Abstract：
:Two-color DNA microarrays are commonly used for the analysis of global gene expression. They provide information on relative abundance of thousands of mRNAs. However, the generated data need to be normalized to minimize systematic variations so that biologically significant differences can be more easily identified. A large number of normalization procedures have been proposed and many softwares for microarray data analysis are available. Here, we have applied two normalization methods (median and loess) from two packages of microarray data analysis softwares. They were examined using a sample data set. We found that the number of genes identified as differentially expressed varied significantly depending on the method applied. The obtained results, i.e. lists of differentially expressed genes, were consistent only when we used median normalization methods. Loess normalization implemented in the two software packages provided less coherent and for some probes even contradictory results. In general, our results provide an additional piece of evidence that the normalization method can profoundly influence final results of DNA microarray-based analysis. The impact of the normalization method depends greatly on the algorithm employed. Consequently, the normalization procedure must be carefully considered and optimized for each individual data set.
journal_name
Acta Biochim Poljournal_title
Acta biochimica Polonicaauthors
Schmidt MT,Handschuh L,Zyprych J,Szabelska A,Olejnik-Schmidt AK,Siatkowski I,Figlerowicz Msubject
Has Abstractpub_date
2011-01-01 00:00:00pages
573-80issue
4eissn
0001-527Xissn
1734-154Xpii
201114943journal_volume
58pub_type
杂志文章abstract：:Growth arrest and DNA damage-inducible (GADD) 45 proteins are regulators of cell death and survival. The proinflammatory cytokine IL-1β strongly increases the level of the transcript encoding GADD45α in rat insulin-producing INS-1E cells. The activation of Gadd45α gene is clearly dependent on JNK and NF-κB activation ...
journal_title：Acta biochimica Polonica
pub_type： 杂志文章
doi：
更新日期：2013-01-01 00:00:00
abstract：:1. The interaction of copper(II) with inosine, 2'-deoxyinosine, 1-methylinosine, 7-deazainosine, 6-methoxypurine riboside and IMP was examined. 2. Copper binds with the purine base of the nucleosides, and in IMP also with the phosphate group. Non interaction with ribose hydroxyl groups was observed. 3. In non-aqueous ...
journal_title：Acta biochimica Polonica
pub_type： 杂志文章
doi：
更新日期：1978-01-01 00:00:00
abstract：:Annexins belong to a family of multi-functional membrane- and Ca(2+)-binding proteins. The characteristic feature of these proteins is that they can bind membrane phospholipids in a reversible, Ca(2+)-dependent manner. While animal annexins have been known for a long time and are fairly well characterized, their plant...
journal_title：Acta biochimica Polonica
pub_type： 杂志文章,评审
doi：
更新日期：2009-01-01 00:00:00
abstract：:Changes in the composition of fatty acids (FA) were determined in lipid extracts isolated from developing ovaries containing ovules and developing seeds of Echium vulgare L. The samples were collected successively over 20 days beginning with the first day after flowering. The contents of the n-6 FA family members, i.e...
journal_title：Acta biochimica Polonica
pub_type： 杂志文章
doi：
更新日期：2007-01-01 00:00:00
abstract：:Secondary structure of alpha (light) and beta (heavy) chains of human haptoglobin was proposed. The Chou-Fasman predictive method was used in conjunction with the hydrophobic character and hydropathy scale value assigned to each amino acid residue in the primary sequence of the protein. Moreover, by means of hydrophil...
journal_title：Acta biochimica Polonica
pub_type： 杂志文章
doi：
更新日期：1987-01-01 00:00:00
abstract：:Selectivity of amidination using ornithine as model amino acid was investigated in detail. The results obtained were taken advantage of for studying the reactions with other polyfunctional amino acids: beta-tyrosine, isoserine, 2,3-diaminopropionic acid, 2,6-diamino-7-hydroxyazelaic acid and with the pentapeptide amid...
journal_title：Acta biochimica Polonica
pub_type： 杂志文章
doi：
更新日期：1982-01-01 00:00:00
abstract：:We here report the influence of the cell cycle abrogator UCN-01 on RKO human colon carcinoma cells differing in p53 status following exposure to two DNA damaging agents, the topoisomerase inhibitors etoposide and camptothecin. Cells were treated with the two drugs at the IC90 concentration for 24 h followed by post-in...
journal_title：Acta biochimica Polonica
pub_type： 杂志文章
doi：
更新日期：2002-01-01 00:00:00
abstract：:We investigated the effect of the cyclic AMP-protein kinase A (PKA) signalling pathway on renal Na(+),K(+)-ATPase and ouabain-sensitive H(+),K(+)-ATPase. Male Wistar rats were anaesthetized and catheter was inserted through the femoral artery into the abdominal aorta proximally to the renal arteries for infusion of th...
journal_title：Acta biochimica Polonica
pub_type： 杂志文章
doi：035001103
更新日期：2003-01-01 00:00:00
abstract：:RNA nucleoside triphosphatases (NTPase)/helicases represent a large family of proteins that are ubiquitously distributed over a wide range of organisms. The enzymes play essential role in cell development and differentiation, and some of them are involved in transcription and replication of viral single-stranded RNA g...
journal_title：Acta biochimica Polonica
pub_type： 杂志文章,评审
doi：024903597
更新日期：2002-01-01 00:00:00
abstract：:Public and private EST (Expressed Sequence Tag) programs provide access to a large number of ESTs from a number of plant species, including Arabidopsis, corn, soybean, rice, wheat. In addition to the homology of each EST to genes in GenBank, information about homology to all other ESTs in the data base can be obtained...
journal_title：Acta biochimica Polonica
pub_type： 杂志文章,评审
doi：
更新日期：1998-01-01 00:00:00
abstract：:The root system of rice is influenced by various environmental factors. However, how the root system responds to abiotic stress has not yet been fully understood. A zinc finger protein gene, OsZFP350, is exclusively expressed in the rice root, but its biological function needs to be investigated. Expression of OsZFP35...
journal_title：Acta biochimica Polonica
pub_type： 杂志文章
doi：10.18388/abp.2018_2765
更新日期：2019-05-24 00:00:00
abstract：:Human haptoglobin (Hp) of the 1-1 type incorporated one spin or fluorescence marker per molecule; the markers were found in the beta chain. Formation of the complex between spin-labelled Hp and haemoglobin or antibody caused conformational changes in the Hp molecular, evidenced by increased participation in the electr...
journal_title：Acta biochimica Polonica
pub_type： 杂志文章
doi：
更新日期：1978-01-01 00:00:00
abstract：:Several mammalian enzymes are anchored to the outer surface of the plasma membrane by a covalently attached glycosylphosphatidylinositol (GPI) structure. These include acetylcholinesterase, alkaline phosphatase (AP) and 5'-nucleotidase among other enzymes. Recently, it has been reported that these membrane enzymes can...
journal_title：Acta biochimica Polonica
pub_type： 杂志文章
doi：
更新日期：2007-01-01 00:00:00
abstract：:The photochemical characteristics of mesophyll and bundle sheath chloroplasts isolated from the leaves of C4 species were investigated in Zea mays (NADP-ME type), Panicum miliaceum (NAD-ME type) and Panicum maximum (PEP-CK type) plants. The aim of this work was to gain information about selected photochemical properti...
journal_title：Acta biochimica Polonica
pub_type： 杂志文章
doi：
更新日期：2006-01-01 00:00:00
abstract：:Nowadays, scientists may learn a lot about the organisms studied just by analyzing their genetic material. This requires the development of methods of reading genomes with high accuracy. It has become clear that the knowledge of the changes occurring within a viral genome is indispensable for effective fighting of the...
journal_title：Acta biochimica Polonica
pub_type： 杂志文章
doi：045104983
更新日期：2004-01-01 00:00:00
abstract：:In situ PCR and in situ reverse transcription PCR (RT-PCR) were applied to discriminate between latent and productive infection of human cytomegalovirus (HCMV) in leukocytes. We investigated 28 samples, in which viral pp65 antigen was detected only in the cytoplasm of leukocytes. Additionally we assayed 12 specimens l...
journal_title：Acta biochimica Polonica
pub_type： 杂志文章
doi：
更新日期：2006-01-01 00:00:00
abstract：:The aim of this study was to investigate the antimicrobial effect of lipopeptide biosurfactants from surfactin, iturin and fengycin families, synthesised by the Bacillus subtilis I'1a strain, on uropathogenic bacteria, including the effects on planktonic growth, processes of biofilm formation and dislodging. Antimicro...
journal_title：Acta biochimica Polonica
pub_type： 杂志文章
doi：10.18388/abp.2015_1120
更新日期：2015-01-01 00:00:00
abstract：:X-ray crystallography provides important insights into structure-function relationship in biomolecules. However, protein crystals are usually hard to obtain which hinders our understanding of multiple important processes. Crystallization requires large amount of protein sample, whereas recombinant proteins are often u...
journal_title：Acta biochimica Polonica
pub_type： 杂志文章
doi：10.18388/abp.2015_1026
更新日期：2015-01-01 00:00:00
abstract：:Although both uveal (UM) and cutaneous (CM) melanoma cells derive from the transformed melanocytes, their biology varies significantly in several aspects. Malignant transformation is frequently associated with alternations in cell glycosylation, in particular those concerning branched complex-type N-glycans. These cha...
journal_title：Acta biochimica Polonica
pub_type： 杂志文章
doi：10.18388/abp.2015_1050
更新日期：2015-01-01 00:00:00
abstract：:This study examined the antiproliferative effects of β-escin (E) in cancer cells. The study showed that E inhibited cancer cells growth in a dose-dependent manner. The flow cytometric analysis revealed an escin-induced increase in the sub-G1 DNA content, which is considered to be a marker of apoptosis. Apoptosis was a...
journal_title：Acta biochimica Polonica
pub_type： 杂志文章
doi：10.18388/abp.2015_1013
更新日期：2016-01-01 00:00:00
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journal_title：Acta biochimica Polonica
pub_type： 杂志文章
doi：10.18388/abp.2015_1165
更新日期：2015-01-01 00:00:00
abstract：:Trans-diamminedichloroplatinum(II) (trans-DDP) forms with DNA at 37 degrees C, more numerous interstrand cross-links than cis-DDP in the isolated DNA and DNA in the chromatin complex. An increase in the temperature to 42.5 degrees C had no effect on the interstrand cross-links of DND-Pt-DNA formed by the two isomers, ...
journal_title：Acta biochimica Polonica
pub_type： 杂志文章
doi：
更新日期：1990-01-01 00:00:00
abstract：:A protease with a molecular mass of 30 kDa and the N-terminal sequence of GLQTNAPWGLARSS, was isolated from fresh fruiting bodies of the wild edible mushroom Termitomyces albuminosus. The purification protocol included ion exchange chromatography on DEAE-cellulose, Q-Sepharose, SP-Sepharose and FPLC-gel filtration on ...
journal_title：Acta biochimica Polonica
pub_type： 杂志文章
doi：
更新日期：2011-01-01 00:00:00
abstract：:1. The insoluble collagen from Guerin epithelioma was isolated and its chemical composition was determined. The unusually high histidine content is accompanied in tumour collagen by a relatively small amount of lysine and arginine. 2. The isolated protein was strongly bound to glycoprotein, which could not be removed ...
journal_title：Acta biochimica Polonica
pub_type： 杂志文章
doi：
更新日期：1975-01-01 00:00:00
abstract：:Staphylococcus aureus is responsible for many types of infections related to biofilm presence. As the early diagnostics remains the best option for prevention of biofilm infections, the aim of the work presented was to search for differences in metabolite patterns of S. aureus ATCC6538 biofilm vs. free-swimming S. aur...
journal_title：Acta biochimica Polonica
pub_type： 杂志文章
doi：
更新日期：2013-01-01 00:00:00
abstract：:The VEGF family members are important factors in promoting angiogenesis and lymphangiogenesis in malignant processes. The aim of this study was to investigate plasma concentrations of VEGF-A, VEGF-B and their soluble VEGFR-1 receptor and their diagnostic utility and potency as compared to CA 15-3 in breast cancer pati...
journal_title：Acta biochimica Polonica
pub_type： 杂志文章
doi：10.18388/abp.2018_2713
更新日期：2018-12-13 00:00:00
abstract：:Spontaneous mutations arise not only in exponentially growing bacteria but also in non-dividing or slowly dividing stationary-phase cells. In the latter case mutations are called adaptive or stationary-phase mutations. High spontaneous mutability has been observed in temperature sensitive Escherichia coli dnaQ49 strai...
journal_title：Acta biochimica Polonica
pub_type： 杂志文章
doi：045103683
更新日期：2004-01-01 00:00:00
abstract：:Endogenous peptide antibiotics are known as evolutionarily old components of innate immunity. Due to interaction with cell membrane these peptides cause permeabilization of the membrane and lysis of invading microbes. However, some studies proved that antimicrobial peptides are universal multifunctional molecules and ...
journal_title：Acta biochimica Polonica
pub_type： 杂志文章,评审
doi：035002461
更新日期：2003-01-01 00:00:00
abstract：:Nano- and microemulsions containing as the oil phase caprylic/capric propylene glycol diesters (Crodamol PC) were investigated as potential vehicle for controlled release of geranic acid. The influence of emulsifiers and co-surfactants on stability of the emulsions was investigated. Different kind of polysorbates (eth...
journal_title：Acta biochimica Polonica
pub_type： 杂志文章
doi：10.18388/abp.2014_926
更新日期：2015-01-01 00:00:00
abstract：:The PCR conditions have been optimized to make the process faster and more economical. When short DNA fragments are to be amplified, the time of denaturation, annealing and extension steps can be as short as 1 s each, and the yield of PCR product is still high, sufficient for many types of analysis. The PCR can be don...
journal_title：Acta biochimica Polonica
pub_type： 杂志文章
doi：
更新日期：1995-01-01 00:00:00
