Additional file 2 of Identification of biological pathways and processes regulated by NEK5 in breast epithelial cells via an integrated proteomic approach
Creators: name: de Castro Ferezin, Camila
name: Lim Kam Sian, Terry C. C.
name: Wu, Yunjian
name: Ma, Xiuquan
name: Chüeh, Anderly C.
name: Huang, Cheng
name: Schittenhelm, Ralf B.
name: Kobarg, Jörg
name: Daly, Roger J.
Publisher: name: figshare
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Molecular Biology
subject: Environmental Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Plant Biology
subject: FOS: Biological sciences

description: Additional file 1. Figure S1. Characterization of the NEK5 interactome via BioID. A Schematic of BioID workflow. B Volcano plot highlighting proteins with enhanced biotinylation that represent NEK5 interactors. Dotted lines indicate the applied cut-offs of fold change &gt; 2 and p &lt; 0.05. Labelled proteins with pink dots are enriched at these cut-offs. Note that these have negative log 2 values. Figure S2. Expression of NEK5 and its interactors in breast cancer cell lines. A Expression of NEK5 and its relationship to ER status. RNA-seq data deposited in the Cancer Cell Line Encyclopedia (CCLE) and Cancer Dependency Map (DepMap) databases were used to determine the mRNA expression of NEK5 in a panel of 60 breast cancer cell lines, grouped based on ER expression status, and the human immortalized breast epithelial cell line HMEL. Error bars represent mean ± SEM (Standard Error of the Mean), ***Indicates p &lt; 0.001 (Student’s t-test). ER, Estrogen receptor; TPM, Transcripts per million. B Expression of NEK5 and NEK5 interactors identified by BioID in ER-positive breast cancer cell lines. The Violin plot shows the distribution of expression levels of NEK5 and its interacting proteins based on RNA-seq data deposited in the CCLE and DepMap databases. Figure S3. Volcano plot highlighting differentially-expressed proteins in NEK5 overexpressing cells versus MCF-10A control cells. Proteins that are significantly increased or decreased in abundance upon overexpression of NEK5 at cut-offs of FC &gt; 1.5 and p &lt; 0.05 are represented by pink and blue dots, respectively. Labelled proteins are the 5 proteins with the largest significant fold changes in either direction and key proteins indicated in the Cytoscape protein-protein interaction networks. Figure S4. Validation of MS-based proteomic data. Western blot analysis of MCAM and NCAPD3 expression in control and NEK5-overexpressing MCF-10A cells. The asterisk indicates a non-specific band at 100 kDa. Positions of size markers are indicated. Figure S5. Volcano plot highlighting differentially abundant phosphosites in NEK5-overexpressing cells versus MCF-10A control cells. Phosphosites that are significantly increased or decreased in abundance upon overexpression of NEK5 at cut-offs of FC &gt; 1.5 and p &lt; 0.05 are represented by pink and blue dots, respectively. Labelled phosphosites are the 5 sites with the largest significant fold changes in either direction and key phosphosites indicated in the Cytoscape protein-protein interaction networks.