Adhikari K, Fontanil T, Cal S, Mendoza-Revilla J, Fuentes-Guajardo M, Chacón-Duque J-C, Al-Saadi F, Johansson JA, Quinto-Sanchez M, Acuña-Alonzo V, et al. 2016. A genome-wide association scan in admixed Latin Americans identifies loci influencing facial and scalp hair features. Nat Commun 7: 10815. https://www.nature.com/articles/ncomms10815 (Accessed June 30, 2022).
Arnaiz E, Miar A, Dias Junior AG, Prasad N, Schulze U, Waithe D, Nathan JA, Rehwinkel J, Harris AL. 2021. Hypoxia Regulates Endogenous Double-Stranded RNA Production via Reduced Mitochondrial DNA Transcription. Frontiers in Oncology 11. https://www.frontiersin.org/article/10.3389/fonc.2021.779739 (Accessed March 29, 2022).
Bono H. 2020. All of gene expression (AOE): An integrated index for public gene expression databases. PLOS ONE 15: e0227076. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0227076 (Accessed February 27, 2021).
Bono H, Hirota K. 2020. Meta-Analysis of Hypoxic Transcriptomes from Public Databases. Biomedicines 8: 10. https://www.mdpi.com/2227-9059/8/1/10 (Accessed February 27, 2021)
Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, et al. 2001. Minimum information about a microarray experiment (MIAME)—toward standards for microarray data. Nat Genet 29: 365–371. https://www.nature.com/articles/ng1201-365 (Accessed June 19, 2022).
Caplan LR, Hennerici M. 1998. Impaired clearance of emboli (washout) is an important link between hypoperfusion, embolism, and ischemic stroke. Arch Neurol 55: 1475–1482.
Carlevaro-Fita J, Rahim A, Guigó R, Vardy LA, Johnson R. 2016. Cytoplasmic long noncoding RNAs are frequently bound to and degraded at ribosomes in human cells. RNA 22: 867. https://www.ncbi.nlm.nih.gov/labs/pmc/articles/PMC4878613/ (Accessed March 10, 2022).
Carter AJ, Kraemer O, Zwick M, Mueller-Fahrnow A, Arrowsmith CH, Edwards AM. 2019. Target 2035: probing the human proteome. Drug Discovery Today 24: 2111–2115. https://www.sciencedirect.com/science/article/pii/S1359644619301382 (Accessed February 27, 2021).
Deng M, Zhang W, Yuan L, Tan J, Chen Z. 2020. HIF-1a regulates hypoxia-induced autophagy via translocation of ANKRD37 in colon cancer. Exp Cell Res 395: 112175.
Ebert BL, Bunn HF. 1998. Regulation of Transcription by Hypoxia Requires a Multiprotein Complex That Includes Hypoxia-Inducible Factor 1, an Adjacent Transcription Factor, and p300/CREB Binding Protein. Mol Cell Biol 18: 4089–4096. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC108993/ (Accessed May 11, 2021).
Fatima A, Tariq F, Malik MFA, Qasim M, Haq F. 2017. Copy Number Profiling of MammaPrintTM Genes Reveals Association with the Prognosis of Breast Cancer Patients. J Breast Cancer 20: 246–253.
Frontini M, Soutoglou E, Argentini M, Bole-Feysot C, Jost B, Scheer E, Tora L. 2005. TAF9b (Formerly TAF9L) Is a Bona Fide TAF That Has Unique and Overlapping Roles with TAF9. Molecular and Cellular Biology 25: 4638–4649. https://journals.asm.org/doi/10.1128/MCB.25.11.4638-4649.2005 (Accessed April 10, 2022).
Ghajar J. 2000. Traumatic brain injury. The Lancet 356: 923–929. https://www.sciencedirect.com/science/article/pii/S0140673600026891 (Accessed June 28, 2022).
Gordan JD, Bertout JA, Hu C-J, Diehl JA, Simon MC. 2007. HIF-2α Promotes Hypoxic Cell Proliferation by Enhancing c-Myc Transcriptional Activity. Cancer Cell 11: 335–347. https://www.sciencedirect.com/science/article/pii/S1535610807000591 (Accessed February 27, 2021).
Hirota K, Semenza GL. 2006. Regulation of angiogenesis by hypoxia-inducible factor 1. Critical Reviews in Oncology/Hematology 59: 15–26. https://www.sciencedirect.com/science/article/pii/S1040842806000138 (Accessed February 27, 2021).
Ho K, Shih C, Liu A, Chen K. 2022. Hypoxia‐inducible lncRNA MIR210HG interacting with OCT1 is involved in glioblastoma multiforme malignancy. Cancer Sci 113: 540–552. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8819343/ (Accessed July 3, 2022).
Imada EL, Sanchez DF, Collado-Torres L, Wilks C, Matam T, Dinalankara W, Stupnikov A, Lobo-Pereira F, Yip C-W, Yasuzawa K, et al. 2020. Recounting the FANTOM CAGE- Associated Transcriptome. Genome Res 30: 1073–1081.
Imada EL, Sanchez DF, Dinalankara W, Vidotto T, Ebot EM, Tyekucheva S, Franco GR, Mucci LA, Loda M, Schaeffer EM, et al. 2021. Transcriptional landscape of PTEN loss in primary prostate cancer. BMC Cancer 21: 856.
Jaakkola P, Mole DR, Tian YM, Wilson MI, Gielbert J, Gaskell SJ, von Kriegsheim A, Hebestreit HF, Mukherji M, Schofield CJ, et al. 2001. Targeting of HIF-alpha to the von Hippel-Lindau ubiquitylation complex by O2-regulated prolyl hydroxylation. Science 292: 468–472.
Katayama S, Tomaru Y, Kasukawa T, Waki K, Nakanishi M, Nakamura M, Nishida H, Yap CC, Suzuki M, Kawai J, et al. 2005. Antisense Transcription in the Mammalian Transcriptome. Science 309: 1564–1566. https://www.science.org/doi/10.1126/science.1112009 (Accessed April 2, 2022).
Knaup KX, Monti J, Hackenbeck T, Jobst-Schwan T, Klanke B, Schietke RE, Wacker I, Behrens J, Amann K, Eckardt K-U, et al. 2014. Hypoxia regulates the sperm associated antigen 4 (SPAG4) via HIF, which is expressed in renal clear cell carcinoma and promotes migration and invasion in vitro. Mol Carcinog 53: 970–978.
Kodama Y, Mashima J, Kosuge T, Ogasawara O. 2019. DDBJ update: the Genomic Expression Archive (GEA) for functional genomics data. Nucleic Acids Research 47: D69– D73. https://doi.org/10.1093/nar/gky1002 (Accessed February 27, 2021).
Koshiji M, Kageyama Y, Pete EA, Horikawa I, Barrett JC, Huang LE. 2004. HIF-1α induces cell cycle arrest by functionally counteracting Myc. The EMBO Journal 23: 1949–1956. https://www.embopress.org/doi/full/10.1038/sj.emboj.7600196 (Accessed February 27, 2021).
Labrecque MP, Takhar MK, Nason R, Santacruz S, Tam KJ, Massah S, Haegert A, Bell RH, Altamirano-Dimas M, Collins CC, et al. 2016. The retinoblastoma protein regulates hypoxia- inducible genetic programs, tumor cell invasiveness and neuroendocrine differentiation in prostate cancer cells. Oncotarget 7: 24284–24302. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5029701/ (Accessed February 27, 2021).
Li H, Ko HP, Whitlock JP. 1996. Induction of Phosphoglycerate Kinase 1 Gene Expression by Hypoxia. Journal of Biological Chemistry 271: 21262–21267. https://linkinghub.elsevier.com/retrieve/pii/S0021925819746444 (Accessed April 2, 2022).
Mahon PC, Hirota K, Semenza GL. 2001. FIH-1: a novel protein that interacts with HIF- 1alpha and VHL to mediate repression of HIF-1 transcriptional activity. Genes Dev 15: 2675–2686.
Mathieu J, Zhang Z, Zhou W, Wang AJ, Heddleston JM, Pinna CMA, Hubaud A, Stadler B, Choi M, Bar M, et al. 2011. HIF Induces Human Embryonic Stem Cell Markers in Cancer Cells. Cancer Research 71: 4640–4652. https://doi.org/10.1158/0008-5472.CAN-10-3320 (Accessed March 19, 2022).
Mihai IS, Das D, Maršalkaite G, Henriksson J. 2021. Meta-Analysis of Gene Popularity: Less Than Half of Gene Citations Stem from Gene Regulatory Networks. Genes 12. https://www.ncbi.nlm.nih.gov/labs/pmc/articles/PMC7926953/ (Accessed February 25, 2022).
Morse JM. 2010. “Cherry picking”: writing from thin data. Qual Health Res 20: 3.
Nieminen T, Scott TA, Lin F-M, Chen Z, Yla-Herttuala S, Morris KV. 2018. Long Non- Coding RNA Modulation of VEGF-A during Hypoxia. Non-Coding RNA 4. https://www.ncbi.nlm.nih.gov/labs/pmc/articles/PMC6315885/ (Accessed March 14, 2022).
Okada Y, Tashiro C, Numata K, Watanabe K, Nakaoka H, Yamamoto N, Okubo K, Ikeda R, Saito R, Kanai A, et al. 2008. Comparative expression analysis uncovers novel features of endogenous antisense transcription. Hum Mol Genet 17: 1631–1640.
Oki S, Ohta T, Shioi G, Hatanaka H, Ogasawara O, Okuda Y, Kawaji H, Nakaki R, Sese J, Meno C. 2018. ChIP-Atlas: a data-mining suite powered by full integration of public ChIP- seq data. EMBO reports 19: e46255. https://www.embopress.org/doi/full/10.15252/embr.201846255 (Accessed February 27, 2021).
Ono H, Ogasawara O, Okubo K, Bono H. 2017. RefEx, a reference gene expression dataset as a web tool for the functional analysis of genes. Scientific Data 4: 170105. https://www.nature.com/articles/sdata2017105 (Accessed February 3, 2021).
Ono Y, Bono H. 2022. Exploratory Meta-Analysis of Hypoxic Transcriptomes Using a Precise Transcript Reference Sequence Set. 2022.05.01.489280. https://www.biorxiv.org/content/10.1101/2022.05.01.489280v1 (Accessed July 11, 2022).
Ono Y, Bono H. 2021. Multi-Omic Meta-Analysis of Transcriptomes and the Bibliome Uncovers Novel Hypoxia-Inducible Genes. Biomedicines 9: 582. https://www.mdpi.com/2227-9059/9/5/582 (Accessed August 9, 2021).
Ozsolak F, Kapranov P, Foissac S, Kim SW, Fishilevich E, Monaghan AP, John B, Milos PM. 2010. Comprehensive Polyadenylation Site Maps in Yeast and Human Reveal Pervasive Alternative Polyadenylation. Cell 143: 1018–1029. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3022516/ (Accessed April 2, 2022).
Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C. 2017. Salmon provides fast and bias- aware quantification of transcript expression. Nature Methods 14: 417–419. https://www.nature.com/articles/nmeth.4197 (Accessed February 27, 2021).
Pelechano V, Steinmetz LM. 2013. Gene regulation by antisense transcription. Nat Rev Genet 14: 880–893. https://www.nature.com/articles/nrg3594 (Accessed February 2, 2022).
Peng C, Wu J, Zheng S. 2018. Hypoxia Induced ANKRD37 Promotes Angiogenesis and Reprograms Glucose Metabolism in Hepatocellular Carcinoma Following Liver Transplantation. Transplantation 102: S683. https://journals.lww.com/transplantjournal/Abstract/2018/07001/Hypoxia_Induced_ANKRD 37_Promotes_Angiogenesis_and.1098.aspx (Accessed June 29, 2022).
Qi J, Nakayama K, Cardiff RD, Borowsky AD, Kaul K, Williams R, Krajewski S, Mercola D, Carpenter PM, Bowtell D, et al. 2010. Siah2-Dependent Concerted Activity of HIF and FoxA2 Regulates Formation of Neuroendocrine Phenotype and Neuroendocrine Prostate Tumors. Cancer Cell 18: 23–38. https://www.cell.com/cancer-cell/abstract/S1535-6108(10)00236-9 (Accessed February 27, 2021).
Ramilowski JA, Yip CW, Agrawal S, Chang J-C, Ciani Y, Kulakovskiy IV, Mendez M, Ooi JLC, Ouyang JF, Parkinson N, et al. 2020. Functional annotation of human long noncoding RNAs via molecular phenotyping. Genome Res 30: 1060–1072. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7397864/ (Accessed July 3, 2022).
Richards JP, Yosten GLC, Kolar GR, Jones CW, Stephenson AH, Ellsworth ML, Sprague RS. 2014. Low O2-induced ATP release from erythrocytes of humans with type 2 diabetes is restored by physiological ratios of C-peptide and insulin. American Journal of Physiology- Regulatory, Integrative and Comparative Physiology 307: R862–R868. https://journals.physiology.org/doi/full/10.1152/ajpregu.00206.2014 (Accessed February 27, 2021).
Rustici G, Williams E, Barzine M, Brazma A, Bumgarner R, Chierici M, Furlanello C, Greger L, Jurman G, Miller M, et al. 2021. Transcriptomics data availability and reusability in the transition from microarray to next-generation sequencing. 2020.12.31.425022. https://www.biorxiv.org/content/10.1101/2020.12.31.425022v1 (Accessed June 19, 2022).
Schmitz K-M, Mayer C, Postepska A, Grummt I. 2010. Interaction of noncoding RNA with the rDNA promoter mediates recruitment of DNMT3b and silencing of rRNA genes. Genes Dev 24: 2264–2269. http://genesdev.cshlp.org/content/24/20/2264 (Accessed April 9, 2022).
Semenza GL. 2003. Angiogenesis in ischemic and neoplastic disorders. Annu Rev Med 54: 17–28.
Semenza GL, Wang GL. 1992. A nuclear factor induced by hypoxia via de novo protein synthesis binds to the human erythropoietin gene enhancer at a site required for transcriptional activation. Mol Cell Biol 12: 5447–5454. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC360482/ (Accessed August 14, 2021).
Shoji K, Murayama T, Mimura I, Wada T, Kume H, Goto A, Ohse T, Tanaka T, Inagi R, van der Hoorn FA, et al. 2013. Sperm-associated antigen 4, a novel hypoxia-inducible factor 1 target, regulates cytokinesis, and its expression correlates with the prognosis of renal cell carcinoma. Am J Pathol 182: 2191–2203.
Stoeger T, Amaral LAN. 2022. The characteristics of early-stage research into human genes are substantially different from subsequent research. PLoS Biology 20. https://www.ncbi.nlm.nih.gov/labs/pmc/articles/PMC8769369/ (Accessed February 8, 2022).
Tora L. 2002. A unified nomenclature for TATA box binding protein (TBP)-associated factors (TAFs) involved in RNA polymerase II transcription. Genes Dev 16: 673–675. http://genesdev.cshlp.org/content/16/6/673 (Accessed April 2, 2022).
Valentin C, Birgens H, Craescu CT, Brødum-Nielsen K, Cohen-Solal M. 1998. A phosphoglycerate kinase mutant (PGK Herlev; D285V) in a Danish patient with isolated chronic hemolytic anemia: mechanism of mutation and structure-function relationships. Hum Mutat 12: 280–287.
Wang GL, Jiang BH, Rue EA, Semenza GL. 1995. Hypoxia-inducible factor 1 is a basic- helix-loop-helix-PAS heterodimer regulated by cellular O2 tension. Proc Natl Acad Sci U S A 92: 5510–5514.
Wang GL, Semenza GL. 1995. Purification and Characterization of Hypoxia-inducible Factor 1 (∗). Journal of Biological Chemistry 270: 1230–1237. https://www.jbc.org/article/S0021-9258(18)82990-8/abstract (Accessed August 14, 2021).
Wasserstein RL, Lazar NA. 2016. The ASA Statement on p -Values: Context, Process, and Purpose. The American Statistician 70: 129–133. https://www.tandfonline.com/doi/full/10.1080/00031305.2016.1154108 (Accessed June 28, 2022).
Wong WJ, Qiu B, Nakazawa MS, Qing G, Simon MC. 2013. MYC Degradation under Low O2 Tension Promotes Survival by Evading Hypoxia-Induced Cell Death. Molecular and Cellular Biology 33: 3494–3504. https://mcb.asm.org/content/33/17/3494 (Accessed February 27, 2021).
Yu H, Rimbert A, Palmer AE, Toyohara T, Xia Y, Xia F, Ferreira LMR, Chen Z, Chen T, Loaiza N, et al. 2019. GPR146 Deficiency Protects Against Hypercholesterolemia and Atherosclerosis. Cell 179: 1276-1288.e14. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6889877/ (Accessed February 27, 2021).
Zhang H, Bosch-Marce M, Shimoda LA, Tan YS, Baek JH, Wesley JB, Gonzalez FJ, Semenza GL. 2008. Mitochondrial Autophagy Is an HIF-1-dependent Adaptive Metabolic Response to Hypoxia. J Biol Chem 283: 10892–10903. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447655/ (Accessed March 29, 2022).
Zhang H, Gao P, Fukuda R, Kumar G, Krishnamachary B, Zeller KI, Dang CV, Semenza GL. 2007. HIF-1 inhibits mitochondrial biogenesis and cellular respiration in VHL-deficient renal cell carcinoma by repression of C-MYC activity. Cancer Cell 11: 407–420.
Zhang X, Le W. 2010. Pathological role of hypoxia in Alzheimer’s disease. Experimental Neurology 223: 299–303. https://www.sciencedirect.com/science/article/pii/S0014488609003057 (Accessed June 28, 2022).
Zhang Y, Gu J, Wang L, Zhao Z, Pan Y, Chen Y. 2017. Ablation of PPP1R3G reduces glycogen deposition and mitigates high-fat diet induced obesity. Molecular and Cellular Endocrinology 439: 133–140. https://www.sciencedirect.com/science/article/pii/S0303720716304476 (Accessed June 30, 2022).
Zhang Y, Xu D, Huang H, Chen S, Wang L, Zhu L, Jiang X, Ruan X, Luo X, Cao P, et al. 2014. Regulation of glucose homeostasis and lipid metabolism by PPP1R3G-mediated hepatic glycogenesis. Mol Endocrinol 28: 116–126.
Zhou Y, Zhou B, Pache L, Chang M, Khodabakhshi AH, Tanaseichuk O, Benner C, Chanda SK. 2019. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nature Communications 10: 1523. https://www.nature.com/articles/s41467-019-09234-6 (Accessed February 27, 2021).
佐藤俊哉. 2018. ASA声明と疫学研究におけるP値. 計量生物学 38: 109–115.