Limits...
Human metabolic atlas: an online resource for human metabolism.

Pornputtapong N, Nookaew I, Nielsen J - Database (Oxford) (2015)

Bottom Line: A web interface for Hreed facilitates an access to the Hreed reaction data, which can be easily retrieved by using specific keywords or names of related genes, proteins, compounds and cross-references.The HMA is a unique tool for studying human metabolism, ranging in scope from an individual cell, to a specific organ, to the overall human body.This resource is freely available under a Creative Commons Attribution-NonCommercial 4.0 International License.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg 41269, Sweden nielsenj@chalmers.se.

No MeSH data available.


Related in: MedlinePlus

Summary of Atlas map viewer functions. (A) The main view of Atlas with control panel comprises a pathway input box for selecting specific sub metabolic map to be opened. The pathway input box provides an autocompleting search by pathway names. Atlas starts with a global metabolic pathway map by default. (B) Sub metabolic map with data overlaid and bar plot representing the number of genes that are present in this pathway map for each cell type can be opened by the control panel, clicking on pathway name in every map and clicking on pathway id in the information window. (C) The information window represents information of reactions from the KEGG database and provides link to external databases for further information.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4513696&req=5

bav068-F2: Summary of Atlas map viewer functions. (A) The main view of Atlas with control panel comprises a pathway input box for selecting specific sub metabolic map to be opened. The pathway input box provides an autocompleting search by pathway names. Atlas starts with a global metabolic pathway map by default. (B) Sub metabolic map with data overlaid and bar plot representing the number of genes that are present in this pathway map for each cell type can be opened by the control panel, clicking on pathway name in every map and clicking on pathway id in the information window. (C) The information window represents information of reactions from the KEGG database and provides link to external databases for further information.

Mentions: To visualize and compare h-tGEMs among different cell types, a visualization system was implemented providing a better view of tissue-specific metabolic models. A web-based visualization system, called Atlas, was developed with an interactive interface representing information from the latest release of INIT normal models on KEGG metabolic maps (17). The Atlas is designed as a web application with an intuitive, clean graphical user interface. The user interface comprises a pathway input box with an ‘Open’ button (a), ‘Tissue filter tree’ (b) and ‘Map viewer’ tabs (c) as shown in Figure 2. Users can easily open a map by typing pathway name or KEGG pathway id, which begins with ‘path:map’ followed by a five digit number in the pathway input box and then click ‘Open’ button or enter. A new map can also be opened by clicking on the corresponding pathway name in a map. To overlay maps with selected tissue information, selecting or deselecting the checkboxes can change the tissue list filter. Only the selected tissue information will be overlaid on maps.Figure 2.


Human metabolic atlas: an online resource for human metabolism.

Pornputtapong N, Nookaew I, Nielsen J - Database (Oxford) (2015)

Summary of Atlas map viewer functions. (A) The main view of Atlas with control panel comprises a pathway input box for selecting specific sub metabolic map to be opened. The pathway input box provides an autocompleting search by pathway names. Atlas starts with a global metabolic pathway map by default. (B) Sub metabolic map with data overlaid and bar plot representing the number of genes that are present in this pathway map for each cell type can be opened by the control panel, clicking on pathway name in every map and clicking on pathway id in the information window. (C) The information window represents information of reactions from the KEGG database and provides link to external databases for further information.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4513696&req=5

bav068-F2: Summary of Atlas map viewer functions. (A) The main view of Atlas with control panel comprises a pathway input box for selecting specific sub metabolic map to be opened. The pathway input box provides an autocompleting search by pathway names. Atlas starts with a global metabolic pathway map by default. (B) Sub metabolic map with data overlaid and bar plot representing the number of genes that are present in this pathway map for each cell type can be opened by the control panel, clicking on pathway name in every map and clicking on pathway id in the information window. (C) The information window represents information of reactions from the KEGG database and provides link to external databases for further information.
Mentions: To visualize and compare h-tGEMs among different cell types, a visualization system was implemented providing a better view of tissue-specific metabolic models. A web-based visualization system, called Atlas, was developed with an interactive interface representing information from the latest release of INIT normal models on KEGG metabolic maps (17). The Atlas is designed as a web application with an intuitive, clean graphical user interface. The user interface comprises a pathway input box with an ‘Open’ button (a), ‘Tissue filter tree’ (b) and ‘Map viewer’ tabs (c) as shown in Figure 2. Users can easily open a map by typing pathway name or KEGG pathway id, which begins with ‘path:map’ followed by a five digit number in the pathway input box and then click ‘Open’ button or enter. A new map can also be opened by clicking on the corresponding pathway name in a map. To overlay maps with selected tissue information, selecting or deselecting the checkboxes can change the tissue list filter. Only the selected tissue information will be overlaid on maps.Figure 2.

Bottom Line: A web interface for Hreed facilitates an access to the Hreed reaction data, which can be easily retrieved by using specific keywords or names of related genes, proteins, compounds and cross-references.The HMA is a unique tool for studying human metabolism, ranging in scope from an individual cell, to a specific organ, to the overall human body.This resource is freely available under a Creative Commons Attribution-NonCommercial 4.0 International License.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg 41269, Sweden nielsenj@chalmers.se.

No MeSH data available.


Related in: MedlinePlus