Web Interface

HAHMIR.DB has a user-friendly web interface to make the database more useful for the research community. There are many options in HAHMIR.DB to serve the needs and requirements of the users. The web Interface of HAHMIR.DB is simple and user ready with many options such as Browse, Explore, Tutorials, Contacts to provide the users with the most relevant information.

Browse

Users can Browse the data present in HAHMIRDB directly from the database or using different filter option. The complete data of HAHMIRDB was manually reviewed and divided into the various category as follows:

  1. Level of Expression
  2. Duration of Experiment
  3. Experimental Altitude
  4. Browse by Association

Level of Expression: Using this option the user can retrieve a list of miRNAs that are up regulated or downregulated during high altitude ascent. Click on any of two option opens a table of miRNA that are either upregulated or downregulated. Each miRNA in the table is being hyperlinked to the individual miRNA information page 

Duration of experiment:

User can browse differentially expressed high altitude miRNAs based on its temporal behavior . This option enables the user to retrieve a list of specific miRNAs that are found differentially expressed in days, months and years. Each miRNA in the table is being hyperlinked to the individual miRNA information page. Each table can be downloaded in Excel and PDF format.

The Experimental Altitude:

This option provide user to retrieve human miRNAs expressed at different altitude. The option contains a range bar, where user can select maximum (7600m) and minimum (3600m) altitude range to get desire set of miRNAs expressed in that range. Each miRNA in the table is being hyperlinked to the individual miRNA information page. Each table can be downloaded in Excel and PDF format

Other Search options

This database enables user with special search options:

  1. Search miRNA from Gene set
  2. Search miRNAs as Biomarker
  3. Search miRNAs Associated with a Drug
  4. Search miRNAs Associated with a GO ID
  5. Search miRNAs Associated with a GO term
  6. Search miRNAs Associated with a Kegg ID
  7. Search miRNAs Associated with a Pathway

Search miRNA from Gene set:

User can select multiple genes from the database and search related high altitude specific miRNAs. On clicking the search button the new page will appear having tabular representation of input genes and corresponding miRNAs. All the miRNA are hyperlinked to their miRNA information page. The table can be downloaded in excel as well as PDF format.

Search miRNA as biomarker:

User can see miRNA that are known to be biomarker for high altitude stress. On clicking the search button the new page will appear having tabular representation of miRNAs associated as biomarker. All the miRNA are hyperlinked to their miRNA information page. The table can be downloaded in excel as well as PDF format.

Search miRNA associated with drug:

User can select any drug stored in the database and search related high altitude miRNAs. On clicking the search button the new page will appear having tabular representation of input drug and corresponding miRNAs. All the miRNA are hyperlinked to their miRNA information page. The table can be downloaded in excel as well as PDF format.

Search miRNA associated with GO ID:

User can select any GO ID stored in the database and search related high altitude miRNAs. On clicking the search button the new page will appear having tabular representation of input GO ID and corresponding miRNAs. All the miRNA are hyperlinked to their miRNA information page. The table can be downloaded in excel as well as PDF format.

Search miRNA associated with GO term:

User can select any GO term stored in the database and search related high altitude miRNAs. On clicking the search button the new page will appear having tabular representation of input GO term and corresponding miRNAs. All the miRNA are hyperlinked to their miRNA information page. The table can be downloaded in excel as well as PDF format.

Search miRNA associated with Kegg ID:

User can select any GO term stored in the database and search related high altitude miRNAs. On clicking the search button the new page will appear having tabular representation of input GO term and corresponding miRNAs. All the miRNA are hyperlinked to their miRNA information page. The table can be downloaded in excel as well as PDF format.

Search miRNA associated with Kegg Term:

User can select any GO term stored in the database and search related high altitude miRNAs. On clicking the search button the new page will appear having tabular representation of input GO term and corresponding miRNAs. All the miRNA are hyperlinked to their miRNA information page. The table can be downloaded in excel as well as PDF format.

miRNA Information Page

Users can Browse the any miRNA present in the HAHMIR.DB. On clicking search Button the page browse to information page of that miRNA for e.g. hsa-let-7a-5p. The information page contains details stored from knowledge databases such as miRBase Accession, miRNA family, miRNA 5’,3’ ID etc. After knowledge data it contains information about precursor and mature sequences of miRNA. The database also identifies miRNA target genes and transcription factors(TFs) and forms miRNA-TF gene co-regulatory network. This network is being visualize using vis.js package. The graph visualization is dynamic in nature. In network graph user can move nodes in the space, also network graph can be Zoom In and Zoom out. User can also Download the excel file in (.sif) format. This file can be exported to visualize network in visualization software like cytoscape. The information on miRNA page can be divided into four categories.

  1. Knowledge based: miRNA Accession, miRNA family, chromosome number, precursor and mature sequence
  2. Association with High Altitude:
  3. Feed Forward Loops:
  4. Association of miRNA with Drugs, Tissues and Other Diseases:
  5. Association with Gene Ontology and Pathways

Association with High Altitude

User can scroll down to see information related to miRNA association with High Altitude Experiment. This information involves experimental group, altitude and duration of experiment, level of Expression, fold change, GEO No., associated as biomarker, reference.

Feed Forward Loops:

This section provides associated miRNA-FFL and TF-FFL motif subgraphs to the user. Section displays them in two different tables and each row of the table defines a FFL and the complete table can be downloaded in Excel/PDF format. User can also visualize tripartite graph by clicking on the miRNA name in the table. The tripartite graphs will appear as a pop-ups

Association of miRNA with Drugs, Tissues and Other Diseases:

User can further scroll down to see information related to miRNA association drug, disease and tissue. In disease and tissue association table the user can search for specific disease and tissue by name. The data in the table can be downloaded both in excel and PDF format. The Tissue Ids in the tissue association table are hyperlinked to Sequence Read Archive(SRA) database. Every PMIDs in drug and disease association table are hyperlinked to PubMed literature database.

Association with Gene Ontology and Pathways

User can further scroll down to see information related to miRNA association with gene ontology(GO) and pathways. In Gene ontology table at each miRNA page, user get information on category [biological process(BP), molecular Function(MF), Cellular component(CC)], gene counts, genes ensemble ID, GO ID, percentage, Enrichment value, Term. Similar type of information can be get from pathways table that include count, Kegg ID, genes ensemble ID, enrichment score and pathway term. Both the data in the table can be downloaded both in excel and PDF format.. Every PMIDs in drug and disease association table are hyperlinked to PubMed literature database.

Explore

In a explore option user can select multiple miRNA from the database and search them. On searching a complex miRNA TF gene co-regulatory network can be visualize, which includes all input miRNAs, their TFs and genes and other interacting miRNAs. User can also Download the excel file in (.sif) format. This file can be exported to visualize network in visualization software like cytoscape. Using our custom algorithm the Feed Forward Loops(FFLs) in the complex network has been identified at run time and shown in tabular format. User can click on each miRNA in a row to see its tripartite graph as pop-up. User can also search specific FFL based on TF, gene.

Hyperlink to miRBase

Hyperlink to RNA central database

Hyperlink to PubMed literature text

Hyperlink to PubMed literature database

Hyperlink to PubMed literature database

Hyperlink to SRA database