Dengue Human Interaction Database (DenHunt) is a comprehensive and integrated database solely dedicated to dengue-human molecular interactions. Diseases caused by dengue have high global infection rates and affect approximately 2.5 billion people worldwide with 390 million dengue infections are reported per year. This necessitates the need for a Dengue specific resource. It contains verified manually curated interactions from the published literature. It collates published reports of three types of interactions:

• Direct interactions, where the human proteins directly interact with the viral proteins or RNA, (682 direct interactions between 11 viral components and 534 human proteins extracted from 103 publications)
• Indirect interactions, where the human proteins affect viral replication but there exists no current evidence of them directly interacting with the viral components (382 indirect interactions extracted from 151 publications)
• Differentially expressed interactions, genes or proteins whose expression patterns are altered during dengue viral infection, (4120 differentially expressed genes extracted from 41 publications).

Documenting the interaction of dengue virus with the host cell is crucial to understanding the process of viral replication and pathogenesis, and provides an essential foundation for the development of safe and effective therapeutic and prevention strategies to combat dengue viral diseases.

The database is divided into and can be queried in 4 sections that includes:

1. Direct interactions
2. Indirect interactions
3. Expression variations
4. Pathways
5. Dengue virus Host Dependency Factors (DVHFs)

Development of DenHunt database

The abstracts and publications containing original research describing association of human host proteins with dengue virus were searched using the term “dengue” or the specific dengue protein along with other relevant keywords. The interactions retrieved from these publications were segregated manually into direct interactions, indirect interactions and differentially expressed interactions. For majority of abstracts, full-text of the article was reviewed. However, for the abstracts for which full length articles were not available, the interactions were catalogued based on the abstract, only if they contained complete descriptions of the interactions. Since the articles were from peer-reviewed publications, all identified interactions were incorporated into the database without placing further judgment on the scientific validity of the report. Most papers described the protein studied as a gene synonym or alias. In this regards the official human protein symbol, and Entrez GeneID was extracted from online tools such as bioDBnet, Synergizer, GeneCards and NCBI Entrez Gene database. Information retrieved from relevant publications were collected and the interactions were manually catalogued into a table containing all the following fields:

1. Dengue viral component. This dengue viral component involved in the interaction. This field is available only for the direct interactions.
2. Human Gene symbol. The official gene symbol of the human protein interactor.
3. Human gene Entrez Id: The gene identification numbers from Entrez Gene, NCBI's database for gene-specific information.
4. Pubmed Id: PubMed identification numbers (PMIDs) of articles describing the interaction.
5. Patient type or Serotype: There are 4 serotypes of dengue virus (DENV 1, 2, 3, 4). Serotype of the DENV strain or strains used in the study. Dengue infection leads to complications ranging from mild dengue fever (DF) to more severe dengue hemorrhagic fever (DHF) and dengue shock syndrome (DSS). If clinical samples from patients such as serum, whole blood or peripheral blood mononuclear cells (PBMCs) are used, then type of patient the sample is extracted for the study is given.
6. System: This field gives information of the cell line used in the study if it is an in vitro study. If the study uses clinical samples, then the type of sample used such as serum, whole blood or peripheral blood mononuclear cells (PBMCs) is given.
7. Comparision: This field is available only for differentially expressed genes. Here what type of sample is compared to what control. eg. Dengue infected 293T cells vs uninfected cells.
8. Variation: This field is available only for differentially expressed interactions. Its states whether the gene is up regulated or down regulated.
9. Title: Title of the paper where the interaction was extracted.

Database Classification:

There are around 14, 313 publications describing dengue viral research in the PubMed till date. Queries were used to extract the information about dengue-human interactiona. The retrieved interactions were classified into three types:

1. Direct interactions, where the human proteins directly interact with the viral proteins or RNA. Most of the direct interactions reported in the literature have been determined using the small scale studies such as affinity purification, pull down assays and co-localization by microscopic techniques. However, the recent years have seen the use of high-throughput techniques such as yeast two-hybrid and tandem affinity purification followed by mass spectrometry which has enabled detection of PPIs at the proteome scale. The papers containing interactions between viral and human proteins from papers that have been determined through any of the above experiments were extracted and manually cataloged.
2. Indirect interactions, where the human proteins affect viral replication but there has been no evidence of directly interacting with the viral components. A commonly used experimental approach to elucidate the function of a gene, in this case the role of a human protein in viral replication or pathogenesis, is the selective deletion of its expression or activity. This can be achieved by one of the approaches, which include mutational studies, small-interfering RNAs (siRNAs), small molecule inhibitors. There have been many studies that use any one or more of the above mentioned approaches to determine dengue virus host dependency factors. Apart from in vitro studies, there have been many studies carried out using patient’s blood or serum in order to determine biomarkers in dengue infection.
3. Differentially expressed interactions, genes or proteins whose expression patterns are altered during dengue viral infection. With the development of high-throughput transcriptomic and proteomic technologies such as microarrays, MALDI and mass spectrometry, it has become possible to identify genes that are differentially expressed on a transcriptome or proteome wide scale in virus-infected cells in vitro, dengue infected patient whole blood and peripheral blood mononuclear cells (PBMCs), serum of patients and secretome of dengue infected cells. The differentially expressed proteins obtained using such approaches provides valuable insights into the dynamic relationships between host cell and the virus during the course of infection. The differentially expressed interactions have two additional fields: Comparison (eg. Dengue infected 293T cells vs uninfected cells) and variation, that states whether the gene is up regulated or down regulated in the study.

Statistics

Type of Interaction	Dengue viral components	Total number of unique interactions	Number of PMID references
Direct Interactions of human protein with dengue viral components		682	103
	5'- and 3'-UTR, DENV RNA	31	15
	C	66	19
	E	34	14
	M	24	8
	NS1	162	21
	NS2A	43	3
	NS2B	23	4
	NS3	126	19
	NS4A	15	7
	NS4B	27	5
	NS5	131	18
Indirect interactions through siRNA and small scale studies		382	151
Differentially Expressed Genes (DEGs) identified in DENV infected cell lines and patients		4120	41
Total number of human genes or proteins involved the above interactions		4613
Total number of PubMed articles			287

Contact details and submission of interaction details

Researchers may submit novel interactions after publications in the following formats given below. Authors who have previously published dengue-human interactions would be called upon to submit interaction details to the following mail id:
karyalaprashanthi@gmail.com
The authors have to identify which category their interactions belong to. The basic format for submission of interactions is given below.
For direct physical interactions the authors have to submit the following details:

Dengue viral interactor

Human Gene interactor

Pubmed Id

Serotype

System

Experiment

For indirect interactions the authors have to submit the following details:

Human Gene interactor

Pubmed Id

Serotype

System

Experiment

For differentially expressed genes the authors have to submit the following details:

Human Gene interactor

Pubmed id

Patient type

System

Experiment

Comparision

Variation or Serotype

The meaning of each field required:

1. Dengue viral interactor: This dengue viral component involved in the interaction.
2. Human Gene interactor: The official gene symbol of the human protein interactor.
3. Pubmed ID: PMID of the article describing the interaction.
4. Serotype or Patient type: The serotype of the DENV strain or strains (DENV1, 2, 3, 4) used in the study. If clinical samples from patients such as serum, whole blood or peripheral blood mononuclear cells (PBMCs) are used, then type of patient (DF, DHF and DSS) used in the study is given.
5. System: This field gives information of the cell line used in the study if it is an in vitro study. If the study uses clinical samples, then the type of sample used such as serum, whole blood or peripheral blood mononuclear cells (PBMCs) is given.
6. Experiment: The experiments used to identify the interaction.
7. Comparison: This field is available only for differentially expressed genes where the expression of genes in infected samples is compared with controls. eg. Dengue infected 293T cells vs uninfected 293T cells)
8. Variation: This field is available only for differentially expressed interactions. It states whether the gene is up regulated or down regulated. In dengue infected samples.