In trvinh/PhyloProfileData: Data package for phylogenetic profile analysis using PhyloProfile tool

Introduction

The PhyloProfileData package contains two experimental datasets to illustrate running and analysing phylogenetic profiles with PhyloProfile pakage (Tran et al. 2018).

library(PhyloProfileData)
data(package = "PhyloProfileData")

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.

data("ampkTorPhyloProfile")
head(ampkTorPhyloProfile)

• A multiple fasta object contains the FASTA sequences for all the proteins present in the data set.

data("ampkTorFasta")
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.

data("ampkTorDomain")
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.

data("arthropodaPhyloProfile")
head(arthropodaPhyloProfile)

• A multiple fasta object contains the FASTA sequences for all the proteins present in the data set.

data("arthropodaFasta")
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.

data("arthropodaDomain")
head(arthropodaDomain)

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. (2010) FACT: functional annotation transfer between proteins with similar feature architectures. BMC Bioinformatics, 11, 417.
6. Kriventseva, EK. et al.(2018) OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs. Nucleic Acids Res., 47(D1), D807-D811.
7. Krogh, A. et al. (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol., 305(3), 567-80.
8. Letunic, I. et al. (2012) SMART 7: recent updates to the protein domain annotation resource. Nucleic Acids Res., 40, D302-5.
9. Lupas, A. et al. (1991) Predicting Coiled Coils from Protein Sequences. Science, 252, 1162-1164.
10. Promponas, VJ. et al. (2000) CAST: an iterative algorithm for the complexity analysis of sequence tracts. Bioinformatics, 16(10), 915–922.
11. Roustan, V. et al. (2016) An evolutionary perspective of AMPK–TOR signaling in the three domains of life. Journal of Experimental Botany, 67(13), 3897–3907.
12. Simão, F. et al. (2015) BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics, 31(19), 3210-2.
13. Tran, NV. et al. (2018) PhyloProfile: dynamic visualization and exploration of multi-layered phylogenetic profiles. Bioinformatics, 34(17), 3041–3043.
14. Wootton, J. and Federhen, S. (1996) Analysis of compositionally biased regions in sequence databases. Methods in Enzymol., 266, 554-571.

trvinh/PhyloProfileData documentation built on June 6, 2019, 8:36 p.m.