References

The original publication of hPRINT:
Large-scale de novo prediction of physical protein-protein association.
Elefsinioti A, Sarac OS, Hegele A, Plake C, Hubner NC, Poser I, Sarov M, Hyman A, Mann M, Schroeder M, Stelzl U, Beyer A. Mol Cell Proteomics. 2011

Simple Search


Simple search

The search panel on the home page of hPRINT allows the user to enter a set of genes. After pressing 'Send' the database will return all interactions of the query genes with any other genes in the database. These settings can be changed by clicking on 'Advanced search'. The query form accepts gene symbols, as well as Ensembl and Entrez gene IDs. Gene names can be separated with any white space or comma, they can be listed in one or many lines.

Advanced Search


Advanced search

When pressing "Advanced search" a more detailed query form appears providing the following options:

Results page


Results page

Description of evidence columns

s.gfus

Gene fusion (STRING). Based on observed fusion of the two candidate interactors in one gene in a different species. (Derived from STRING score).

s.gneighbor

Genomic neigborhood (STRING). Scores genes that occur repeatedly in close neighborhood in genome sequences. (Derived from STRING score).

s.phyl

Phylogenetic profile (STRING). Based on presence or absence of linked proteins across species. (Derived from STRING score).

s.coex

Coexpression (STRING). Based on co-expression in the same or in other species (transferred by homology). (Derived from STRING score).

s.exp

Experimental (STRING). Based on a list of protein interaction datasets, gathered from other databases reporting experimentally tested interactions. (Derived from STRING score).

s.db

Database (STRING). Based on other curated databases. (Derived from STRING score).

s.txt

Text mining (STRING). The text mining sore is extracted from the abstracts of scientific literature (Derived from STRING score).

s.combined

STRING. This score is derived from the "combined score" reported in STRING. It

HiMAP

Gene-gene associations reported in the HiMAP database.

Bioverse

Gene-gene associations reported in the Bioverse database.

txt.CC

Text mining: cellular component. Gene association with a GO cellular component is predicted based on co-occurrences in the literature database PubMed. Gene-Gene scores are based on association with a common GO cellular component.

txt.MF

Text mining: molecular function. Gene association with a GO biological process is predicted based on co-occurrences in the literature database PubMed. Gene-Gene scores are based on association with a common GO biological process.

txt.BP

txt.cooc

Text mining: biological process. Gene association with a GO biological process is predicted based on co-occurrences in the literature database PubMed. Gene-Gene scores are based on association with a common GO biological process. |

txt.disease

Text mining: disease. Gene-gene association scores sharing a common disease annotation. Evidence of a gene associated with a disease is based on co-occurrences in the literature database PubMed.

KEGG.bin

KEGG binary Binary interactions reported in KEGG.

KEGG.cpx

KEGG complex. Protein complex association reported in KEGG.

KEGG.fun

KEGG functional Pathway co-membership based on KEGG.

HPRDiV

HPRD in vivo Binary interactions tha t are validated via in vivo experiments (based on HPRD)

HPRDniV

HPRD not in vivo Binary interactions that are tested in vitro or via yeast two-hybrid experiments (based on HPRD).

IntAct

Direct interactions or physical associations reported in IntAct.

CORUM

Protein complex association reported in CORUM (core set complexes for ''homo sapiens'').

CRGhigh

CRG high confidence High confidence score selected from the paper of Bossi et al., 2009

domp

Domain pairs Protein sequence-based prediction of matching domain pairs in the two proteins. Profile HMMs are constructed using structural information about protein interaction interfaces (see Henschel et al. 2007).

ccf

Network feature: clustering coefficient Average clustering coefficient of the two genes. Clustering coefficients are computed based on the functional network's topology.

mst

Network feature: minimum spanning tree Based on whether or not the respective edge is part of the minimum spanning tree in the functional network. Given a connected, undirected graph, a spanning tree of that graph is a subgraph which is a tree and connects all the vertices together. A minimum spanning tree is then a spanning tree with weight less than or equal to the weight of every other spanning tree.

mst.ex

Network feature: extended minimum spanning tree. A minimum spanning tree (MST) is extended such that if an edge is not in the MST and the weight of the shortest path in the MST between the vertices that the edge connects is larger than the weight of the edge itself, than the edge is added to the extended MST.

ratio.neigh

Network feature: neighborhood ratio Ratio of the common neighbors of the vertices connected by the edge to the total number of neighbors of that two vertices (in the functional network).

ratio.sp

Network feature: shortest path to weight ratio. Ratio of the weight of the shortest path between two vertices to the weight of the edge connecting them.

btw.loc

Network feature: local betweenness. Ratio of shortest paths going through the edge to the number of possible pairs of vertices in the local neighborhood of the edge (based on functional network).

btw.glo

Ratio of shortest paths going through the edge to the number of possible pairs of vertices in the graph (based on functional network).

rf.phys

Random Forest score for physical interactions. For computing Random Forest scores we used only non-experimental evidences.

rf.fun

Random Forest functional. Random Forest functional Random Forest score for functional interactions. For computing Random Forest scores we used only non-experimental evidences.

bay.phys

Bayesian physical. Bayesian score for physical interactions. For predicting Bayesian score we used Random Forest physical score as input evidence and we combined it with experimental evidences.

Details page


Detailed view

The details page displays information about the interacting genes. A short description and cross references to other databases such as Entrez Ensembl and HGNC are provided.

hPRINT is being developed at BIOTEC.