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Literature phenotype analysis (LPA)

AC Antonio Colaprico
CO Catharina Olsen
MB Matthew H. Bailey
GO Gabriel J. Odom
TT Thilde Terkelsen
TS Tiago C. Silva
AO André V. Olsen
LC Laura Cantini
AZ Andrei Zinovyev
EB Emmanuel Barillot
HN Houtan Noushmehr
GB Gloria Bertoli
IC Isabella Castiglioni
CC Claudia Cava
GB Gianluca Bontempi
XC Xi Steven Chen
EP Elena Papaleo
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As described in the Biological Processes section, we extracted 101 BPs (reported in Supplementary Data 5) using IPA91 that were successively used for the downstream analysis. LPA interrogates PubMed to obtain a table with information for each gene and a particular BP such as apoptosis or proliferation to understand the number of publications reporting the relationship of a gene-BP (increasing, decreasing, or affected). To filter out false positives obtained from text co-occurrence, it is possible to integrate Beegle’s92 results applied on individual BP, considering the overlapping results. Here with the LPA function, it is possible to extract a BP-genes database from the literature with a twofold aim: (i) producing updated literature information, and (ii) flexibility for BPs of relevant interest.

Copyright and License information: The Author(s) ©2020
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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