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return kwic search for effects out of >500 occurrences
566982 occurrences (No.17 in the rank) during 5 years in the PubMed. [cache]

434) We leverage Bisbee's prediction of protein level effects as a benchmark of its capabilities using matched sets of RNAseq and mass spectrometry data from normal tissues.

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PMID:34031440 DOI:10.1038/s41598-021-89938-2

2021 Scientific reports

* Improved methods for RNAseq-based alternative splicing analysis.

- The robust detection of disease-associated splice events from RNAseq data is challenging due to the potential confounding effect of gene expression levels and the often limited number of patients with relevant RNAseq data. Here we present a novel statistical approach to splicing outlier detection and differential splicing analysis. Our approach tests for differences in the percentages of sequence reads representing local splice events. We describe a software package called Bisbee which can predict the protein-level effect of splice alterations, a key feature lacking in many other splicing analysis resources. We leverage Bisbee's prediction of protein level effects as a benchmark of its capabilities using matched sets of RNAseq and mass spectrometry data from normal tissues. Bisbee exhibits improved sensitivity and specificity over existing approaches and can be used to identify tissue-specific splice variants whose protein-level expression can be confirmed by mass spectrometry. We also applied Bisbee to assess evidence for a pathogenic splicing variant contributing to a rare disease and to identify tumor-specific splice isoforms associated with an oncogenic mutation. Bisbee was able to rediscover previously validated results in both of these cases and also identify common tumor-associated splice isoforms replicated in two independent melanoma datasets.

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(1)230 of	(8)6 between	(15)3 may	(22)2 from
(2)71 on	(9)6 such	(16)3 model	(23)2 meta-analysis
(3)34 null	(10)5 is	(17)3 that	(24)2 or
(4)22 in	(11)3 at	(18)3 with	(25)2 reported
(5)12 were	(12)3 but	(19)2 against
(6)11 and	(13)3 by	(20)2 as
(7)10 are	(14)3 can	(21)2 for

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--- WordNet output for effects --- =>個人資産 Overview of noun effects The noun effects has 1 sense (no senses from tagged texts) 1. effects, personal effects -- (property of a personal character that is portable but not used in business; "she left some of her personal effects in the house"; "I watched over their effects until they returned") Overview of noun effect The noun effect has 6 senses (first 5 from tagged texts) 1. (101) consequence, effect, outcome, result, event, issue, upshot -- (a phenomenon that follows and is caused by some previous phenomenon; "the magnetic effect was greater when the rod was lengthwise"; "his decision had depressing consequences for business"; "he acted very wise after the event") 2. (11) impression, effect -- (an outward appearance; "he made a good impression"; "I wanted to create an impression of success"; "she retained that bold effect in her reproductions of the original painting") 3. (9) effect -- (an impression (especially one that is artificial or contrived); "he just did it for effect") 4. (2) effect, essence, burden, core, gist -- (the central meaning or theme of a speech or literary work) 5. (1) effect, force -- ((of a law) having legal validity; "the law is still in effect") 6. effect -- (a symptom caused by an illness or a drug; "the effects of sleep loss"; "the effect of the anesthetic") Overview of verb effect The verb effect has 2 senses (first 2 from tagged texts) 1. (17) effect, effectuate, set up -- (produce; "The scientists set up a shock wave") 2. (3) effect -- (act so as to bring into existence; "effect a change") --- WordNet end ---