TY - JOUR
T1 - The TissueNet v.3 Database
T2 - Protein-protein Interactions in Adult and Embryonic Human Tissue contexts
AU - Ziv, Maya
AU - Gruber, Gil
AU - Sharon, Moran
AU - Vinogradov, Ekaterina
AU - Yeger-Lotem, Esti
N1 - Funding Information:
This study was funded by the Israel Science Foundation [317/19 to E.Y.-L].
Publisher Copyright:
© 2022 Elsevier Ltd
PY - 2022/6/15
Y1 - 2022/6/15
N2 - Tissue contexts are extremely valuable when studying protein functions and their associated phenotypes. Recently, the study of proteins in tissue contexts was greatly facilitated by the availability of thousands of tissue transcriptomes. To provide access to these data we developed the TissueNet integrative database that displays protein-protein interactions (PPIs) in tissue contexts. Through TissueNet, users can create tissue-sensitive network views of the PPI landscape of query proteins. Unlike other tools, TissueNet output networks highlight tissue-specific and broadly expressed proteins, as well as over- and under-expressed proteins per tissue. The TissueNet v.3 upgrade has a much larger dataset of proteins and PPIs, and represents 125 adult tissues and seven embryonic tissues. Thus, TissueNet provides an extensive, quantitative, and user-friendly interface to study the roles of human proteins in adulthood and embryonic stages. TissueNet v3 is freely available at https://netbio.bgu.ac.il/tissuenet3.
AB - Tissue contexts are extremely valuable when studying protein functions and their associated phenotypes. Recently, the study of proteins in tissue contexts was greatly facilitated by the availability of thousands of tissue transcriptomes. To provide access to these data we developed the TissueNet integrative database that displays protein-protein interactions (PPIs) in tissue contexts. Through TissueNet, users can create tissue-sensitive network views of the PPI landscape of query proteins. Unlike other tools, TissueNet output networks highlight tissue-specific and broadly expressed proteins, as well as over- and under-expressed proteins per tissue. The TissueNet v.3 upgrade has a much larger dataset of proteins and PPIs, and represents 125 adult tissues and seven embryonic tissues. Thus, TissueNet provides an extensive, quantitative, and user-friendly interface to study the roles of human proteins in adulthood and embryonic stages. TissueNet v3 is freely available at https://netbio.bgu.ac.il/tissuenet3.
KW - data integration
KW - gene expression
KW - interaction networks
KW - protein-protein interactions
KW - tissue interactomes
KW - tissue-specificity
UR - http://www.scopus.com/inward/record.url?scp=85127341291&partnerID=8YFLogxK
U2 - 10.1016/j.jmb.2022.167532
DO - 10.1016/j.jmb.2022.167532
M3 - Article
C2 - 35662455
AN - SCOPUS:85127341291
VL - 434
JO - Journal of Molecular Biology
JF - Journal of Molecular Biology
SN - 0022-2836
IS - 11
M1 - 167532
ER -