Table of Contents
PrePhyloPro is host at http://prephylopro.org/phyloprofile/ and a backup link.
- Linkages number
The threshold of linkages number for each gene could be randomly chose between 1 and 500(even a float number like 5.4). A smaller vaule means a more stringent threshold of predicted linkages.
If you want to get less but more reliable linkages, please try a small value, for example 20. Please be aware, a small value may be at a risk of missing some potential and novel linkages which do not have very strong evidence.
- BLAST Evalue
Three BLAST E-value threshold, 0.001, 0.0005, 0.0001, were provided. This threshold was used in choosing homologous proteins. For a pair proteins (the referenced protein and test protein), if the blast E-value that is smaller than the threshold, the homologs is through to be present; otherwise, the homologs is absent. Correspondingly, in the phylogenetic profile, "1" and "0" are used to denote the presence and absence.
- Organism
Homo sapiens (human) and Arabidopsis thaliana (thale cress) are now supported.
Please try default plot parameters at first. If you are not satisfied with output figures, please adjust the parameters and run it again.
Only the txt (with the separator of "Tab") or the csv (with the separator of ",") format is allowed for the input files. Please do not try to upload other types of files (like test.html). Otherwise, an error webpage may return.
The number of input genes is supposed to be at least two. Otherwise, an error message will return. There are several reasons. The important one is our algorithm is based on the whole genome, and the prediction results are more reliable when taking into account a cluster of genes like genes from a complex or a biological pathway.
- 1st column
1st column contains the input genes. The "GeneID" is used as the unique gene name for each gene, for example hsa:513 denotes the human gene "ATP5D" (ATP synthase, H+ transporting, mitochondrial F1 complex, delta subunit (EC:3.6.1.14)). Please refer the "Input gene list" to set your own input genes. Other formats of gene names may be supported in the future.
- 2nd column
2nd column contains the colours for each input genes. Colour modes like the hex triplet and colour names are both supported. For example, the "red" and #ff0000 are legal input colours. If you do not want to show the colour for a gene, an easy way is to set the colour as white or #FFFFFF.
- 3rd column
3rd column defines linkages colours, which uses the same colour format as the 2nd column. You may want to hidden the linkaged for certain genes, just use NA (not "na", not "white", not "Na") as the link color. But, at least one genes should have proper linkage colour.An internal Circos gene list is used for Circos plot, and any genes not in this list will be neglected. The D3 interactive network is also constructed based on the 3rd column data. It is designed as an alternative way to show the linkages network.
- 4th column
4th column allows pre-defined gene names (optional). As the GeneID (e.g., hsa:513) is hard to get its meaning, the 4th column could provide a way to transfer the GeneID to other formats (Example). The pre-defined gene names will be used inboth phylogenetic profile and correlation figures. This column is optional; if you want to keep the GeneID in figures, please leave it as blank (no column names and no values).
| Organism | Input gene list (1st column) | Circos gene list |
|---|---|---|
| Homo sapiens | 20127 Download | 19077 Download |
| Arabidopsis thaliana | 27396 Download | 27394 Download |
We provide two ways to illustrate the prediction results. A webpage merged the all the figures and tables will be returned at first. At the bottom of the webpage, a linkage will guide you to download all the results into your local computer.
- Webpage
The webpage contains visualization of phylogenetic profiles, correlation matrix, Circos plot, D3 interactive network, and list of prediction linkages. A grey block will be used to represent the negative correlation value in the correlation matrix plot.
- Download folder
The downloaded folder includes published quality of figures mentioned above in both "pdf" and "jpg" formats. The correlation matrix and prediction linkages are stored in a "csv" file that can be easily used for other analysis and validation experiments. Moreover, the same webage is stored in a "html" file used for a overview of the results.
Please download and save your results (at the end of the return webpage), the result files will be kept on the web-server only 2 hours.
PrePhyloPro is peer-reviewed and officially published on PeerJ. Please cite the following article if you use PrePhyloPro in your project.
Niu Y, Liu C, Moghimyfiroozabad S, Yang Y, Alavian KN. (2017) PrePhyloPro: phylogenetic profile-based prediction of whole proteome linkages. PeerJ 5:e3712.
PrePhyloProis used to investigate the modular evolution of the F1Fo ATP synthase.
Niu Y, Moghimyfiroozabad S, Safaie S, Yang Y, Jonas EA, Alavian KN (2017) Phylogenetic Profiling of Mitochondrial Proteins and Integration Analysis of Bacterial Transcription Units Suggest Evolution of F1Fo ATP Synthase from Multiple Modules. J Mol Evol 85: 219.
