HPIDB3.0
Predicting Host-Pathogen Interactions
Click here to Download HPIDB predicted interologs
HPIDB biocurators curate host-pathogen interaction (HPI) data from published literature using the International Molecular Exchange Consortium (IMEx) guidelines. However, since there is no experimental evidence available for HPI of many economically important agricultural pathogens, HPIDB also predicts HPI. Currently, we predict HPI using a modified version of the interolog method described by Yu et al., 2004.
Briefly, HPI Interologs are determined by creating a subset of all experimentally validated HPI from IMEx. Host proteins from this subset are then mapped to production animal proteins based upon orthology. Since orthology is not available for pathogen proteins, we use Blast based upon manually reviewed Blast parameters (>= 74 % identity, >= 50% coverage, Eval <= 6e-180 for bacteria, Eval <= 2e-161 for other pathogens) to identify homology between pathogen proteins. Orthologous host proteins and homologous pathogen proteins are then compared to the subset of experimentally validated HPI to identify new interologs.
| Host | Pathogen | Predicted Interologs |
|---|---|---|
| Bos taurus | Bovine viral diarrhea virus | 19,418 |
| Bos taurus | Histophilus somni | 829 |
| Bos taurus | Salmonella enterica | 291,169 |
| Bos taurus | Babesia bovis | 29 |
| Bos taurus | Mannheimia haemolytica | 954 |
| Bos taurus | Foot-and-Mouth Disease | 5,261 |
| Bos taurus | Mycobacterium avium | 31 |
| Bos taurus | Staphylococcus aureus | 10,094 |
| Bos taurus | Clostridium | 89 |
| Bos taurus | Pasteurella multocida | 2,207 |
| Bos taurus | Babesia bigemina | 25 |
| Bos taurus | Babesia divergens | 6 |
| Bos taurus | herpesvirus | 284 |
| Gallus gallus | Salmonella enterica | 18,231 |
| Gallus gallus | Mycoplasma | 15 |
| Gallus gallus | Clostridium | 527 |
| Gallus gallus | Pasteurella multocida | 2,386 |
| Gallus gallus | herpesvirus | 5,344 |
| Ictalurus punctatus | Edwardsiella ictaluri | 27 |
| Ovis aries | Clostridium | 13 |
| Sus scrofa | Clostridium | 3 |
| Sus scrofa | Porcine reproductive and respiratory syndrome virus | 32,967 |
| TOTAL: | 389,909 |
Downloading Interolog Files
HPIDB predicted interologs are available as downloadable
MITAB files from HPIDB, and can be included in HPIDB searches.
Interologs are reviewed to assign confidence indicators, and these are indicated in the Confidence column of the MITAB file (column 15). Please note that the confidence indicator is not meant to be quantitative, but rather should provide a qualitative assessment of support for the prediction. Interologs are assessed based upon biological characteristics of the proteins and assigned the following codes:
This tab separated file may be used in Cytoscape for network analysis.
The MITAB_plus file contains 11 additional columns which contains information about the interacting proteins taxon category and sequence.
Interolog Confidence Indicators
I: assigned to all interologs to indicate predicted interactions.
L: indicates that host and pathogen proteins are co-localized (based upon GO CC)
M: indicates HPI containing secreted or membrane bacterial proteins, which are more likely to interact with host proteins (based upon GO CC & BP)
P: indicates HPI containing host proteins involved in replication and host cell defenses (based upon GO BP). Pathogens target these processes to evade the immune response.
D: indicates HPI containing pathogen proteins with domains that commonly interact with host proteins (based upon InterPro and Pfam).