Construction of human activity‐based phosphorylation networks by Robert H Newman, Jianfei Hu, Hee‐Sool Rho, Zhi Xie, Crystal Woodard, John Neiswinger, Christopher Cooper, Matthew Shirley, Hillary M Clark, Shaohui Hu, Woochang Hwang, Jun Seop Jeong, George Wu, Jimmy Lin, Xinxin Gao, Qiang Ni, Renu Goel, Shuli Xia, Hongkai Ji, Kevin N Dalby, Morris J Birnbaum, Philip A Cole, Stefan Knapp, Alexey G Ryazanov, Donald J Zack, Seth Blackshaw, Tony Pawson, Anne‐Claude Gingras, Stephen Desiderio, Akhilesh Pandey, Benjamin E Turk, Jin Zhang, Heng Zhu, Jiang Qian

“…Here, we developed a new strategy, called CEASAR, based on functional protein microarrays and bioinformatics to experimentally identify substrates for 289 unique kinases, resulting in 3656 high‐quality KSRs. …”
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The relative resistance of children to sepsis mortality: from pathways to drug candidates by Rose B Joachim, Gabriel M Altschuler, John N Hutchinson, Hector R Wong, Winston A Hide, Lester Kobzik

“…To find drugs that could promote beneficial (child) pathways or inhibit harmful (adult) ones, we built an in silico pathway drug network (PDN) using expression correlation between drug, disease, and pathway gene signatures across 58,475 microarrays. Specific pathway clusters from children or adults were assessed for correlation with drug‐based signatures. …”
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Gene signature based on degradome-related genes can predict distal metastasis in cervical cancer patients by Jorge Fernandez-Retana, Horacio Zamudio-Meza, Miguel Rodriguez-Morales, Abraham Pedroza-Torres, David Isla-Ortiz, Luis Herrera, Nadia Jacobo-Herrera, Oscar Peralta-Zaragoza, César López-Camarillo, Fermin Morales-Gonzalez, David Cantu de Leon, Carlos Pérez-Plasencia

“…In this study, we used high-density microarrays and quantitative reverse transcriptase polymerase chain reaction to evaluate the degradome profile and their inhibitors in 112 samples of patients diagnosed with locally advanced cervical cancer. …”
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Adverse predictive value of ASPM on lung adenocarcinoma overall survival depended on chemotherapy status by Yan Zheng, Baichen Sun, Zhiling Qu

“…This study investigates the expression and prognostic value of ASPM, focusing on its role in chemotherapy outcomes.Methods We analyzed the prognostic relevance of ASPM using bioinformatics, immunohistochemical staining of LUAD tissue microarrays, and proteomics data. Further, in vitro experiments were conducted to evaluate the effects of ASPM overexpression on cell proliferation and sensitivity to cisplatin.Results Bioinformatics analysis revealed that ASPM’s prognostic significance differed between transcriptomic and proteomic datasets. …”
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Comprehensive analysis of the clinical and biological significances of polyamine metabolism in glioma by Fei Bai, Kexin Zhai, Tiantian Yao, Yuxia Zhou, Yongxiang Zhao, Guanghui Yang

“…What’s more, IHC staining was conducted on glioma tissue microarrays to confirm the expression patterns of genes related to polyamine metabolism in glioma tissues. …”
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The transcription factor SOX18 regulates the expression of matrix metalloproteinase 7 and guidance molecules in human endothelial cells. by Martina Hoeth, Heide Niederleithner, Renate Hofer-Warbinek, Martin Bilban, Herbert Mayer, Ulrike Resch, Christof Lemberger, Oswald Wagner, Erhard Hofer, Peter Petzelbauer, Rainer de Martin

“…<h4>Methodology/principal findings</h4>SOX18 was expressed in HUVEC using a recombinant adenoviral vector and the altered gene expression profile was analyzed using microarrays. Expression of several regulated candidate SOX18 target genes was verified by real-time PCR. …”
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Partial IGF-1 deficiency is sufficient to reduce heart contractibility, angiotensin II sensibility, and alter gene expression of structural and functional cardiac proteins. by José Luis González-Guerra, Inma Castilla-Cortazar, Gabriel A Aguirre, Úrsula Muñoz, Irene Martín-Estal, Elena Ávila-Gallego, Miriam Granado, Juan E Puche, Ángel Luis García-Villalón

“…In addition, histology of the heart was performed together with cardiac gene expression for proteins involved in structure and function (extracellular matrix, contractile proteins, active peptides); carried out using microarrays, followed by RT-qPCR confirmation of the three experimental groups. …”
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A cytokine protein-protein interaction network for identifying key molecules in rheumatoid arthritis. by Venugopal Panga, Srivatsan Raghunathan

“…By combining the network centrality measures with the gene expression data from the RA related microarrays that are available in the open source Gene Expression Omnibus (GEO) database, we have identified 24 key proteins of this signaling network. …”
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Comparing the Expression of Genes Related to Serotonin (5-HT) in C57BL/6J Mice and Humans Based on Data Available at the Allen Mouse Brain Atlas and Allen Human Brain Atlas by C. A. Acevedo-Triana, L. A. León, F. P. Cardenas

“…Genes of interest were searched for manually in each case (in situ hybridization for mice and microarrays for humans), normalized expression data (z-scores) were extracted, and the results were graphed. …”
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Milk production in the post-genomic era by Polona FRAJMAN, Peter DOVČ

“…The availability of genomic DNA sequences for a number of potential candidate genes with an impact on production traits allowed construction of cattle genome microarrays. Functional studies of milk protein genes revealed the impact of different genetic variants on technological properties of milk. …”
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Systems biology approaches reveal a specific interferon-inducible signature in HTLV-1 associated myelopathy. by Sonja Tattermusch, Jason A Skinner, Damien Chaussabel, Jacques Banchereau, Matthew P Berry, Finlay W McNab, Anne O'Garra, Graham P Taylor, Charles R M Bangham

“…We used gene expression microarrays followed by flow cytometric and functional assays to investigate global changes in blood transcriptional profiles of HTLV-1-infected and seronegative individuals. …”
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Network analysis of epidermal growth factor signaling using integrated genomic, proteomic and phosphorylation data. by Katrina M Waters, Tao Liu, Ryan D Quesenberry, Alan R Willse, Somnath Bandyopadhyay, Loel E Kathmann, Thomas J Weber, Richard D Smith, H Steven Wiley, Brian D Thrall

“…To understand how integration of multiple data types can help decipher cellular responses at the systems level, we analyzed the mitogenic response of human mammary epithelial cells to epidermal growth factor (EGF) using whole genome microarrays, mass spectrometry-based proteomics and large-scale western blots with over 1000 antibodies. …”
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Epigenomic modifications predict active promoters and gene structure in Toxoplasma gondii. by Mathieu Gissot, Krystyna A Kelly, James W Ajioka, John M Greally, Kami Kim

“…Using the model organism Toxoplasma gondii, we characterized the epigenetic organization and transcription patterns of a contiguous 1% of the T. gondii genome using custom oligonucleotide microarrays. We show that methylation and acetylation of histones H3 and H4 are landmarks of active promoters in T. gondii that allow us to deduce the position and directionality of gene promoters with >95% accuracy. …”
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Tissue factor expression in salivary gland carcinoma: a potential novel therapeutic target for advanced disease by Louis Jansen, Lisa Nachtsheim, Philipp Wolber, Sami Shabli, Julia Eßer, Alexander Quaas, Luc G. T. Morris, Alan L. Ho, Jens Peter Klußmann, Christoph Arolt, Marcel Mayer

“…Methods: TF expression in primaries and lymph node (LN) metastases was assessed using immunohistochemistry on tissue microarrays. Histo-scores were calculated for cytoplasmic and membranous staining and correlated with clinicopathological data. …”
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A morning-specific phytohormone gene expression program underlying rhythmic plant growth. by Todd P Michael, Ghislain Breton, Samuel P Hazen, Henry Priest, Todd C Mockler, Steve A Kay, Joanne Chory

“…To determine the transcriptional component associated with the rhythmic control of growth, we applied temporal analysis of the Arabidopsis thaliana seedling transcriptome under multiple growth conditions and mutant backgrounds using DNA microarrays. We show that a group of plant hormone-associated genes are coexpressed at the time of day when hypocotyl growth rate is maximal. …”
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Improved real-time RT-PCR method for high-throughput measurements using second derivative calculation and double correction by Van Luu-The, Nathalie Paquet, Ezequiel Calvo, Jean Cumps

“…Quantification of mRNA expression levels using real-time reverse transcription PCR (RT-PCR) is increasingly used to validate results of DNA microarrays or GeneChips®. It requires an improved method that is more robust and more suitable for high-throughput measurements. …”
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Coordinate Transcriptomic and Metabolomic Effects of the Insulin Sensitizer Rosiglitazone on Fundamental Metabolic Pathways in Liver, Soleus Muscle, and Adipose Tissue in Diabetic... by Sabrina Le Bouter, Marianne Rodriguez, Nolwen Guigal-Stephan, Sophie Courtade-Gaïani, Laura Xuereb, Catherine de Montrion, Vincent Croixmarie, Thierry Umbdenstock, Claire Boursier-Neyret, Michel Lonchampt, Manuel Brun, Catherine Dacquet, Alain Ktorza, Brian-Paul Lockhart, Jean-Pierre Galizzi

“…For this aim, transcriptional changes were measured in liver, inguinal adipose tissue (IAT) and soleus muscle using microarrays and real-time PCR. In parallel, targeted metabolomic assessment of lipids (triglycerides (TGs) and free fatty acids (FFAs)) in plasma and tissues was performed by UPLC-MS methods. …”
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Prognostic significance of cytotoxic-T-lymphocytes to immunosuppressive lymphocytes ratio (CIL) in laryngeal squamous cell carcinoma by Duo Zhang, Yu Heng, Qiu-yan Jin, Di Tang, Xiao-ke Zhu, Li-ming Lu, Chun-ping Wu, Lei Tao

“…Two cohorts were included in this study: The training cohort (N = 75) consisted of tumor tissue microarrays from LSCC patients in our department, and the validation cohort (N = 116) utilized bulk RNA-seq data from the TCGA database. …”
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A Transcriptomic Signature of Mouse Liver Progenitor Cells by Adam M. Passman, Jasmine Low, Roslyn London, Janina E. E. Tirnitz-Parker, Atsushi Miyajima, Minoru Tanaka, Helene Strick-Marchand, Gretchen J. Darlington, Megan Finch-Edmondson, Scott Ochsner, Cornelia Zhu, James Whelan, Bernard A. Callus, George C. T. Yeoh

“…A transcriptomic meta-analysis of over 400 microarrays was undertaken to compare LPC lines against datasets of muscle and embryonic stem cell lines, embryonic and developed liver (DL), and HCC. …”
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Comprehensive analysis of microRNA expression profile in malignant glioma tissues by Monika Piwecka, Katarzyna Rolle, Agnieszka Belter, Anna Maria Barciszewska, Marek Żywicki, Marcin Michalak, Stanisław Nowak, Mirosława Z. Naskręt-Barciszewska, Jan Barciszewski

“…We investigated the global miRNA profile of malignant glioma tissues with miRNA microarrays, deep sequencing and meta‐analysis. We selected miRNAs that were most frequently deregulated in glioblastoma tissues, as well as in peritumoral areas, in comparison with normal human brain. …”
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