This repository hosts the second release of MITHrIL algorithm
The second releases of MITHrIL also includes support for multiple species, meta-pathway approach, and an implementation of the SPECIFIC algorithm.
- Alaimo, S., Giugno, R., Acunzo, M., Veneziano, D., Ferro, A. and Pulvirenti, A., 2016. Post-transcriptional knowledge in pathway analysis increases the accuracy of phenotypes classification. Oncotarget, 7(34), p.54572.
- Alaimo, S., Marceca, G.P., Ferro, A. and Pulvirenti, A., 2017. Detecting disease specific pathway substructures through an integrated systems biology approach. Non-coding RNA, 3(2), p.20.
| Id | Name | Has miRNA-targets interactions? | Has TF-miRNAs activations? |
|---|---|---|---|
| hsa | Homo sapiens latest version (human) | Yes | Yes |
| hsa2015 | Homo sapiens version 2015 (human) | Yes | Yes |
| hsa2018 | Homo sapiens version 2018 (human) | Yes | Yes |
| mmu | Mus musculus (mouse) | Yes | Yes |
| rno | Rattus norvegicus (rat) | Yes | Yes |
| bmor | Bombyx mori (domestic silkworm) | Yes | No |
| gga | Gallus gallus (chicken) | Yes | Yes |
| sly | Solanum lycopersicum (tomato) | No | No |
| ssc | Sus scrofa (pig) | Yes | No |
| ecb | Equus caballus (horse) | No | No |
| cel | Caenorhabditis elegans (nematode) | Yes | Yes |
| mcc | Macaca mulatta (rhesus monkey) | No | No |
| bta | Bos taurus (cow) | Yes | No |
| ath | Arabidopsis thaliana (thale cress) | Yes | Yes |
| dre | Danio rerio (zebrafish) | Yes | Yes |
| cfa | Canis familiaris (dog) | Yes | No |
| oas | Ovis aries (sheep) | Yes | No |
| tgu | Taeniopygia guttata (zebra finch) | Yes | No |
| ola | Oryzias latipes (Japanese medaka) | Yes | No |
| pau | Pseudomonas aeruginosa UCBPP-PA14 | No | No |
| vvi | Vitis vinifera (wine grape) | No | No |
| pfa | Plasmodium falciparum 3D7 | No | No |
| xla | Xenopus laevis (African clawed frog) | Yes | No |
| ptr | Pan troglodytes (chimpanzee) | No | No |
| pps | Pan paniscus (bonobo) | No | No |
| xtr | Xenopus tropicalis (western clawed frog) | Yes | No |
| dme | Drosophila melanogaster (fruit fly) | Yes | Yes |
MITHrIL 2 includes several services. By running the jar application, a list of available services is displayed:
java -jar MITHrIL2.jarTo run a service you just use its name:
java -jar MITHrIL2.jar <service_name>A list of the major services is displayed in the following table:
| Name | Description |
|---|---|
| batch-mithril | runs MITHrIL 2 algorithm on a batch of log-fold-changes |
| convert | conversion between MITHrIL 2 and MITHrIL 1 |
| exportgraph | export pathway graph. |
| exportstructs | runs SPECIFIC algorithm: exports all specific substructures found in a MITHrIL 2 experiment. |
| mithril | runs MITHrIL 2 algorithm on a sample (use -b option to build SPECIFIC input file) |
| organisms | Lists all organisms and their characteristics |
| pathway-categories | shows all pathway categories for a species |
| version | Shows current version of MITHrIL and checks for updates |