Readme for SupplementaryData2_Dsub_sfp_abundance_172transferred.txt

These are the candidate seminal fluid proteins of D. subobscura. They were identified using a label-free quantitative proteomics approach where proteins with significantly higher abundance in unmated vs mated males were identified to have been transferred during mating. This dataset shows the limma calculation of differential abundance, the annotation of the protein with D. melanogaster and identification of whether the protein is implicated in sexual conflict (whether it is in sex peptide network or has a role in post-copulatory sexual selection).

X = transcript

mated_01 - mated males protein abundance, replicate 1 (vsn normalised reads)
mated_02 - mated males protein abundance, replicate 2
mated_03 - mated males protein abundance, replicate 3
mated_04 - mated males protein abundance, replicate 4
mated_05 - mated males protein abundance, replicate 5
unmated_01 - unmated males protein abundance, replicate 1
unmated_02 - unmated males protein abundance, replicate 2
unmated_03 - unmated males protein abundance, replicate 3
unmated_04 - unmated males protein abundance, replicate 4
unmated_05 - unmated males protein abundance, replicate 5

logFC - log fold change calculation from limma, specifying unmated - mated (i.e. positive values mean unmated males had higher abundance than mated males and this protein was likely transferred to the female during mating and is a Sfp)

AveExpr - Average expression of all samples, calculating in limma

t - calculated in limma

P.Value - significant different in mated and unmated samples, calculated in limma
adj.P.Val - p value after for correction for multiple testing

B - calculated in limma, log odds that it is differentially expressed

DE - Differential expression - denotes is adj.P.Val < 0.05

Dirn - Direction of difference in differential expression (Up = higher in unmated ie transferred - all proteins in this .csv are transferred so all will be "Up")

SFprotein - Seminal fluid protein is defined by DE and Dirn = Up

log_adj_pval - log adjusted p.value used for plotting in volcano plot

Av_unmated_allproteins - mean of unmated samples

rank_allproteins - ranking of unmated samples from 1 to 1389 for all proteins

protein_group - protein ID from the BLAST analysis with D.melanogaster

prot_id - unique protein identification. If name starts with XP the protein can be found in the official D. subobscura genome. If name starts with a number, the protein was found in the D. subobscura transcriptome from male reproductive tract that was made as part of this study (ie from the improved gene models)

gene.y_BLASTPtoDmel - the best BLAST hit to D. melanogaster. Some Dsub proteins had the same best BLAST hit to a Dmel protein so some names are repeated

SPN - if protein belongs to Sex Peptide Network or not

PCSS - if proteins belongs to group of proteins previously identified as having a role in post-copulatory sexual selection

protein_unique - derives from gene.y_BLASTPtoDmel but if protein maps to the same Dmel protein it is appended with ".1" to make a unique ID