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Of Triple Negative Breast Cancer (TNBC)

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Of Triple Negative Breast Cancer (TNBC) Supplementary Methods Gene set enrichment analysis (GSEA) of triple negative breast cancer (TNBC) We obtained the primary gene expression data of breast cancer patients and breast cancer cell lines from Gene Expression Omnibus (GEO; http://www.ncbi.nlm.nih.gov/geo/) and analyzed the gene signature with Gene Set Enrichment Analysis (GSEA), as described in our previous report [1]. Briefly, the clinical data of breast cancer patients were obtained from the GEO database under series accession no. GSE27447, and human breast cancer cell line data were obtained from GSE32474. We utilized GEO2R (https://www.ncbi.nlm.nih.gov/geo/geo2r/) to compare TNBC and non‐TNBC groups to identify differentially expressed genes. From GSE27447, we compared the gene expression profiles of five TNBC patient tumors with those of fourteen non‐TNBC patient tumors, and we identified 1972 genes that were differentially expressed between TNBC and non‐TNBC patients (p‐value<5E‐02, Supplementary Table 1). From the GSE32474 dataset, we compared the genomic signature of TNBC cell lines (BT549, HS578T, and MDA‐MB‐231) with that of non‐TNBC cell lines (MCF7 and T47D), and we identified a total of 653 annotated genes that were differentially expressed between human TNBC and non‐TNBC cell lines (p‐value<1E‐08, Supplementary Table 2). Then, GSEA of the ranked gene list was performed using the Java implementation of GSEA obtained from http://www.broadinstitute.org/gsea/ (5000 permutations, minimum term size of 15, and maximum term size of 500). The entire gene lists for TNBC patients as well as for TNBC cell lines were pre‐ranked based on the mean fold change. The analysis included gene sets from MSigDB pathways and C2: curated gene sets (c2.all.v6.2.symbols.gmt), and an FDR q‐value < 0.05 was set as the significance threshold. Supplementary Tables Supplementary Table 1. Differentially expressed gene list of TNBC patient tumors (n=5) versus non‐ TNBC patient tumors (n=14). Supplementary Table 2. Differentially expressed gene list of TNBC cell lines (BT549, HS578T, and MDA‐MB‐231) versus non‐TNBC cell lines (MCF7 and T47D). Supplementary Tables are attached as excel files. References 1. Kim J.‐H.; Park S.‐Y; Jun Y.; Kim J.‐Y.; Nam J.‐S. Roles of Wnt Target Genes in the Journey of Cancer Stem Cells. International Journal of Molecular Sciences 2017, 18, pii: E1604 Supplementary Table 1. Differentially expressed gene list of TNBC patient tumors (n=5) versus non-TNBC patient tumors (n=14). # ID Gene.symbTNBC group non-TNBC group logFC P.Value Gene.title 1 8103706 AADAT 2.272663 -3.5244 1.667202 0.0348422 aminoadipate aminotransferase 2 7989953 AAGAB -2.9889457 -2.4408 -0.59936 0.0075418 alpha- and gamma-adaptin binding protein 3 8052798 AAK1 2.220929 -3.5981 0.519726 0.0387047 AP2 associated kinase 1 4 8100478 AASDH -2.1427178 -3.7078 -0.60192 0.0452934 aminoadipate-semialdehyde dehydrogenase 5 8070708 AATBC 2.2450704 -3.5638 0.524513 0.0368558 apoptosis associated transcript in bladder cancer 6 8131682 ABCB5 -2.1401391 -3.7114 -1.18796 0.0455271 ATP binding cassette subfamily B member 5 7 7975607 ACOT4 -2.8771048 -2.6158 -1.45266 0.0096492 acyl-CoA thioesterase 4 8 7952503 ACRV1 2.1522735 -3.6945 0.541704 0.0444369 acrosomal vesicle protein 1 9 8137474 ACTR3B 2.497213 -3.196 0.932199 0.0218645 ARP3 actin related protein 3 homolog B 10 8092002 ACTRT3 2.1043293 -3.761 0.477936 0.0488877 actin related protein T3 11 7955535 ACVR1B -3.4919358 -1.6429 -0.7804 0.0024384 activin A receptor type 1B 12 8066431 ADA 2.5949572 -3.0493 0.613998 0.0177718 adenosine deaminase 13 7983191 ADAL -3.6757514 -1.3502 -1.13951 0.0016052 adenosine deaminase like 14 8115490 ADAM19 2.2082558 -3.616 0.784916 0.0397089 ADAM metallopeptidase domain 19 15 7979927 ADAM20 -2.5968716 -3.0464 -0.97852 0.0176993 ADAM metallopeptidase domain 20 16 7979925 ADAM20P1 -3.1352823 -2.21 -1.10773 0.0054469 ADAM metallopeptidase domain 20 pseudogene 1 17 7990736 ADAMTS7 2.7036207 -2.8839 0.471716 0.0140756 ADAM metallopeptidase with thrombospondin type 1 motif 7 18 7952752 ADAMTS8 2.267395 -3.5319 0.373428 0.0352187 ADAM metallopeptidase with thrombospondin type 1 motif 8 19 8088560 ADAMTS9 2.223479 -3.5944 0.814403 0.0385054 ADAM metallopeptidase with thrombospondin type 1 motif 9 20 8132667 ADCY1 -2.3826722 -3.3652 -2.13113 0.027783 adenylate cyclase 1 21 7999079 ADCY9 -2.178401 -3.658 -0.68505 0.0421698 adenylate cyclase 9 22 8052882 ADD2 2.3413871 -3.4253 0.920914 0.0302602 adducin 2 23 8157777 ADGRD2 3.0434101 -2.3551 0.753347 0.006684 adhesion G protein-coupled receptor D2 24 7996064 ADGRG5 2.6787531 -2.9219 0.748457 0.0148507 adhesion G protein-coupled receptor G5 25 7902565 ADGRL2 3.1775711 -2.143 1.370978 0.0049553 adhesion G protein-coupled receptor L2 26 8106827 ADGRV1 -2.9017974 -2.5773 -2.19419 0.0091399 adhesion G protein-coupled receptor V1 27 7928882 ADIRF -2.6158137 -3.0177 -1.52148 0.0169976 adipogenesis regulatory factor 28 7928471 ADK -2.4563235 -3.2568 -0.54747 0.0238268 adenosine kinase 29 8005134 ADORA2B 2.5798829 -3.072 0.501918 0.0183519 adenosine A2b receptor 30 7925550 ADSS -2.2428494 -3.5669 -0.80113 0.0370224 adenylosuccinate synthase 31 7977273 ADSSL1 -3.924199 -0.9566 -1.24256 0.0009105 adenylosuccinate synthase like 1 32 8106429 AGGF1 -2.3379787 -3.4303 -0.45223 0.0304736 angiogenic factor with G-patch and FHA domains 1 33 8130628 AGPAT4 2.2572734 -3.5464 1.030554 0.0359524 1-acylglycerol-3-phosphate O-acyltransferase 4 34 8138381 AGR2 -3.034222 -2.3696 -4.76127 0.0068217 anterior gradient 2, protein disulphide isomerase family member 35 8138392 AGR3 -2.8541838 -2.6514 -3.82108 0.0101462 anterior gradient 3, protein disulphide isomerase family member 36 7896822 AGRN -3.6272845 -1.4273 -1.2464 0.0017926 agrin 37 8169492 AGTR2 -2.350242 -3.4125 -0.79261 0.0297122 angiotensin II receptor type 2 38 8049737 AGXT 2.147625 -3.701 0.561296 0.0448517 alanine-glyoxylate aminotransferase 39 8122396 AIG1 -2.8242038 -2.698 -0.85036 0.0108335 androgen induced 1 40 8011912 AIPL1 2.428713 -3.2976 0.446297 0.0252438 aryl hydrocarbon receptor interacting protein like 1 41 8112458 AK6///TAF9 -2.1319152 -3.7228 -0.37853 0.0462798 adenylate kinase 6///TATA-box binding protein associated factor 9 42 8177635 AK6///TAF9 -2.1319152 -3.7228 -0.37853 0.0462798 adenylate kinase 6///TATA-box binding protein associated factor 9 43 8164766 AK8 -2.2637759 -3.5371 -0.58121 0.0354794 adenylate kinase 8 44 8128777 AK9 -4.3419818 -0.3051 -6.19443 0.0003509 adenylate kinase 9 45 8128788 AK9 -2.2081295 -3.6162 -0.79441 0.0397191 adenylate kinase 9 46 7975066 AKAP5 -2.1550402 -3.6907 -1.10602 0.0441917 A-kinase anchoring protein 5 47 8163569 AKNA 2.3821898 -3.3659 0.831578 0.0278109 AT-hook transcription factor 48 7904084 AKR7A2P1 -2.0949187 -3.7739 -0.5781 0.0498074 aldo-keto reductase family 7 member A2 pseudogene 1 49 7913146 AKR7A3 -2.1430004 -3.7074 -1.01223 0.0452679 aldo-keto reductase family 7 member A3 50 7994737 ALDOA -2.6232516 -3.0064 -0.86986 0.0167294 aldolase, fructose-bisphosphate A 51 7936923 ALDOAP2 -2.1384024 -3.7138 -0.76954 0.0456851 aldolase, fructose-bisphosphate A pseudogene 2 52 7969228 ALG11///U -2.5976779 -3.0452 -0.49494 0.0176689 ALG11, alpha-1,2-mannosyltransferase///UTP14, small subunit proces 53 8141757 ALKBH4 2.769381 -2.7828 0.541324 0.0122074 alkB homolog 4, lysine demethylase 54 8040053 ALLC 3.2541557 -2.0215 1.017958 0.0041729 allantoicase 55 8004221 ALOX12 2.1981782 -3.6302 0.453382 0.0405245 arachidonate 12-lipoxygenase, 12S type 56 8012309 ALOX12B 2.2575772 -3.546 0.439605 0.0359302 arachidonate 12-lipoxygenase, 12R type 57 8001477 AMFR -2.6542221 -2.9593 -0.77238 0.0156549 autocrine motility factor receptor 58 8090852 AMOTL2 -3.0848012 -2.2898 -0.7071 0.0060961 angiomotin like 2 59 8090866 ANAPC13 -3.0338613 -2.3702 -0.95255 0.0068272 anaphase promoting complex subunit 13 60 8033892 ANGPTL6 2.1121698 -3.7501 0.470955 0.0481332 angiopoietin like 6 61 8150439 ANK1 2.3629479 -3.394 0.46731 0.028942 ankyrin 1 62 7984227 ANKDD1A 3.0400253 -2.3605 0.497822 0.0067344 ankyrin repeat and death domain containing 1A 63 8060949 ANKEF1 -5.0439266 0.7419 -1.35595 0.000072 ankyrin repeat and EF-hand domain containing 1 64 7943943 ANKK1 2.3528345 -3.4087 0.400823 0.0295535 ankyrin repeat and kinase domain containing 1 65 7934979 ANKRD1 2.1881199 -3.6443 0.493973 0.0413538 ankyrin repeat domain 1 66 7927033 ANKRD30A -3.1461142 -2.1929 -6.27253 0.0053167 ankyrin repeat domain 30A 67 8069499 ANKRD30B -3.3952732 -1.7969 -3.55391 0.0030354 ankyrin repeat domain 30B 68 8112672 ANKRD31 2.493414 -3.2017 0.877722 0.0220402 ankyrin repeat domain 31 69 8016725 ANKRD40 -2.728627 -2.8455 -0.59072 0.0133352 ankyrin repeat domain 40 70 7942858 ANKRD42 -2.3024942 -3.4816 -1.0422 0.0327798 ankyrin repeat domain 42 71 7965686 ANKS1B -2.3903619 -3.3539 -1.47992 0.027343 ankyrin repeat and sterile alpha motif domain containing 1B 72 7993815 ANKS4B 2.6442458 -2.9745 0.669602 0.0159937 ankyrin repeat and sterile alpha motif domain containing 4B 73 7938951 ANO5 -2.3424692 -3.4238 -1.12212 0.0301927 anoctamin 5 74 8049799 ANO7 2.1350723 -3.7184 0.452277 0.0459895 anoctamin 7 75 7905283 ANXA9 -2.4597308 -3.2517 -2.26573 0.0236572 annexin A9 76 8034084 AP1M2 -2.7490871 -2.814 -2.50749 0.0127571 adaptor related protein complex 1 mu 2 subunit 77 8161618 APBA1 3.5176519 -1.6019 0.960177 0.0023002 amyloid beta precursor protein binding family A member 1 78 8099982 APBB2 -2.5988325 -3.0434 -0.94924 0.0176255 amyloid beta precursor protein binding family B member 2 79 7897632 APITD1-CO -2.8836635 -2.6055 -1.1645 0.0095113
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