Pathway databases
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This study aims to investigate the role and mechanism of tubiquitin-conjugating enzyme E2 C (UBE2C) in acute myeloid leukemia (AML). Initially, UBE2C expression in leukemia was analyzed using the Cancer Genome Atlas database. Further, we silenced UBE2C expression using small-hairpin RNA (sh-RNA).
11p vishanshan 27-06-2024 1 1 Download
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Precision oncology involves analysis of individual cancer samples to understand the genes and pathways involved in the development and progression of a cancer. To improve patient care, knowledge of diagnostic, prognostic, predisposing, and drug response markers is essential.
16p vibransone 28-03-2024 4 2 Download
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We present PhenCards (https://phencards.org), a database and web server intended as a one-stop shop for previously disconnected biomedical knowledge related to human clinical phenotypes. Users can query human phenotype terms or clinical notes. PhenCards obtains relevant disease/phenotype prevalence and co-occurrence, drug, procedural, pathway, literature, grant, and collaborator data.
9p vibransone 28-03-2024 7 1 Download
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The ends of linear chromosomes, the telomeres, comprise repetitive DNA sequences in complex with proteins that protects them from being processed by the DNA repair machinery. Cancer cells need to counteract the shortening of telomere repeats during replication for their unlimited proliferation by reactivating the reverse transcriptase telomerase or by using the alternative lengthening of telomeres (ALT) pathway.
10p vinarcissa 21-03-2023 2 1 Download
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This study aimed to explore the molecular mechanism of estrogen-mediated neuroprotection in the relief of cerebral ischemic injury. The gene expression profiles were downloaded from Gene Expression Omnibus database, and differentially expressed genes (DEGs) were identified using limma package in R software.
10p vihagrid 30-01-2023 5 3 Download
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Metabolism including anabolism and catabolism is a prerequisite phenomenon for all living organisms. Anabolism refers to the synthesis of the entire compound needed by a species. Catabolism refers to the breakdown of molecules to obtain energy.
7p vihagrid 30-01-2023 11 3 Download
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To identify candidate key genes and pathways related to resting mast cells in meningioma and the underlying molecular mechanisms of meningioma. Gene expression profiles of the used microarray datasets were obtained from the Gene Expression Omnibus (GEO) database.
12p vimahuateng 26-11-2021 6 1 Download
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This study aimed to explore and identify key genes and signaling pathways that contribute to the progression of cervical cancer to improve prognosis. Three gene expression profiles (GSE63514, GSE64217 and GSE138080) were screened and downloaded from the Gene Expression Omnibus database (GEO).
15p vimahuateng 26-11-2021 2 0 Download
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Liver cancer is the sixth most commonly diagnosed cancer and the fourth most common cause of cancer death. The purpose of this work is to find new diagnostic biomarkers or prognostic biomarkers and explore the biological functions related to the prognosis of liver cancer.
15p vimahuateng 26-11-2021 8 1 Download
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The stabilization and three-dimensional modeling of mutant proteins were also determined by using the I-Mutant 2.0 and Project HOPE webservers, respectively. In total, 772 missense SNPs were found in the APAF1 gene from the NCBI dbSNP database, 18 SNPs of which were demonstrated to be deleterious or damaging. Of those, 13 SNPs had a decreasing effect on protein stability, while the other 5 SNPs had an increasing effect. Based on the modeling results, some dissimilarities of mutant type amino acids from wild-type amino acids such as size, charge, and hydrophobicity were revealed.
11p thiencuuchu 27-11-2021 12 3 Download
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Polyhydroxyalkanoate (PHA) is stored as an important carbon and energy source in bacterial cells. For biomedical applications, gram-positive bacteria can be better sources of PHAs, since they lack outer membrane lipopolysaccharide. Although gram-positive Streptomyces coelicolor A3(2) has been indicated as a high potential PHA producer, phaC gene that encodes the key enzyme PHA synthase in the metabolic pathway is not determined in its genome.
12p thiencuuchu 27-11-2021 17 1 Download
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Brain cancer is one of the eight most common cancers occurring in people aged 40+ and is the fifthleading cause of cancer-related deaths for males aged 40–59. Accurate subtype identification is crucial for precise therapeutic treatment, which largely depends on understanding the biological pathways and regulatory mechanisms associated with different brain cancer subtypes.
11p vilichoo2711 25-06-2021 7 1 Download
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Plants have adapted to survive under adverse conditions or exploit favorable conditions in response to their environment as sessile creatures. In a way of plant adaptation, plant hormones have been evolved to efficiently use limited resources.
6p vijichea2711 28-05-2021 10 1 Download
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The concept of orthology is key to decoding evolutionary relationships among genes across different species using comparative genomics. QuartetS is a recently reported algorithm for large-scale orthology detection.
9p viwyoming2711 16-12-2020 5 0 Download
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The MetaCyc and KEGG projects have developed large metabolic pathway databases that are used for a variety of applications including genome analysis and metabolic engineering. We present a comparison of the compound, reaction, and pathway content of MetaCyc version 16.0 and a KEGG version downloaded on Feb-27-2012 to increase understanding of their relative sizes, their degree of overlap, and their scope.
15p viwyoming2711 16-12-2020 14 1 Download
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A central challenge to understanding the ecological and biogeochemical roles of microorganisms in natural and human engineered ecosystems is the reconstruction of metabolic interaction networks from environmental sequence information.
10p viwyoming2711 16-12-2020 13 1 Download
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Biologists make frequent use of databases containing large and complex biological networks. One popular database is the Kyoto Encyclopedia of Genes and Genomes (KEGG) which uses its own graphical representation and manual layout for pathways.
17p viwyoming2711 16-12-2020 12 1 Download
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Given the estimate that 30% of our genes are controlled by microRNAs, it is essential that we understand the precise relationship between microRNAs and their targets. OncomiRs are microRNAs (miRNAs) that have been frequently shown to be deregulated in cancer.
12p vikentucky2711 26-11-2020 13 0 Download
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Increasing resistance to anti-tuberculosis drugs has driven the need for developing new drugs. Resources such as the tropical disease research (TDR) target database and AssessDrugTarget can help to prioritize putative drug targets.
10p vioklahoma2711 19-11-2020 6 2 Download
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When modeling in Systems Biology and Systems Medicine, the data is often extensive, complex and heterogeneous. Graphs are a natural way of representing biological networks. Graph databases enable efficient storage and processing of the encoded biological relationships. They furthermore support queries on the structure of biological networks.
9p vioklahoma2711 19-11-2020 10 0 Download