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README.md

Gene-Ages

A consensus approach to estimating gene ages for model organisms

DOI This repository contains scripts, data, and ipython notebooks in support of our manuscript:

"Towards Consensus Gene Ages" Benjamin J. Liebeskind, Claire D. McWhite, and Edward M. Marcotte

If you use any of the information or code in this repository, please cite the paper above.

How old is my gene?

If you study a certain gene or gene family, you might be interested in knowing how many other organisms share orthologs of that gene. Or maybe you want to annotate genomic datasets with gene ages to get an idea of how deep in evolutionary time different pathways were assembled. If so, look no further!

We took orthology calls from 13 popular orthology inference algorithms and estimated consensus gene ages for a variety of model eukaryotes. Because orthology inference is notoriously difficult, we also annotated our datasets with various error terms so that you can propagate uncertainty through your downstream analyses.

Organisms with gene-age information

You can find consensus tables for the following organisms in the Main/ directory. They are named main_<UniprotID>.csv

Common Name Uniprot ID
Anopheles gambiae (Mosquito) ANOGA
Bos taurus (Cattle) BOVIN
Branchiostoma floridae (Lancelet) BRAFL
Caenorhabditis elegans (Worm) CAEEL
Candida albicans CANAL
Canis lupus familiaris (Dog) CANFA
Gallus gallus (Chicken) CHICK
Ciona intestinalis (Tunicate) CIOIN
Cryptococcus neoformans CRYNJ
Danio rerio (Zebrafish) DANRE
Drosophila melanogaster (Fly) DROME
Homo sapiens (Human) HUMAN
Ixodes scapularis (Tick) IXOSC
Macaca mulatta (Rhesus macaque) MACMU
Monosiga brevicollis (Choanoflagellate) MONBE
Monodelphis domestica (Opossum) MONDO
Mus musculus (Mouse) MOUSE
Nematostella vectensis (Sea anemone) NEMVE
Neurospora crassa (Bread mold) NEUCR
Ornithorhynchus anatinus (Platypus) ORNAN
Pan troglodytes (Chimp) PANTR
Phaeosphaeria nodorum (Wheat fungus) PHANO
Rattus rattus (Rat) RAT
Saccaromyces cerevisiae (Budding yeast) YEAST
Schistosoma mansoni (Blood fluke) SCHMA
Schizosaccharomyces pombe (Fission yeast) SCHPO
Sclerotinia sclerotiorum (White mold) SCLS1
Takifugu rubripes (Pufferfish) TAKRU
Ustilago maydis (Corn smut/Huitlacoche USTMA
Xenopus tropicalis (Frog) XENTR
Yarrowia lipolytica YARLI

Age-categories

These files contain the following information:

  • First, they contain a distribution over gene ages estimated by 13 orthology algorithms after trimming errors (see manuscript for details). This distribution can be viewed as a posterior.
  • Next, they contain the mode age of the gene
  • The next 6 columns contain details on various sources of error in the age-call

Error statistics

Name Description
NumDBsContributing How many databases/algorithms contribute to final estimate. More is better
NumDBsFiltered How many databases/algorithms were trimmed out. Less is better
entropy Shannon's entropy over final age-call distribution. Lower is better
NodeError Average patristic distance between age calls before filtering. Lower is better
Bimodality How bimodal the age call is (see manuscript). Lower is better
HGT_flag Whether or not this gene was flagged as being a recent horizontal gene transfer

Replicating the analysis

We provide scripts and ipython notebooks if you're interested in replicating the analysis or running again with some different parameters. You should run the code using scripts in CannedScripts/. Raw orthology prediction alignments are available from https://github.com/qfo/OrthologTables/. Here's a flowchart to show how the scripts in CannedScripts/, some of the ipyton notebooks in Notebooks/, and the output files in Data/ are all related:

Flowchart

And because you can now add emojis to GitHub markdown, I will 🃏

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