Abugessaisa I, Ramilowski JA, Lizio M, Severin J, Hasegawa A, Harshbarger J, ... Ooi JLC (2021) FANTOM enters 20th year: expansion of transcriptomic atlases and functional annotation of non-coding RNAs. Nucleic Acids Res 49(D1):D892-D898

Ballantyne RL, Zhang X, Nunez S, Xue C, Zhao W, Reed E, ... Reilly MP (2016) Genome-wide interrogation reveals hundreds of long intergenic noncoding RNAs that associate with cardiometabolic traits. Hum Mol Genet 25(14):3125–3141

Bar-Joseph Z, Gerber GK, Lee TI, Rinaldi NJ, Yoo JY, Robert F, ... Gifford DK (2003) Computational discovery of gene modules and regulatory networks. Nat Biotechnol 21(11):1337–1342. https://doi.org/10.1038/nbt890

Bhardwaj B, Klassen J, Cossette N, Sterns E, Tuck A, Deeley R, ... Elliott B (1996) Localization of platelet-derived growth factor beta receptor expression in the periepithelial stroma of human breast carcinoma. Clin Cancer Res 2(4):773–782

Braschi B, Denny P, Gray K, Jones T, Seal R, Tweedie S, ... Bruford E (2019) Genenames.org: the HGNC and VGNC resources in 2019. Nucleic Acids Res 47(D1):D786-d792. https://doi.org/10.1093/nar/gky930

Campbell CI, Moorehead RA (2011) Mammary tumors that become independent of the type I insulin-like growth factor receptor express elevated levels of platelet-derived growth factor receptors. BMC Cancer 11:480. https://doi.org/10.1186/1471-2407-11-480

Article  CAS  PubMed  PubMed Central  Google Scholar 

Carvalho I, Milanezi F, Martins A, Reis RM, Schmitt F (2005) Overexpression of platelet-derived growth factor receptor alpha in breast cancer is associated with tumour progression. Breast Cancer Res 7(5):R788-795. https://doi.org/10.1186/bcr1304

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chin CH, Chen SH, Wu HH, Ho CW, Ko MT, Lin CY (2014) cytoHubba: identifying hub objects and sub-networks from complex interactome. BMC Syst Biol 8 Suppl 4(Suppl 4):S11. https://doi.org/10.1186/1752-0509-8-s4-s11

Coltrera MD, Wang J, Porter PL, Gown AM (1995) Expression of platelet-derived growth factor B-chain and the platelet-derived growth factor receptor beta subunit in human breast tissue and breast carcinoma. Cancer Res 55(12):2703–2708

CAS  PubMed  Google Scholar 

Condorelli R, Vaz-Luis I (2018) Managing side effects in adjuvant endocrine therapy for breast cancer. Expert Rev Anticancer Ther 18(11):1101–1112. https://doi.org/10.1080/14737140.2018.1520096

Article  CAS  PubMed  Google Scholar 

Delgir S, Ilkhani K, Safi A, Rahmati Y, Montazari V, Zaynali-Khasraghi Z, ... Alivand MR (2021) The expression of miR-513c and miR-3163 was downregulated in tumor tissues compared with normal adjacent tissue of patients with breast cancer. BMC Med Genomics 14(1):180. https://doi.org/10.1186/s12920-021-01029-3

Denley A, Cosgrove LJ, Booker GW, Wallace JC, Forbes BE (2005) Molecular interactions of the IGF system. Cytokine Growth Factor Rev 16(4–5):421–439. https://doi.org/10.1016/j.cytogfr.2005.04.004

Article  CAS  PubMed  Google Scholar 

Fattahi Dolatabadi N, Dehghani A, Shahand E, Yazdanshenas M, Tabatabaeian H, Zamani A, ... Ghaedi K (2020) The interaction between MALAT1 target, miR-143–3p, and RALGAPA2 is affected by functional SNP rs3827693 in breast cancer. Human Cell 33(4):1229–1239

Goh CY, Patmore S, Smolenski A, Howard J, Evans S, O’Sullivan J, McCann A (2021) The role of von Willebrand factor in breast cancer metastasis. Transl Oncol 14(4):101033. https://doi.org/10.1016/j.tranon.2021.101033

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hu X, Villodre ES, Larson R, Rahal OM, Wang X, Gong Y, ... Debeb BG (2021) Decorin-mediated suppression of tumorigenesis, invasion, and metastasis in inflammatory breast cancer. Commun Biol 4(1):72. https://doi.org/10.1038/s42003-020-01590-0

Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, ... Morgan M (2015) Orchestrating high-throughput genomic analysis with Bioconductor. Nat Methods 12(2):115–121. https://doi.org/10.1038/nmeth.3252

Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4(2):249–264. https://doi.org/10.1093/biostatistics/4.2.249

Article  PubMed  Google Scholar 

Jechlinger M, Sommer A, Moriggl R, Seither P, Kraut N, Capodiecci P, ... Grünert S (2006) Autocrine PDGFR signaling promotes mammary cancer metastasis. J Clin Invest 116(6):1561–1570. https://doi.org/10.1172/jci24652

Jin K-T, Lu Z-B, Lv J-Q, Zhang J-G (2020) The role of long non-coding RNAs in mediating chemoresistance by modulating autophagy in cancer. RNA Biol 17(12):1727–1740

Article  CAS  PubMed  PubMed Central  Google Scholar 

Johnsson P, Lipovich L, Grandér D, Morris KV (2014) Evolutionary conservation of long non-coding RNAs; sequence, structure, function. Biochim Biophys Acta 1840(3):1063–1071. https://doi.org/10.1016/j.bbagen.2013.10.035

Kanduri C (2016) Long noncoding RNAs: lessons from genomic imprinting. Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms 1859(1):102–111

Article  CAS  PubMed  Google Scholar 

Koboldt DC, Fulton RS, McLellan MD, Schmidt H, Kalicki-Veizer J, McMichael JF, ... Center MDAC (2012) Comprehensive molecular portraits of human breast tumours. Nature. 490(7418):61–70. https://doi.org/10.1038/nature11412

Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, Lin L, ... Wilson RK (2012) VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res 22(3):568–576

Langfelder P, Horvath S (2008) WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics 9:559. https://doi.org/10.1186/1471-2105-9-559

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lima SM, Kehm RD, Terry MB (2021) Global breast cancer incidence and mortality trends by region, age-groups, and fertility patterns. EClinicalMedicine 38:100985. https://doi.org/10.1016/j.eclinm.2021.100985

Liu J, Wang Q, Zhang R, Zhang C, Lin J, Huang X (2018) Identification of LINC01279 as a cell cycle-associated long non-coding RNA in endometriosis with GBA analysis. Mol Med Rep 18(4):3850–3858. https://doi.org/10.3892/mmr.2018.9387

Article  CAS  PubMed  PubMed Central  Google Scholar 

López-Romero P (2011) Pre-processing and differential expression analysis of Agilent microRNA arrays using the AgiMicroRna Bioconductor library. BMC Genomics 12(1):1–8

Article  Google Scholar 

Ma Y, Liu W, Li J, Xu Y, Wang H (2018) Gastric cancer with breast metastasis: clinical features and prognostic factors. Oncol Lett 16(5):5565–5574. https://doi.org/10.3892/ol.2018.9383

Article  PubMed  PubMed Central  Google Scholar 

Mahmoud MM, Sanad EF, Elshimy RA, Hamdy NM (2021) Competitive endogenous role of the LINC00511/miR-185-3p axis and miR-301a-3p from liquid biopsy as molecular markers for breast cancer diagnosis. Front Oncol 11:749753

Article  CAS  PubMed  PubMed Central  Google Scholar 

Makki J (2015) Diversity of breast carcinoma: histological subtypes and clinical relevance. Clin Med Insights Pathol 8:CPath-S31563. https://doi.org/10.4137/CPath.S31563

Meng S, Dolo PR, Guo P, Hong J, Li C, Zhu X, Zhou D (2022a) The expression of long non-coding RNA LINC01279 in gastric adenocarcinoma and its clinical significance. Asian J Surg 45(6):1231–1236. https://doi.org/10.1016/j.asjsur.2021.08.031

Article  PubMed  Google Scholar 

Meng S, Dolo PR, Guo P, Hong J, Li C, Zhu X, Zhou D (2022b) The expression of long non-coding RNA LINC01279 in gastric adenocarcinoma and its clinical significance. Asian J Surg 45(6):1231–1236

Article  PubMed  Google Scholar 

Mochizuki S, Soejima K, Shimoda M, Abe H, Sasaki A, Okano HJ, ... Okada Y (2012) Effect of ADAM28 on carcinoma cell metastasis by cleavage of von Willebrand factor. J Natl Cancer Inst 104(12):906–922

Mochizuki S, Soejima K, Shimoda M, Abe H, Sasaki A, Okano HJ, ... Okada Y (2012) Effect of ADAM28 on carcinoma cell metastasis by cleavage of von Willebrand factor. J Natl Cancer Inst 104(12):906–922. https://doi.org/10.1093/jnci/djs232

Mouttet D, Laé M, Caly M, Gentien D, Carpentier S, Peyro-Saint-Paul H, ... Sastre-Garau X (2016) Estrogen-receptor, progesterone-receptor and HER2 status determination in invasive breast cancer. Concordance between immuno-histochemistry and MapQuant™ microarray based assay. PLoS One 11(2):e0146474

Nakamura T, Sakai K, Nakamura T, Matsumoto K (2010) Anti-cancer approach with NK4: bivalent action and mechanisms. Anticancer Agents Med Chem 10(1):36–46. https://doi.org/10.2174/1871520611009010036

Article  CAS  PubMed  Google Scholar 

O’Sullivan JM, Preston RJS, Robson T, O’Donnell JS (2018) Emerging Roles for von Willebrand Factor in Cancer Cell Biology. Semin Thromb Hemost 44(2):159–166. https://doi.org/10.1055/s-0037-1607352

Article  CAS  PubMed  Google Scholar 

Padmanaban V, Krol I, Suhail Y, Szczerba BM, Aceto N, Bader JS, Ewald AJ (2019) E-cadherin is required for metastasis in multiple models of breast cancer. Nature 573(7774):439–444. https://doi.org/10.1038/s41586-019-1526-3

Article  CAS  PubMed  PubMed Central  Google Scholar 

Philippou A, Maridaki M, Pneumaticos S, Koutsilieris M (2014) The complexity of the IGF1 gene splicing, posttranslational modification and bioactivity. Mol Med 20(1):202–214. https://doi.org/10.2119/molmed.2014.00011

Article  CAS  PubMed  PubMed Central  Google Scholar 

Pondé NF, Zardavas D, Piccart M (2019) Progress in adjuvant systemic therapy for breast cancer. Nat Rev Clin Oncol 16(1):27–44. https://doi.org/10.1038/s41571-018-0089-9

Article  CAS  PubMed  Google Scholar 

Qian XL, Pan YH, Huang QY, Shi YB, Huang QY, Hu ZZ, Xiong LX (2019) Caveolin-1: a multifaceted driver of breast cancer progression and its application in clinical treatment. Onco Targets Ther 12:1539–1552. https://doi.org/10.2147/ott.S191317

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, Smyth GK (2015) limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res 43(7):e47. https://doi.org/10.1093/nar/gkv007

Article  CAS  PubMed  PubMed Central  Google Scholar 

Salama S, El-shimy R, El-Mesallamy H, Hamdy NM (2021) Clinical significance of the transcription factor sox11, cell-cell adhesion protein e-cadherin and zinc finger protein bcl11a in the diagnosis of breast cancer. Arch Pharmaceut Sci Ain Shams Univ 5(1):97–110