and 11-12 (prior distributions), and Supplementary Figure 1-19.
Supplementary Figure 2 from Enhanced Acid Sphingomyelinase Activity Drives Immune Evasion and Tumor Growth in Non–Small Cell Lung Carcinoma
Authors: Kachler Katerina , Bailer Maximilian , Heim Lisanne , Schumacher Fabian , Reichel Martin , Holzinger Corinna D. , Trump Sonja , Mittler Susanne , Monti Juliana , Trufa Denis I. , Rieker Ralf J. , Hartmann Arndt , Sirbu Horia , Kleuser Burkhard , Kornhuber Johannes , Finotto Susetta
Published: March 2023

Cell survival and apoptosis, ASM-activity, Ceramide and Sphingomyelin levels after siRNA-mediated ASM depletion in NSCLC cell lines.
Supplementary Table S2 from Clinical Proteomics of Breast Cancer Reveals a Novel Layer of Breast Cancer Classification
Authors: Yanovich Gali , Agmon Hadar , Harel Michal , Sonnenblick Amir , Peretz Tamar , Geiger Tamar
Published: March 2023

Comparison of healthy samples to each cancer subtype
Supplementary Table S1 from Clinical Proteomics of Breast Cancer Reveals a Novel Layer of Breast Cancer Classification
Authors: Yanovich Gali , Agmon Hadar , Harel Michal , Sonnenblick Amir , Peretz Tamar , Geiger Tamar
Published: March 2023

Sample summary table
Table S5 from Tau Mutations Serve as a Novel Risk Factor for Cancer
Authors: Rossi Giacomina , Redaelli Veronica , Contiero Paolo , Fabiano Sabrina , Tagliabue Giovanna , Perego Paola , Benussi Luisa , Bruni Amalia C. , Filippini Graziella , Farinotti Mariangela , Giaccone Giorgio , Buiatiotis Simona , Manzoni Claudia , Ferrari Raffaele , Tagliavini Fabrizio
Published: March 2023

Table S5 shows the strong and unbiased specificity of tau's interactome, by generating 25 random protein sets with similar size to the tau's interactome and their functional enrichment
Supplementary Materials and Methods from Actin Cytoskeleton Remodeling Drives Breast Cancer Cell Escape from Natural Killer–Mediated Cytotoxicity
Authors: Al Absi Antoun , Wurzer Hannah , Guerin Coralie , Hoffmann Celine , Moreau Flora , Mao Xianqing , Brown-Clay Joshua , Petrolli Rémi , Casellas Carla Pou , Dieterle Monika , Thiery Jean-Paul , Chouaib Salem , Berchem Guy , Janji Bassam , Thomas Clément
Published: March 2023

Supplementary Materials and Methods
Table S3 from miRNA Profiling of Magnetic Nanopore–Isolated Extracellular Vesicles for the Diagnosis of Pancreatic Cancer
Authors: Ko Jina , Bhagwat Neha , Black Taylor , Yee Stephanie S. , Na Young-Ji , Fisher Stephen , Kim Junhyong , Carpenter Erica L. , Stanger Ben Z. , Issadore David
Published: March 2023

Workflow and the corresponding result.
Supplementary Materials and Methods and References from Identification of a Small Molecule That Selectively Inhibits ERG-Positive Cancer Cell Growth
Authors: Mohamed Ahmed A. , Xavier Charles P. , Sukumar Gauthaman , Tan Shyh-Han , Ravindranath Lakshmi , Seraj Nishat , Kumar Vineet , Sreenath Taduru , McLeod David G. , Petrovics Gyorgy , Rosner Inger L. , Srivastava Meera , Strovel Jeffrey , Malhotra Sanjay V. , LaRonde Nicole A. , Dobi Albert , Dalgard Clifton L. , Srivastava Shiv
Published: March 2023

Reagents. Antibodies for Immunoblot, methods for qPCR, Tunnel assay and Determination of equilibrium dissociation constant (Kd) of RIOK proteins and Additional references supporting the ERGi-USU manuscript
Figure S3 from miRNA Profiling of Magnetic Nanopore–Isolated Extracellular Vesicles for the Diagnosis of Pancreatic Cancer
Authors: Ko Jina , Bhagwat Neha , Black Taylor , Yee Stephanie S. , Na Young-Ji , Fisher Stephen , Kim Junhyong , Carpenter Erica L. , Stanger Ben Z. , Issadore David
Published: March 2023

Diagnostic performance of individual miRNAs.
Supplementary Tables S1-3 from SPON2 Promotes M1-like Macrophage Recruitment and Inhibits Hepatocellular Carcinoma Metastasis by Distinct Integrin–Rho GTPase–Hippo Pathways
Authors: Zhang Yan-Li , Li Qing , Yang Xiao-Mei , Fang Fang , Li Jun , Wang Ya-Hui , Yang Qin , Zhu Lei , Nie Hui-Zhen , Zhang Xue-Li , Feng Ming-Xuan , Jiang Shu-Heng , Tian Guang-Ang , Hu Li-Peng , Lee Ho-Young , Lee Su-Jae , Xia Qiang , Zhang Zhi-Gang
Published: March 2023

Supplementary tables of correlation of clinicopathological features with SPON2 expression, primers for PCR, and sequence of shRNA and siRNA
Figure S4 from Glycoprotein nmb Is Exposed on the Surface of Dormant Breast Cancer Cells and Induces Stem Cell–like Properties
Authors: Chen Chen , Okita Yukari , Watanabe Yukihide , Abe Fumie , Fikry Muhammad Ali , Ichikawa Yumu , Suzuki Hiroyuki , Shibuya Akira , Kato Mitsuyasu
Published: March 2023

Expression levels of EMT marker genes in cell surface-GPNMBlow/high breast cancer cells.
Table S3 from A Transcriptome-Wide Association Study Among 97,898 Women to Identify Candidate Susceptibility Genes for Epithelial Ovarian Cancer Risk
Authors: Lu Yingchang , Beeghly-Fadiel Alicia , Wu Lang , Guo Xingyi , Li Bingshan , Schildkraut Joellen M. , Im Hae Kyung , Chen Yian A. , Permuth Jennifer B. , Reid Brett M. , Teer Jamie K. , Moysich Kirsten B. , Andrulis Irene L. , Anton-Culver Hoda , Arun Banu K. , Bandera Elisa V. , Barkardottir Rosa B. , Barnes Daniel R. , Benitez Javier , Bjorge Line , Brenton James , Butzow Ralf , Caldes Trinidad , Caligo Maria A. , Campbell Ian , Chang-Claude Jenny , Claes Kathleen B.M. , Couch Fergus J. , Cramer Daniel W. , Daly Mary B. , deFazio Anna , Dennis Joe , Diez Orland , Domchek Susan M. , Dörk Thilo , Easton Douglas F. , Eccles Diana M. , Fasching Peter A. , Fortner Renée T. , Fountzilas George , Friedman Eitan , Ganz Patricia A. , Garber Judy , Giles Graham G. , Godwin Andrew K. , Goldgar David E. , Goodman Marc T. , Greene Mark H. , Gronwald Jacek , Hamann Ute , Heitz Florian , Hildebrandt Michelle A.T. , Høgdall Claus K. , Hollestelle Antoinette , Hulick Peter J. , Huntsman David G. , Imyanitov Evgeny N. , Isaacs Claudine , Jakubowska Anna , James Paul , Karlan Beth Y. , Kelemen Linda E. , Kiemeney Lambertus A. , Kjaer Susanne K. , Kwong Ava , Le Nhu D. , Leslie Goska , Lesueur Fabienne , Levine Douglas A. , Mattiello Amalia , May Taymaa , McGuffog Lesley , McNeish Iain A. , Merritt Melissa A. , Modugno Francesmary , Montagna Marco , Neuhausen Susan L. , Nevanlinna Heli , Nielsen Finn C. , Nikitina-Zake Liene , Nussbaum Robert L. , Offit Kenneth , Olah Edith , Olopade Olufunmilayo I. , Olson Sara H. , Olsson Håkan , Osorio Ana , Park Sue K. , Parsons Michael T. , Peeters Petra H.M. , Pejovic Tanja , Peterlongo Paolo , Phelan Catherine M. , Pujana Miquel Angel , Ramus Susan J. , Rennert Gad , Risch Harvey , Rodriguez Gustavo C. , Rodríguez-Antona Cristina , Romieu Isabelle , Rookus Matti A. , Rossing Mary Anne , Rzepecka Iwona K. , Sandler Dale P. , Schmutzler Rita K. , Setiawan Veronica W. , Sharma Priyanka , Sieh Weiva , Simard Jacques , Singer Christian F. , Song Honglin , Southey Melissa C. , Spurdle Amanda B. , Sutphen Rebecca , Swerdlow Anthony J. , Teixeira Manuel R. , Teo Soo H. , Thomassen Mads , Tischkowitz Marc , Toland Amanda E. , Trichopoulou Antonia , Tung Nadine , Tworoger Shelley S. , van Rensburg Elizabeth J. , Vanderstichele Adriaan , Vega Ana , Edwards Digna Velez , Webb Penelope M. , Weitzel Jeffrey N. , Wentzensen Nicolas , White Emily , Wolk Alicja , Wu Anna H. , Yannoukakos Drakoulis , Zorn Kristin K. , Gayther Simon A. , Antoniou Antonis C. , Berchuck Andrew , Goode Ellen L. , Chenevix-Trench Georgia , Sellers Thomas A. , Pharoah Paul D.P. , Zheng Wei , Long Jirong
Published: March 2023

Known common variants identified from genome-wide assocation studies and their bioinformatically predicted target genes.
GA - author version from Hypoxic Tumor-Derived Exosomal miR-301a Mediates M2 Macrophage Polarization via PTEN/PI3Kγ to Promote Pancreatic Cancer Metastasis
Authors: Wang Xiaofeng , Luo Guangtao , Zhang Kundong , Cao Jun , Huang Chen , Jiang Tao , Liu Bingya , Su Liping , Qiu Zhengjun
Published: March 2023

Hypoxia PC cells-derived exosomal miR-301a induced M2 macrophages polarization via the PTEN/PI3Kγ pathway and polarized macrophages promoted cancer cells metastasis.
Supplementary Data from The NCI Transcriptional Pharmacodynamics Workbench: A Tool to Examine Dynamic Expression Profiling of Therapeutic Response in the NCI-60 Cell Line Panel
Authors: Monks Anne , Zhao Yingdong , Hose Curtis , Hamed Hossein , Krushkal Julia , Fang Jianwen , Sonkin Dmitriy , Palmisano Alida , Polley Eric C. , Fogli Laura K. , Konaté Mariam M. , Miller Sarah B. , Simpson Melanie A. , Voth Andrea Regier , Li Ming-Chung , Harris Erik , Wu Xiaolin , Connelly John W. , Rapisarda Annamaria , Teicher Beverly A. , Simon Richard , Doroshow James H.
Published: March 2023

This file contains Supplementary Figure S1 (Correlation between downregulation of EGFR transcriptional target genes, and sensitivity to erlotinib at the high concentration after 6 hours); Supplementary Figure S2 (EGFR inhibitor and DNA damaging agents induce directionally opposing changes in EGR1 expression that are differentially associated with drug sensitivity); Supplementary Figure S3 (Representative 3D response surface plots for the gemcitabine-erlotinib combination in the indicated cell lines); Supplementary Figure S4 (Representative 3D response surface plots for the vorinostat-talazoparib combination in the indicated cell lines); Supplementary Table S1 (Validation of array-based measurements by qRT-PCR); Supplementary Table S2 (Genes with concerted changes in the same direction [upregulation or downregulation] 24 hours after treatment with each of the 15 drugs); and Supplementary Table S4 (Selected genes potentially mediating drug insensitivity to agents in the NCI TPW dataset).
Supplementary Fig Legends from SETD2 Haploinsufficiency for Microtubule Methylation Is an Early Driver of Genomic Instability in Renal Cell Carcinoma
Authors: Chiang Yun-Chen , Park In-Young , Terzo Esteban A. , Tripathi Durga Nand , Mason Frank M. , Fahey Catherine C. , Karki Menuka , Shuster Charles B. , Sohn Bo-Hwa , Chowdhury Pratim , Powell Reid T. , Ohi Ryoma , Tsai Yihsuan S. , de Cubas Aguirre A. , Khan Abid , Davis Ian J. , Strahl Brian D. , Parker Joel S. , Dere Ruhee , Walker Cheryl L. , Rathmell W. Kimryn
Published: March 2023

fig legends for sup figures
Supplementary Data from Genomic Characterization of Six Virus-Associated Cancers Identifies Changes in the Tumor Immune Microenvironment and Altered Genetic Programs
Authors: Varn Frederick S. , Schaafsma Evelien , Wang Yue , Cheng Chao
Published: March 2023

Supplementary Table S4: Infiltration score validation using lymphocyte fractions inferred from hematoxylin and eosin-stained tissue slides.
Supplementary Figure 5 from Elevation of Stromal-Derived Mediators of Inflammation Promote Prostate Cancer Progression in African-American Men
Authors: Gillard Marc , Javier Rodrigo , Ji Yuan , Zheng S. Lilly , Xu Jianfeng , Brendler Charles B. , Crawford Susan E. , Pierce Brandon L. , Griend Donald J. Vander , Franco Omar E.
Published: March 2023

RNASeq quality control data
Figure S6 from The Circular RNA circPRKCI Promotes Tumor Growth in Lung Adenocarcinoma
Authors: Qiu Mantang , Xia Wenjia , Chen Rui , Wang Siwei , Xu Youtao , Ma Zhifei , Xu Weizhang , Zhang Erbao , Wang Jie , Fang Tian , Hu Jingwen , Dong Gaochao , Yin Rong , Wang Jun , Xu Lin
Published: March 2023

circPRKCI exerts biological function independent of PRKCI. Correlation between circPRKCI and PRKCI (A) and SOX2 (B). Impact of circPRKCI on expression of SOX2 and HHAT in A549 (C) and SPC-A1 (D) cells. Silence of circPRKCI and SOX2 in A549 (E, F) and SPC-A1 (G, H) cells. *P <0.05; ** P <0.01; NC: negative control; EV: empty vector
Supplementary Figure 2 from Elevation of Stromal-Derived Mediators of Inflammation Promote Prostate Cancer Progression in African-American Men
Authors: Gillard Marc , Javier Rodrigo , Ji Yuan , Zheng S. Lilly , Xu Jianfeng , Brendler Charles B. , Crawford Susan E. , Pierce Brandon L. , Griend Donald J. Vander , Franco Omar E.
Published: March 2023

In vitro proliferation of fibroblasts from AA and EA patients. Proliferation of PCa cell lines exposed to CM from AA and EA prostate fibroblasts
Supplementary Table from Mathematical Modeling Predicts Response to Chemotherapy and Drug Combinations in Ovarian Cancer
Authors: Kozłowska Emilia , Färkkilä Anniina , Vallius Tuulia , Carpén Olli , Kemppainen Jukka , Grénman Seija , Lehtonen Rainer , Hynninen Johanna , Hietanen Sakari , Hautaniemi Sampsa
Published: March 2023

Clinical data for calibration and validation cohorts.
Figure S1 from Macrophage-Derived Neuropilin-2 Exhibits Novel Tumor-Promoting Functions
Authors: Roy Sohini , Bag Arup K. , Dutta Samikshan , Polavaram Navatha Shree , Islam Ridwan , Schellenburg Samuel , Banwait Jasjit , Guda Chittibabu , Ran Sophia , Hollingsworth Michael A. , Singh Rakesh K. , Talmadge James E. , Muders Michael H. , Batra Surinder K. , Datta Kaustubh
Published: March 2023

NRP2 expression in alternative and classical type of macrophages
Supplementary Figure S4 from The MDA-9/Syntenin/IGF1R/STAT3 Axis Directs Prostate Cancer Invasion
Authors: Das Swadesh K. , Pradhan Anjan K. , Bhoopathi Praveen , Talukdar Sarmistha , Shen Xue-Ning , Sarkar Devanand , Emdad Luni , Fisher Paul B.
Published: March 2023

IGFBP-2 expression is regulated by MDA-9/Syntenin.
Supplementary Tables S1 and S2 from Transcription Factor YY1 Promotes Cell Proliferation by Directly Activating the Pentose Phosphate Pathway
Authors: Wu Shourong , Wang Huimin , Li Yanjun , Xie Yudan , Huang Can , Zhao Hezhao , Miyagishi Makoto , Kasim Vivi
Published: March 2023

Supplementary Tables S1 and S2 - S1. Primer pairs used for quantitative PCR; S2. Antibodies used for western blotting, chromatin immunoprecipitation, immunofluorescence, and immunohistochemistry.
Table S2 from Epigenetic Regulation of CXCL12 Plays a Critical Role in Mediating Tumor Progression and the Immune Response In Osteosarcoma
Authors: Li Binghao , Wang Zhan , Wu Hao , Xue Mingfeng , Lin Peng , Wang Shengdong , Lin Nong , Huang Xin , Pan Weibo , Liu Meng , Yan Xiaobo , Qu Hao , Sun Lingling , Li Hengyuan , Wu Yan , Teng Wangsiyuan , Wang Zenan , Zhou Xingzhi , Chen Huabiao , Poznansky Mark C. , Ye Zhaoming
Published: March 2023

Supplementary Table S2. Patient characteristics
Figure S5 from Epigenetic Regulation of CXCL12 Plays a Critical Role in Mediating Tumor Progression and the Immune Response In Osteosarcoma
Authors: Li Binghao , Wang Zhan , Wu Hao , Xue Mingfeng , Lin Peng , Wang Shengdong , Lin Nong , Huang Xin , Pan Weibo , Liu Meng , Yan Xiaobo , Qu Hao , Sun Lingling , Li Hengyuan , Wu Yan , Teng Wangsiyuan , Wang Zenan , Zhou Xingzhi , Chen Huabiao , Poznansky Mark C. , Ye Zhaoming
Published: March 2023

Supplementary figure S5. DAC treatment did not increase the risk of osteosarcoma proliferation.
Figure S3 from Epigenetic Regulation of CXCL12 Plays a Critical Role in Mediating Tumor Progression and the Immune Response In Osteosarcoma
Authors: Li Binghao , Wang Zhan , Wu Hao , Xue Mingfeng , Lin Peng , Wang Shengdong , Lin Nong , Huang Xin , Pan Weibo , Liu Meng , Yan Xiaobo , Qu Hao , Sun Lingling , Li Hengyuan , Wu Yan , Teng Wangsiyuan , Wang Zenan , Zhou Xingzhi , Chen Huabiao , Poznansky Mark C. , Ye Zhaoming
Published: March 2023

Supplementary figure S3. Flow cytometry analyses of tumor draining lymph nodes.
Supplementary Figure S3 from Amplification of Glyceronephosphate O-Acyltransferase and Recruitment of USP30 Stabilize DRP1 to Promote Hepatocarcinogenesis
Authors: Gu Li , Zhu Yahui , Lin Xi , Li Yajun , Cui Kaisa , Prochownik Edward V. , Li Youjun
Published: March 2023

Supplementary Figure S3 presents the data of GNPAT recruiting USP30 to deubiquitinate and stabilize DRP1.
Figure S5 from YAP/TAZ Initiates Gastric Tumorigenesis via Upregulation of MYC
Authors: Choi Wonyoung , Kim Jeongsik , Park Jaeoh , Lee Da-Hye , Hwang Daehee , Kim Jeong-Hwan , Ashktorab Hassan , Smoot Duane , Kim Seon-Young , Choi Chan , Koh Gou Young , Lim Dae-Sik
Published: March 2023

MYC is post-transcriptionally upregulated by YAP
Supplementary Figure S2 from Amplification of Glyceronephosphate O-Acyltransferase and Recruitment of USP30 Stabilize DRP1 to Promote Hepatocarcinogenesis
Authors: Gu Li , Zhu Yahui , Lin Xi , Li Yajun , Cui Kaisa , Prochownik Edward V. , Li Youjun
Published: March 2023

Supplementary Figure S2 shows that GNPAT interacts with DRP1 to regulate mitochondrial morphology.
Supplementary Figure S1 from Amplification of Glyceronephosphate O-Acyltransferase and Recruitment of USP30 Stabilize DRP1 to Promote Hepatocarcinogenesis
Authors: Gu Li , Zhu Yahui , Lin Xi , Li Yajun , Cui Kaisa , Prochownik Edward V. , Li Youjun
Published: March 2023

Supplementary Figure S1 illustrates that GNPAT is amplified and upregulated in HCCs.
Figure S6 from The miR-371∼373 Cluster Represses Colon Cancer Initiation and Metastatic Colonization by Inhibiting the TGFBR2/ID1 Signaling Axis
Authors: Ullmann Pit , Rodriguez Fabien , Schmitz Martine , Meurer Steffen K. , Qureshi-Baig Komal , Felten Paul , Ginolhac Aurélien , Antunes Laurent , Frasquilho Sonia , Zügel Nikolaus , Weiskirchen Ralf , Haan Serge , Letellier Elisabeth
Published: March 2023

Investigation of SOX2 and BMP signaling as potential miR-371~373/TGFBR2 targets
Supplementary from A Novel Mechanism for Activation of GLI1 by Nuclear SMO That Escapes Anti-SMO Inhibitors
Authors: Rahman Muhammad M. , Hazan Allon , Selway Joanne L. , Herath Dimalee S. , Harwood Catherine A. , Pirzado Muhammad S. , Atkar Ravinder , Kelsell David P. , Linton Kenneth J. , Philpott Mike P. , Neill Graham W.
Published: March 2023

Single supplementary figure
Table S3 from Metabolic and Physiologic Imaging Biomarkers of the Tumor Microenvironment Predict Treatment Outcome with Radiation or a Hypoxia-Activated Prodrug in Mice
Authors: Matsumoto Shingo , Kishimoto Shun , Saito Keita , Takakusagi Yoichi , Munasinghe Jeeva P. , Devasahayam Nallathamby , Hart Charles P. , Gillies Robert J. , Mitchell James B. , Krishna Murali C.
Published: March 2023

Benefit of combination therapy over monotherapy.
Supplementary Figure Legends from NFATc1 Promotes Antitumoral Effector Functions and Memory CD8+ T-cell Differentiation during Non–Small Cell Lung Cancer Development
Authors: Heim Lisanne , Friedrich Juliane , Engelhardt Marina , Trufa Denis I. , Geppert Carol I. , Rieker Ralf J. , Sirbu Horia , Finotto Susetta
Published: March 2023

Decreased NFATc1 in T cells in the tumoural region of NSCLC patients with advanced disease stages.Cytokines secreted from NFATc1Î"CD4 total lung cells did not influence lung tumour cell growth. Representative dot plots of NFATc1 levels in T cells of lung tumor-bearing B6 WT mice in vivo treated and in vitro re-challenged with Î±PD-1antibodies.
FigureS7 from Inhibition of Nr4a Receptors Enhances Antitumor Immunity by Breaking Treg-Mediated Immune Tolerance
Authors: Hibino Sana , Chikuma Shunsuke , Kondo Taisuke , Ito Minako , Nakatsukasa Hiroko , Omata-Mise Setsuko , Yoshimura Akihiko
Published: March 2023

Camptothecin and a COX-2 inhibitor regulate Treg-mediated down-regulation of costimulatory molecules on tumor-infiltrating DCs
Supplementary Table 1-3 from CDKN2A/p16 Deletion in Head and Neck Cancer Cells Is Associated with CDK2 Activation, Replication Stress, and Vulnerability to CHK1 Inhibition
Authors: Gadhikar Mayur A. , Zhang Jiexin , Shen Li , Rao Xiayu , Wang Jing , Zhao Mei , Kalu Nene N. , Johnson Faye M. , Byers Lauren A. , Heymach John , Hittelman Walter N. , Udayakumar Durga , Pandita Raj K. , Pandita Tej K. , Pickering Curtis R. , Redwood Abena B. , Piwnica-Worms Helen , Schlacher Katharina , Frederick Mitchell J. , Myers Jeffrey N.
Published: March 2023

This file contains tabulated data on genomic associations with prexasertib sensitivity in HNSCC cells. This file is linked to main figure 4.
CAN-17-3953 SI tables and figures from Dual Inhibition of DNA and Histone Methyltransferases Increases Viral Mimicry in Ovarian Cancer Cells
Authors: Liu Minmin , Thomas Stacey L. , DeWitt Ashley K. , Zhou Wanding , Madaj Zachary B. , Ohtani Hitoshi , Baylin Stephen B. , Liang Gangning , Jones Peter A.
Published: March 2023

Includes one supplementary table, 13 supplementary figures and figure legends for supplementary figures
Supplementary table S1 from Matrix Stiffening and EGFR Cooperate to Promote the Collective Invasion of Cancer Cells
Authors: Grasset Eloise M. , Bertero Thomas , Bozec Alexandre , Friard Jonas , Bourget Isabelle , Pisano Sabrina , Lecacheur Margaux , Maiel Majdi , Bailleux Caroline , Emelyanov Alexander , Ilie Marius , Hofman Paul , Meneguzzi Guerrino , Duranton Christophe , Bulavin Dmitry V. , Gaggioli Cedric
Published: March 2023

Relative mitochondrial activity of SCC12 cells or CAF in presence of inhibitors
Supplementary figures and legends from Matrix Stiffening and EGFR Cooperate to Promote the Collective Invasion of Cancer Cells
Authors: Grasset Eloise M. , Bertero Thomas , Bozec Alexandre , Friard Jonas , Bourget Isabelle , Pisano Sabrina , Lecacheur Margaux , Maiel Majdi , Bailleux Caroline , Emelyanov Alexander , Ilie Marius , Hofman Paul , Meneguzzi Guerrino , Duranton Christophe , Bulavin Dmitry V. , Gaggioli Cedric
Published: March 2023

Supplemental data
Table S5 from RNF6 Promotes Colorectal Cancer by Activating the Wnt/β-Catenin Pathway via Ubiquitination of TLE3
Authors: Liu Lei , Zhang Yanquan , Wong Chi Chun , Zhang Jingwan , Dong Yujuan , Li Xiangchun , Kang Wei , Chan Francis K.L. , Sung Joseph J.Y. , Yu Jun
Published: March 2023

Univariate and Multivariate analysis of different prognostic parameters for patients with colorectal cancer in the Beijing cohort 2, n=148
Figure S7 from The Small GTPase ARF6 Activates PI3K in Melanoma to Induce a Prometastatic State
Authors: Yoo Jae Hyuk , Brady Samuel W. , Acosta-Alvarez Lehi , Rogers Aaron , Peng Jingfu , Sorensen Lise K. , Wolff Roger K. , Mleynek Tara , Shin Donghan , Rich Coulson P. , Kircher David A. , Bild Andrea , Odelberg Shannon J. , Li Dean Y. , Holmen Sheri L. , Grossmann Allie H.
Published: March 2023

Figure S7. Low expression of ARF GAP genes correlates with reduced overall survival. (a) Individual gene plots of four ARF6 GAPs (ACAP1, ADAP1, ARAP2, SMAP2), an ARF1/ARF5 GAP (AGAP2) and one predicted ARF GAP (AGFG2). n = 439 patients. (b) Individual gene plots in Stage III specific cohort, n=142 patients. Log-rank (Mantel-Cox) test.
Figure S2 from The Small GTPase ARF6 Activates PI3K in Melanoma to Induce a Prometastatic State
Authors: Yoo Jae Hyuk , Brady Samuel W. , Acosta-Alvarez Lehi , Rogers Aaron , Peng Jingfu , Sorensen Lise K. , Wolff Roger K. , Mleynek Tara , Shin Donghan , Rich Coulson P. , Kircher David A. , Bild Andrea , Odelberg Shannon J. , Li Dean Y. , Holmen Sheri L. , Grossmann Allie H.
Published: March 2023

Figure S2. Primary tumor incidence and growth in BrafCA;Cdkn2af/f mice is not altered by ARF6-GTP. (a) Primary tumor incidence (% = # of mice that developed a tumor / # TVA positive, injected mice) in control and overlapping Arf6Q67L cohorts. Two Arf6Q67L cohorts, classified according to detectable or undetectable HA-tagged Arf6Q67L expression by qRT-PCR and/or by anti-HA immunohistochemistry (see Figure S1). Cohort A includes all mice injected with RCAS Cre + Arf6Q67L. Cohort B is limited to only those mice from cohort A with detectable Arf6Q67L in tumors. Fisher's exact test, two tailed,a<0.05. b) Primary tumor growth upon tumor onset, bars = SD. (c) Overall survival upon tumor onset, log-rank (Mantel-Cox) test. (d) Metastatic incidence (# mice with metastasis / # mice with primary tumors). (e) Proliferation, BrafCA;Cdkn2af/f mouse melanoma cells. (f). Apoptosis, BrafCA;Cdkn2af/f mouse melanoma cells. (g) Representative images of Ki67 immunostains, 200x magnification, scale bars = 50um.
Figure S1 from The Small GTPase ARF6 Activates PI3K in Melanoma to Induce a Prometastatic State
Authors: Yoo Jae Hyuk , Brady Samuel W. , Acosta-Alvarez Lehi , Rogers Aaron , Peng Jingfu , Sorensen Lise K. , Wolff Roger K. , Mleynek Tara , Shin Donghan , Rich Coulson P. , Kircher David A. , Bild Andrea , Odelberg Shannon J. , Li Dean Y. , Holmen Sheri L. , Grossmann Allie H.
Published: March 2023

Figure S1. Detection of HA-tagged ARF6Q67L in BrafCA;Cdkn2af/f melanoma. a) Anti-HA immunostain of FFPE sections of primary tumors with variable levels of detection of ARF6Q67L -HA. The strongest staining was observed in tumors with the highest level of mRNA detected by qRT-PCR (b). Absent staining of FFPE tumors was observed in tumors with low (6456) and undetectable (6457) levels of mRNA by qRT-PCR of frozen tumors. Scale bars = 20mm, 400x magnification. Control = BrafCA;Cdkn2af/f (Cre-only injection). b) qRT-PCR of Arf6 Q67L-HA from fresh, frozen primary tumor fragments. Bars represent the absolute difference in crossing threshold (Ct) between Arf6Q67L-HA and Gapdh. The Ct threshold that defines detection was established above the background signal for controls in both the BrafCA;Cdkn2af/f and the BrafCA;Cdkn2af/f ;Ptenf/f cohorts (see Figures 1g and S3). With rare exception, positive tumors demonstrated Arf6 Q67L-HA expression levels lower than Gapdh.
Video S3 from The Cancer Editome Atlas: A Resource for Exploratory Analysis of the Adenosine-to-Inosine RNA Editome in Cancer
Authors: Lin Chui-Hsien , Chen Sean Chun-Chang
Published: March 2023

Tutorial on the EdmiR module
Video S2 from The Cancer Editome Atlas: A Resource for Exploratory Analysis of the Adenosine-to-Inosine RNA Editome in Cancer
Authors: Lin Chui-Hsien , Chen Sean Chun-Chang
Published: March 2023

Tutorial on the EdCancer module
Supplementary Table 2 from Retinoblastoma Inactivation Induces a Protumoral Microenvironment via Enhanced CCL2 Secretion
Authors: Li Fengkai , Kitajima Shunsuke , Kohno Susumu , Yoshida Akiyo , Tange Shoichiro , Sasaki Soichiro , Okada Nobuhiro , Nishimoto Yuuki , Muranaka Hayato , Nagatani Naoko , Suzuki Misa , Masuda Sayuri , Thai Tran C. , Nishiuchi Takumi , Tanaka Tomoaki , Barbie David A. , Mukaida Naofumi , Takahashi Chiaki
Published: March 2023

RPKM value of CCL2, CCL5 and RB1 gene in each breast cancer cell line based on Cancer Cell Line Encyclopedia (CCLE) database.