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●遺伝子発現カスケード解析をご利用いただいた弊社お客様による論文

Fra-1 Regulates the Expression of HMGA1, Which is Associated with a Poor Prognosis in Human Esophageal Squamous Cell Carcinoma., Toyozumi, T., Hoshino, I., Takahashi, M., Usui, A., Akutsu, Y., Hanari, N., Murakami, K., Kano, M., Akanuma, N., Suitoh, H., Matsumoto, Y., Sekino, N., Komatsu, A., Matsubara, H., Ann Surg Oncol. 24, 3446-3455 (2017) doi: 10.1245/s10434-016-5666-5.

Hyperactive mTOR induces neuroendocrine differentiation in prostate cancer cell with concurrent up-regulation of IRF1., Kanayama, M., Hayano, T., Koebis, M., Maeda, T., Tabe, Y., Horie, S., Aiba, A., Prostate. 77, 1489-1498 (2017) doi: 10.1002/pros.23425.

Diminished DYRK2 sensitizes hormone receptor-positive breast cancer to everolimus by the escape from degrading mTOR., Mimoto, R., Nihira, NT., Hirooka, S., Takeyama, H., Yoshida, K., Cancer Lett. 384, 27-38 (2017) doi: 10.1016/j.canlet.2016.10.015.

Genome-wide DNA methylation profiling of CpG islands in a morpholino anthracycline derivative-resistant leukemia cell line: p38α as a novel candidate for resistance., Asano, T., Narazaki, H., Fujita, A., Pharmacol Res Perspect. 5, e00285 (2016) doi: 10.1002/prp2.285.

Evaluation of the effects of quercetin on damaged salivary secretion., Takahashi, A., Inoue, H., Mishima, K., Ide, F., Nakayama, R., Hasaka, A., Ryo, K., Ito, Y., Sakurai, T., Hasegawa, Y., Saito, I., PLoS One. 10, e0116008 (2015) doi: 10.1371/journal.pone.0116008. eCollection 2015.

遺伝子発現カスケード解析によるトコトリエノールエーテル誘導体の抗中皮腫作用に関与するシグナル分子の推定, 菅原綾介, 佐藤綾美, 内田明日香, 塩澤信哉, 河野翔, 宮越雄一, 安藤章, 太田昌子, 矢野友啓, ビタミン 88, 610 -615 (2014)

 

●geneXplain社・Biobase社の顧客・関係者によるUpstream Analysis(遺伝子発現カスケード解析)を使用した論文

Gender-Specific Expression of Ubiquitin-Specific Peptidase 9 Modulates Tau Expression and Phosphorylation: Possible Implications for Tauopathies., Köglsberger, S,, Cordero-Maldonado, M. L., Antony,P., Forster, J. I., Garcia, P., Buttini, M., Crawford, A., Glaab, E., Mol Neurobiol. 54, 7979-7993 (2017) doi: 10.1007/s12035-016-0299-z.

Study on a novel polymorphism in the VKORC1 promoter region using bioinformatic tools and warfarin dosing data., Askari, B., Khaleqsefat, E., Khalafkhani, D., Khalaj-Kondori, M., Khademvatan, K., Soraya, H., Thromb Res. 158, 76-78 (2017) doi: 10.1016/j.thromres.2017.08.012.

c-Jun N-terminal kinase 2 promotes enterocyte survival and goblet cell differentiation in the inflamed intestine. Mandić AD, Bennek E, Verdier J, Zhang K, Roubrocks S, Davis RJ, Denecke B, Gassler N, Streetz K, Kel A, Hornef M, Cubero FJ, Trautwein C, Sellge G., Mucosal Immunol. 10, 1211-1223 (2017) doi: 10.1038/mi.2016.125.

Decoding Cellular Dynamics in Epidermal Growth Factor Signaling Using a New Pathway-Based Integration Approach for Proteomics and Transcriptomics Data., Wachter, A., Beißbarth, T., Front Genet. 6, 351 (2016) doi: 10.3389/fgene.2015.00351.

Multi-omics “upstream analysis” of regulatory genomic regions helps identifying targets against methotrexate resistance of colon cancer., Kel, A. E., Stegmaier, P., Valeev, T., Koschmann, J., Poroikov, V., Kel-Margoulis, O. V. and Wingender, E., EuPA Open Proteomics 13, 1-13 (2016) doi: 10.1016/j.euprot.2016.09.002.

Prediction of protein-DNA interactions of transcription factors linking proteomics and transcriptomics data., Kondrakhin, Y., Valeev, T., Sharipov, R., Yevshin, I., Kolpakov, F. and Kel, A. E., EuPA Open Proteomics 13, 14-23  (2016) doi: 10.1016/j.euprot.2016.09.001.

Pathways of aging: comparative analysis of gene signatures in replicative senescence and stress induced premature senescence., Kural, K. C., Tandon, N., Skoblov, M., Kel-Margoulis, O. V. and Baranova, A. V.,  BMC Genomics 17, 1030 (2016) doi: 10.1186/s12864-016-3352-4.

Microarray characterization of gene expression changes in blood during acute ethanol exposure., Kupfer, D.M., White, V.L., Strayer, D.L., Crouch, D.J., Burian, D., BMC Med Genomics 6, 26 (2013) doi: 10.1186/1755-8794-6-26.

Tumor suppressor maspin as a rheostat in HDAC regulation to achieve the fine-tuning of epithelial homeostasis., Kaplun, A., Dzinic, S., Bernardo, M., Sheng, S., Crit Rev Eukaryot Gene Expr. 22, 249-258 (2012)

A metabolic prosurvival role for PML in breast cancer., Carracedo, A., Weiss, D., Leliaert, A.K., Bhasin, M., de Boer, V.C., Laurent, G., Adams, A.C., Sundvall, M., Song, S.J., Ito, K., Finley, L.S., Egia, A., Libermann, T., Gerhart-Hines, Z., Puigserver, P., Haigis, M.C., Maratos-Flier, E., Richardson, A.L., Schafer, Z.T., Pandolfi, P.P., J Clin Invest. 122, 3088-3100 (2012) doi: 10.1172/JCI62129. Epub 2012 Aug 13.

Computational predictions of common transcription factor binding sites on the genes of proline metabolism in plants., Kiran, U., Abdin, M.Z., Bioinformation 8, 886-890 (2012) doi: 10.6026/97320630008886. Epub 2012 Sep 21.

Gene set enrichment analysis identifies LIF as a negative regulator of human Th2 cell differentiation., Ullah, U., Tripathi, P., Lahesmaa, R., Rao, K.V., Sci Rep. 2, 464 (2012) doi: 10.1038/srep00464. Epub 2012 Jun 18.

Proteomic analysis (GeLC-MS/MS) of ePFT-collected pancreatic fluid in chronic pancreatitis., Paulo, J.A., Kadiyala, V., Lee, L.S., Banks, P.A., Conwell, D.L., Steen, H., J Proteome Res. 11, 1897-1912 (2012) doi: 10.1021/pr2011022. Epub 2012 Feb 7.

Identification of hypoxia-induced genes in human SGBS adipocytes by microarray analysis., Geiger, K., Leiherer, A., Muendlein, A., Stark, N., Geller-Rhomberg, S., Saely, C.H., Wabitsch, M., Fraunberger, P., Drexel, H., PLoS One 6, e26465 (2011) Epub 2011 Oct 19.

In Silico Analysis of Combinatorial microRNA Activity Reveals Target Genes and Pathways Associated with Breast Cancer Metastasis., Dombkowski, A.A., Sultana, Z., Craig, D.B., Jamil, H., Cancer Inform. 10, 13-29 (2011) doi: 10.4137/CIN.S6631.

Inhibition of glycolytic enzymes mediated by pharmacologically activated p53: targeting Warburg effect to fight cancer., Zawacka-Pankau, J., Grinkevich, V.V., Hünten, S., Nikulenkov, F., Gluch, A., Li, H., Enge, M., Kel, A., Selivanova, G.,  J. Biol. Chem. 286, 41600-41615 (2011)

Early transcriptional regulation by C-peptide in freshly isolated rat proximal tubular cells., Lindahl, E., Nordquist, L., Müller, P. E., Agha, E., Friederich, M., Dahlman-Wright, K., Palm, F., Jörnvall, H., Diabetes Metab Res Rev. 27, 697-704 (2011) doi: 10.1002/dmrr.1220.

Identification of key mechanisms controlling gene expression in Leishmania infected macrophages using genome-wide promoter analysis., Ghedira, K., Hornischer, K., Konovalova, T., Jenhani, A.Z., Benkahlam, A., Kel, A., Infect Genet Evol. 11, 769-77 (2011) doi: 10.1016/j.meegid.2010.10.015. Epub 2010 Nov 18.

Development and evaluation of a genomic signature for the prediction and mechanistic assessment of nongenotoxic hepatocarcinogens in the rat., Fielden, M.R., Adai, A., Dunn, R.T. 2nd, Olaharski, A., Searfoss, G., Sina, J., Aubrecht, J., Boitier, E., Nioi, P., Auerbach, S., Jacobson-Kram, D., Raghavan, N., Yang, Y., Kincaid, A., Sherlock, J., Chen, S.J., Car, B.; Predictive Safety Testing Consortium, Carcinogenicity Working Group., Toxicol Sci. 124, 54-74 (2011) doi: 10.1093/toxsci/kfr202. Epub 2011 Aug 2.

Left ventricular remodeling in swine after myocardial infarction: a transcriptional genomics approach., Kuster, D.W., Merkus, D., Kremer, A., van Ijcken, W.F., de Beer, V.J., Verhoeven, A.J., Duncker, D.J., Basic Res Cardiol. 106, 1269-81 (2011) doi: 10.1007/s00395-011-0229-1. Epub 2011 Nov 5.

Estrogen-regulated genes in rat testes and their relationship to recovery of spermatogenesis after irradiation., Zhou, W., Bolden-Tiller, O.U., Shao, S.H., Weng, C.C., Shetty, G., AbuElhija, M., Pakarinen, P., Huhtaniemi, I., Momin, A.A., Wang, J., Stivers, D.N., Liu, Z., Meistrich, M.L., Biol Reprod. 85, 823-33 (2011) doi: 10.1095/biolreprod.111.091611. Epub 2011 Jun 8.

Specific regulatory motifs predict glucocorticoid responsiveness of hippocampal gene expression., Datson, N.A., Polman, J.A., de Jonge, R.T., van Boheemen, P.T., van Maanen, E.M., Welten, J., McEwen, B.S., Meiland, H.C., Meijer, O.C., Endocrinology. 152, 3749-57 (2011) doi: 10.1210/en.2011-0287. Epub 2011 Aug 16.

Express path analysis identifies a tyrosine kinase Src-centric network regulating divergent host responses to Mycobacterium tuberculosis infection., Karim, A.F., Chandra, P., Chopra, A., Siddiqui, Z., Bhaskar, A., Singh, A., Kumar, D., J Biol Chem. 286, 40307-19 (2011) doi: 10.1074/jbc.M111.266239. Epub 2011 Sep 27.

Proteomic analysis of an immortalized mouse pancreatic stellate cell line identifies differentially-expressed proteins in activated vs nonproliferating cell states., Paulo, J.A., Urrutia, R., Banks, P.A., Conwell, D.L., Steen, H., J Proteome Res. 10, 4835-44 (2011) doi: 10.1021/pr2006318. Epub 2011 Sep 9.

Unique cellular and mitochondrial defects mediate FK506-induced islet β-cell dysfunction., Rostambeigi, N., Lanza, I.R., Dzeja, P.P., Deeds, M.C., Irving, B.A., Reddi, H.V., Madde, P., Zhang, S., Asmann, Y.W., Anderson, J.M., Schimke, J.M., Nair, K.S., Eberhardt, N.L., Kudva, Y.C., Transplantation. 91, 615-23 (2011) doi: 10.1097/TP.0b013e3182094a33.

A20 modulates lipid metabolism and energy production to promote liver regeneration., Damrauer SM1, Studer P, da Silva CG, Longo CR, Ramsey HE, Csizmadia E, Shrikhande GV, Scali ST, Libermann TA, Bhasin MK, Ferran C., PLoS One. 6, e17715 (2011) doi: 10.1371/journal.pone.0017715.

Proteomics and pathway analysis identifies JNK signaling as critical for high linear energy transfer radiation-induced apoptosis in non-small lung cancer cells., Stahl, S., Fung, E., Adams, C., Lengqvist, J., Mork, B., Stenerlow, B., Lewensohn, R., Lehtio, J., Zubarev, R., Viktorsson, K., Mol Cell Proteomics 8, 1117-29 (2009) Epub 2009 Jan 23.

 

●遺伝子発現カスケード解析 (Upstream Analysis) 開発関連論文

Search for Master Regulators in Walking Cancer Pathways., Kel, A. E., Methods Mol Biol. 1613, 161-191 (2017) doi: 10.1007/978-1-4939-7027-8_8.

Data on master regulators and transcription factor binding sites found by upstream analysis of multi-omics data on methotrexate resistance of colon cancer., Kel, A. E. Data Brief. 10, 499-504 (2016) doi: 10.1016/j.dib.2016.11.096.

“Upstream Analysis”: An integrated promoter-pathway analysis approach to causal interpretation of microarray data., Koschmann, J., Bhar, A., Stegmaier,P., Kel, A. E. and Wingender, E.,  Microarrays 4, 270-286 (2015) doi:10.3390/microarrays4020270.

TFClass: a classification of human transcription factors and their rodent orthologs., Wingender, E., Schoeps, T., Haubrock, M., Dönitz, J. Nucleic Acids Res. 43, D97-D102 (2015) doi: 10.1093/nar/gku1064.

Equal impact of diffusion and DNA binding rates on the potential spatial distribution of nuclear factor κB transcription factor inside the nucleus., Sycheva, A.M., Kel, A., Nikolaev, E.N., Moshkovskii, S.A., Biochemistry (Mosc) 79, 577-80 (2014) doi: 10.1134/S0006297914060121.

Toward more transparent and reproducible omics studies through a common metadata checklist and data publications., Kolker, E., Ozdemir, V., Martens, L., Hancock, W., Anderson, G., Anderson, N., Aynacioglu, S., Baranova, A., Campagna, S.R., Chen, R., Choiniere, J., Dearth, S.P., Feng, W.C., Ferguson, L., Fox, G., Frishman, D., Grossman, R., Heath, A., Higdon, R., Hutz, MH., Janko, I., Jiang, L., Joshi, S., Kel, A., Kemnitz, J.W., Kohane, I.S., Kolker, N., Lancet, D., Lee, E., Li, W., Lisitsa, A., Llerena, A., Macnealy-Koch, C., Marshall, J.C., Masuzzo, P., May, A., Mias, G., Monroe, M., Montague, E., Mooney, S., Nesvizhskii, A., Noronha, S., Omenn, G., Rajasimha, H., Ramamoorthy, P., Sheehan, J., Smarr, L., Smith, C.V., Smith, T., Snyder, M., Rapole, S., Srivastava, S., Stanberry, L., Stewart, E., Toppo, S., Uetz, P., Verheggen, K., Voy, B.H., Warnich, L., Wilhelm, S.W. and Yandl, G. OMICS 18, 10-14 (2014) doi:10.1089/omi.2013.0149.

Integrated Bio-Search: challenges and trends for the integration, search and comprehensive processing of biological information., Masseroli, M., Mons, B., Bongcam-Rudloff, E., Ceri, S., Kel, A., Rechenmann, F., Lisacek, F. and Romano, P. BMC Bioinformatics 15 (Suppl. 1), S2 (2014) doi:10.1186/1471-2105-15-S1-S2.

MatrixCatch – a novel tool for the recognition of composite regulatory elements in promoters., Deyneko, I. V., Kel, A. E., Kel-Margoulis, O. V., Deineko, E. V., Wingender, E. and Weiss, S. BMC Bioinformatics 14, 241 (2013)