HIV-1 Interactions Help Documentation

Contents

• Data Sets
• Searching NCBI Gene records
• Query Hints to find related data in NCBI databases
• Browsing and Downloading Interaction data
  • Retrieving protein-interaction data
  • Retrieving replication-interaction data
  • Finding data intersections

Data Sets

Protein interactions

Southern Research Institute (SRI) curates the HIV-1 human protein interaction data set. Interactions reported here are based on literature reports that have used a variety of experimental methods to identify direct or indirect protein-protein interactions. Literature reports often do not include full-length sequence information or specific sequence identifiers (an accession.version, or gi number) and so the SRI curators anchor the interaction on RefSeq accessions based on matching the interacting amino acids reported in the literature to RefSeq protein sequences.  For many genes, there may be more than one RefSeq protein isoform that contains the interacting sequence and we do not know whether these isoforms are indeed interacting with the HIV-1 protein sequence.

Replication interactions

SRI curates the HIV-1 virus human gene replication interaction data set. Interactions reported here are based on literature reports of virus infectivity and replication in different cell lines following siRNA/shRNA-mediated knock-down of human genes.  

Search NCBI Gene records with HIV-1 Interaction Data

This section of the page can be used to build a query to find Gene records that match the selected query options.  To use this form, select the data set(s) of interest, and optionally provide additional details to restrict Gene results to those matching a specific term or property. Clicking on the Search button returns results in NCBI Gene resource. 

Search criteria include:

• Interaction type:  restriction your search to protein interaction data, replication interaction data, or both
• Gene Ontology (GO): enter a GO term; as you type, a list of matching terms is presented for selection. The list of matched terms options are those currently associated with Gene records.
• Protein domain name: enter a protein domain name; this queries Gene for protein domains annotated on RefSeq protein records that are associated with a Gene entry.
• Properties: select 0, 1, or more properties to further restrict your Gene query
  • Has phenotype: the Gene is associated with phenotype data from OMIM, MedGen, or GeneReivews
  • Has gene expression data: GEO Profiles expression data is available for the Gene record
  • Has HomoloGene cluster: the Gene is included in a HomoloGene cluster
  • Has >1 RefSeq transcript: the Gene record contains more than one RefSeq transcript thus the protein-interaction data reported may be applicable to more than one RefSeq protein isoform
  • Has biological pathways: the Gene record is in a known pathway tracked in NCBI's BioSystems database
• Entrez Gene keywords: enter any word or phrase; this is treated as a free text search against all content in Gene. For example, 'virus replication', or 'antimicrobial'

Find Related Data in NCBI Databases

This section provides links to access the different data types listed and also illustrates how the query can be formatted to find this data if directly searching against the indicated database.  Links and query format examples are provided to find HIV-1 sequence, structure, and publication content in several NCBI databases. The format of the URL string example following 'term=' can also be used to directly query the named databases.

Browsing and Downloading Interaction Datasets

This page supports browsing the protein interaction and replication interaction datasets, and identifying intersections between the two. Results are presented in tabular format, and are also available for download. The page also provides a link to view the filtered content in NCBI's Gene database.  Additional data details are included in the download files.

Filters:

As filters are selected the table contents are automatically updated. 

• HIV-1: select individual named proteins, or 'ALL' for the whole virus and all proteins
• Protein interaction:
  • All interaction types - browse or download all protein interactions
  • Do not show - restrict the display and download to only replication interactions
  • specific interaction type (acetylated by, for example) - restrict the display and download to a specific type of protein interaction
• Replication interaction
  • All interaction types - browse or download all replication interactions
  • Do not show - restrict the display and download to only protein interactions
  • specific interaction type (e.g., enhanced by knockdown of human gene) - browse or download a specific type of replication interaction

Tabular report

The table presents 20 rows at a time, sorted on the first column and second columns, with options at the top and bottom of the table to navigate to additional pages.  A row is provided per each distinct interaction description; thus, for a HIV-1 protein and human protein pair, several rows may be presented in the table.  Four columns are provided for the web display:

• HIV-1: for replication interactions, this column reflect the virus; for protein interactions this column reflects a gene product or specific mature peptide product if the gene is associated with more than one functional protein.
• Interaction:  the protein or replication interaction type; terms shown here are also found in a filter menu option
• Human genes: the human gene that is associated with the interaction type. Cells are linked to the NCBI Gene record.
• Details: clicking on the 'more' link opens a pop-up box with information on the the human protein accession, an interaction description, and supporting PubMed ID(s).

Download

The download file corresponds to the results presented in the table and includes additional information. The download button can be used to retrieve all data for one or both interaction types, or a sub-set of the data after filtering for a specific interaction type or HIV-1 protein product.  The download file is in comma separated value (csv) format, is provided as one row per distinct interaction description, and includes the following columns:

• HIV-1 Gene ID
• HIV-1 Protein accession.version
• HIV-1 Protein name
• keyword - e.g., interaction type
• Human Gene ID
• Human Gene symbol
• Human protein accession.version
• PubMed ID(s) comma separated
• Modification date - most recent data release date
• Interaction Description - brief functional description

Retrieving protein-interaction data

To restrict the display and download to only protein-interaction data:

1. Set Replication interaction to 'Do not show'
2. Select 'ALL' or a specific protein product from the HIV-1 filter menu
3. Select 'All interaction types' or a specific interaction type from the Protein interaction filter

Retrieving replication-interaction data

To restrict the display and download to only replication interaction data:

1. Set Protein interaction menu to 'Do not show'
2. Select 'ALL' from the HIV-1 filter menu
3. Select 'All interaction types' or a specific interaction type from the Replication interaction menu

Finding data intersections

The best way to explore protein and replication interaction data intersections is to download the full dataset for further analysis using programming approaches or publicly available tabular display and analysis software such as Microsoft Excel:

1. Select 'ALL' from HIV-1 filter menu
2. Select 'All interaction types' from the Protein interaction menu
3. Select 'All interaction types' from the Replication interaction menu