--- title: "Overview of PhyloProfileData" author: "Hannah Mülbaier & Vinh Tran" date: "`r Sys.Date()`" package: PhyloProfileData output: BiocStyle::html_document: toc: true vignette: > %\VignetteIndexEntry{PhyloProfileData} %\VignetteEngine{knitr::rmarkdown} %\VignetteEncoding{UTF-8} --- # Introduction The PhyloProfileData package contains two experimental datasets to illustrate running and analysing phylogenetic profiles with PhyloProfile pakage (Tran et al. 2018). ```{r} library(ExperimentHub) eh = ExperimentHub() myData <- query(eh, "PhyloProfileData") myData ``` # Phylogenetic profiles of AMPK-TOR pathway The phylogenetic profiles of 147 human proteins in the AMPK-TOR pathway across 83 species in the three domains of life were taken from the study of Roustan et al. 2016. This data set includes 3 files: - A phylogenetic profile input contains the human protein IDs, the taxaonomy IDs of the 83 search species and the corresponding orthologous protein IDs in those species, together with two additional values, the forward and backward feature architecture similarity (FAS) scores. **FAS approach** is an enhancement of **FACT** (Koestler et al. 2010) which give an idea how similar two proteins are in term of functional equivalence. These compared protein features can be the functional PFAM (Finn et al. 2014) or SMART (Letunic et al. 2012) domains, the transmembran domains, secondary structures or low complexity regions of the protein. FAS scores have a range between 0 and 1, where 1 is for a protein pair that have identical architectures, and 0 in cases that two proteins are completely different in their architectures. ```{r, warning = FALSE, message = FALSE} ampkTorPhyloProfile <- myData[["EH2544"]] head(ampkTorPhyloProfile) ``` - A multiple fasta object contains the FASTA sequences for all the proteins present in the data set. ```{r, warning = FALSE, message = FALSE} ampkTorFasta <- myData[["EH2545"]] head(ampkTorFasta) ``` - A data frame contains the domain annotation for the proteins present in the phylogenetic profiles. The protein domain annotations were done using different annotation tools and databases, including *PFAM*, *SMART*, *CAST* (Promponas et al. 2000), *COILS2* (Lupas et al. 1991), *SEG* (Wootton and Federhen 1996), *SignalP* (Armenteros et al. 2019), and *TMHMM* (Krogh et al. 2001). The annotation types together with their domain name and the corresponding start and end positions are stored in this domain data frame. ```{r, warning = FALSE, message = FALSE} ampkTorDomain <- myData[["EH2546"]] head(ampkTorDomain) ``` # Phylogenetic profiles of BUSCO Arthropoda proteins One fundamental step in establishing the phylogenetic profiles is searching orthologs for the query proteins in different taxa of interest. **HaMStR-oneseq**, an extended version of **HaMStR** (Ebersberger et al. 2009), has been shown to be an promising approach for sensitively predicting orthologs even in the distantly related taxa from the query species, which is required for the phylogenetic profiling of a broad range of taxa through all domains of the species tree of life. One main parameter for HaMStR-oneseq is the core ortholog group, the starting point for the orthology search. In order to set up a reliable core ortholog set that can be used for further phylogenetic profiling studies, we made use of the well-known **BUSCO** datasets (Simão et al. 2015). Here we represent the phylogenetic profiles of 1011 ortholog groups across 88 species, which was calculated from the BUSCO arthropoda dataset downloaded from https://busco.ezlab.org/datasets/arthropoda_odb9.tar.gz in Jan. 2018. The 88 species include 10 arthropoda species (*Ladona fulva*, *Agrilus planipennis*, *Polypedilum vanderplanki*, *Daphnia magna*, *Harpegnathos saltator*, *Zootermopsis nevadensis*, *Halyomorpha halys*, *Heliconius melpomene*, *Stegodyphus mimosarum*, *Drosophila willistoni*) downloaded from orthoDB version 10 (https://www.orthodb.org) and 78 species of the Quest for Ortholog dataset (Altenhoff et al. 2016). This dataset includes 3 files: - A phylogenetic profile input contains 1011 BUSCO ortholog group IDs, the taxaonomy IDs of the 88 searched species and the corresponding orthologous protein IDs in those species, together with two additional values, the forward and backward FAS scores which were described above in the description of the AMPK-TOR pathway dataset. ```{r, warning = FALSE, message = FALSE} arthropodaPhyloProfile <- myData[["EH2547"]] head(arthropodaPhyloProfile) ``` - A multiple fasta object contains the FASTA sequences for all the proteins present in the data set. ```{r, warning = FALSE, message = FALSE} arthropodaFasta <- myData[["EH2548"]] head(arthropodaFasta) ``` - A data frame contains the domain annotation for the proteins present in the phylogenetic profiles. The protein domain annotations were done using different annotation tools and databases, including *PFAM*, *SMART*, *CAST*, *COILS2*, *SEG*, *SignalP*, and *TMHMM*. The annotation types together with their domain name and the corresponding start and end positions are stored in this domain data frame. ```{r, warning = FALSE, message = FALSE} arthropodaDomain <- myData[["EH2549"]] head(arthropodaDomain) ``` # SessionInfo() Here is the output of `sessionInfo()` on the system on which this document was compiles: ```{r sessionInfo, echo = FALSE} sessionInfo(package = "PhyloProfileData") ``` # References 1. Armenteros, JJA. et al. (2019) SignalP 5.0 improves signal peptide predictions using deep neural networks. Nature Biotechnology, 37, 420–423. 2. Altenhoff, AM. et al. (2016) Standardized benchmarking in the quest for orthologs. Nature Methods, 13, 425–430. 3. Ebersberger, I. et al. (2009) HaMStR: profile hidden markov model based search for orthologs in ESTs. BMC Evol Biol., 9, 157 4. Finn, RD. (2014) Pfam: The protein families database. Nucleic Acids Res., 42, D222-30 5. Koestler, T. et al. 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