Mass-spectrometry analysis of the human pineal proteome during night and day and in autism.

"to eliminate redundancy we first filtered all the statistically significant gene ontology (go) with less than 10 genes or more than 1000 and then used enrichment map to assess the graph of similarity between the different go terms and to annotate the connected components (p-value cutoff = 0 005; fdr q-value cutoff = 0 01; jaccard coefficient = 0 5) 57 2 9 we concatenated five human interactome datasets provided online by the dana farber cancer institute: four high-quality binary protein-protein interactions (ppi) using a systematic primary yeast two-hybrid assay (y2h): hi-i-05 58 venkatesan-09 59 yu-11 60 and hi-ii-14 61 plus one high-quality binary literature dataset lit-bm-13 comprising all ppi that are binary and supported by at least two traceable pieces of evidence (publications and/or methods) 61 proteins associated with either statistical differences in intensity between day and night or marked as only present during day or during the night were then projected in the ppi network 2 10 the mass-spectrometry proteomics data have been deposited to the proteomexchange consortium via the pride partner repository with the dataset identifier pxd020501 62 all the rest of the data that supports the findings of this study are available in the supplementary material of this article 3 3 1 the protein composition of the pineal gland was examined through gene ontology (go) analysis.; data availability statement the mass spectrometry proteomics data have been deposited to the proteomexchange consortium via the pride partner repository with the dataset identifier pxd020501. to assess the stability of the detected cycling proteins we used an alternative method from astrophysics generalized lomb-scargle periodogram (gls) which allows to detect periodic signals in unevenly sampled data 53 to take into account the replicate and missing value we used a bayesian implementation of gls (code available online here: https://github com/mfouesneau/bgls) 54 2 8 we identified enrichments of genetic ontology (go) terms in gene sets related to the pineal gland itself and on its states during day or night utilizing cytoscape 3 3 0 with the plugin bingo 55 56 we used the genetic background consisting of all the proteins coding genes."

"to assess the stability of the detected cycling proteins we used an alternative method from astrophysics generalized lomb-scargle periodogram (gls) which allows to detect periodic signals in unevenly sampled data 53 to take into account the replicate and missing value we used a bayesian implementation of gls (code available online here: https://github com/mfouesneau/bgls) 54 2 8 we identified enrichments of genetic ontology (go) terms in gene sets related to the pineal gland itself and on its states during day or night utilizing cytoscape 3 3 0 with the plugin bingo 55 56 we used the genetic background consisting of all the proteins coding genes."

"CONFLICT OF INTEREST None of the authors has conflicts of interest pertaining to the present paper."

"This work was supported by the Institut Pasteur, the CNRS, the INSERM, the AP‐HP, the University Paris Diderot, the Cognacq‐Jay foundation, the Bettencourt‐Schueller foundation, the Orange foundation, the FondaMental foundation, the Fondation de France, the Conny‐Maeva foundation, the Eranet‐Neuron ANR (ALTRUISM), and the Labex GenMed and BioPsy. GD is funded by the Institute for Data Valorization (IVADO), Montreal, and the Fonds de recherche du Québec (FRQ). We further wish to thank Véronique Hourdel and Quentin Giai Gianetto for early help regarding MS statistics, as well as Christian Malosse for the first set of sample preparation."