FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2000264668> ?p ?o ?g. }

• W2000264668 abstract "Reproducibility is a fundamental requirement in scientific experiments. Some recent publications have claimed that microarrays are unreliable because lists of differentially expressed genes (DEGs) are not reproducible in similar experiments. Meanwhile, new statistical methods for identifying DEGs continue to appear in the scientific literature. The resultant variety of existing and emerging methods exacerbates confusion and continuing debate in the microarray community on the appropriate choice of methods for identifying reliable DEG lists.Using the data sets generated by the MicroArray Quality Control (MAQC) project, we investigated the impact on the reproducibility of DEG lists of a few widely used gene selection procedures. We present comprehensive results from inter-site comparisons using the same microarray platform, cross-platform comparisons using multiple microarray platforms, and comparisons between microarray results and those from TaqMan - the widely regarded standard gene expression platform. Our results demonstrate that (1) previously reported discordance between DEG lists could simply result from ranking and selecting DEGs solely by statistical significance (P) derived from widely used simple t-tests; (2) when fold change (FC) is used as the ranking criterion with a non-stringent P-value cutoff filtering, the DEG lists become much more reproducible, especially when fewer genes are selected as differentially expressed, as is the case in most microarray studies; and (3) the instability of short DEG lists solely based on P-value ranking is an expected mathematical consequence of the high variability of the t-values; the more stringent the P-value threshold, the less reproducible the DEG list is. These observations are also consistent with results from extensive simulation calculations.We recommend the use of FC-ranking plus a non-stringent P cutoff as a straightforward and baseline practice in order to generate more reproducible DEG lists. Specifically, the P-value cutoff should not be stringent (too small) and FC should be as large as possible. Our results provide practical guidance to choose the appropriate FC and P-value cutoffs when selecting a given number of DEGs. The FC criterion enhances reproducibility, whereas the P criterion balances sensitivity and specificity." @default.
• W2000264668 created "2016-06-24" @default.
• W2000264668 creator A5000862370 @default.
• W2000264668 creator A5001633495 @default.
• W2000264668 creator A5003849228 @default.
• W2000264668 creator A5004979421 @default.
• W2000264668 creator A5006262632 @default.
• W2000264668 creator A5006406931 @default.
• W2000264668 creator A5008243922 @default.
• W2000264668 creator A5009054100 @default.
• W2000264668 creator A5010087179 @default.
• W2000264668 creator A5011251776 @default.
• W2000264668 creator A5015216573 @default.
• W2000264668 creator A5015683073 @default.
• W2000264668 creator A5018882292 @default.
• W2000264668 creator A5020144785 @default.
• W2000264668 creator A5027129016 @default.
• W2000264668 creator A5029076691 @default.
• W2000264668 creator A5031909133 @default.
• W2000264668 creator A5032273680 @default.
• W2000264668 creator A5036021036 @default.
• W2000264668 creator A5043439155 @default.
• W2000264668 creator A5043590676 @default.
• W2000264668 creator A5043867523 @default.
• W2000264668 creator A5044757881 @default.
• W2000264668 creator A5045608420 @default.
• W2000264668 creator A5047497810 @default.
• W2000264668 creator A5047976044 @default.
• W2000264668 creator A5047985749 @default.
• W2000264668 creator A5048655816 @default.
• W2000264668 creator A5056523134 @default.
• W2000264668 creator A5062332192 @default.
• W2000264668 creator A5062984211 @default.
• W2000264668 creator A5064995841 @default.
• W2000264668 creator A5066211240 @default.
• W2000264668 creator A5066599847 @default.
• W2000264668 creator A5067123720 @default.
• W2000264668 creator A5067972591 @default.
• W2000264668 creator A5068886380 @default.
• W2000264668 creator A5075189493 @default.
• W2000264668 creator A5075794110 @default.
• W2000264668 creator A5076838888 @default.
• W2000264668 creator A5077446386 @default.
• W2000264668 creator A5078370697 @default.
• W2000264668 creator A5079261300 @default.
• W2000264668 creator A5079305919 @default.
• W2000264668 creator A5082869942 @default.
• W2000264668 creator A5083301167 @default.
• W2000264668 creator A5086234334 @default.
• W2000264668 creator A5088070159 @default.
• W2000264668 creator A5091238252 @default.
• W2000264668 date "2008-08-01" @default.
• W2000264668 modified "2023-10-17" @default.
• W2000264668 title "The balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studies" @default.
• W2000264668 cites W1484414601 @default.
• W2000264668 cites W1542824894 @default.
• W2000264668 cites W1600272042 @default.
• W2000264668 cites W1967668617 @default.
• W2000264668 cites W1970156673 @default.
• W2000264668 cites W1981963681 @default.
• W2000264668 cites W1984401569 @default.
• W2000264668 cites W1985229138 @default.
• W2000264668 cites W1986381857 @default.
• W2000264668 cites W1995017987 @default.
• W2000264668 cites W1998913367 @default.
• W2000264668 cites W2001627351 @default.
• W2000264668 cites W2004088708 @default.
• W2000264668 cites W2007329423 @default.
• W2000264668 cites W2010305827 @default.
• W2000264668 cites W2010637767 @default.
• W2000264668 cites W2014245116 @default.
• W2000264668 cites W2019586039 @default.
• W2000264668 cites W2020130015 @default.
• W2000264668 cites W2021129827 @default.
• W2000264668 cites W2025618966 @default.
• W2000264668 cites W2039057614 @default.
• W2000264668 cites W2051262326 @default.
• W2000264668 cites W2063912592 @default.
• W2000264668 cites W2065020503 @default.
• W2000264668 cites W2091947792 @default.
• W2000264668 cites W2094801904 @default.
• W2000264668 cites W2097554668 @default.
• W2000264668 cites W2110891968 @default.
• W2000264668 cites W2115226431 @default.
• W2000264668 cites W2115617081 @default.
• W2000264668 cites W2117348786 @default.
• W2000264668 cites W2118957901 @default.
• W2000264668 cites W2119739306 @default.
• W2000264668 cites W2123199013 @default.
• W2000264668 cites W2125826355 @default.
• W2000264668 cites W2129895818 @default.
• W2000264668 cites W2132561013 @default.
• W2000264668 cites W2136746865 @default.
• W2000264668 cites W2141009231 @default.
• W2000264668 cites W2144227498 @default.
• W2000264668 cites W2146264532 @default.
• W2000264668 cites W2147840076 @default.
• W2000264668 cites W2149697028 @default.
• W2000264668 cites W2157132621 @default.
• W2000264668 cites W2159373567 @default.

• next