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Log in credentials

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2. How to edit?

A new markup

SubtiWiki v3 has adapted a new markup system. This markup system not only indicate the style of the page, but also the structure the page. The text below is a part of source text of gene dnaA


* description: AAA  ATPase, replication initiation protein

* locus: BSU00010

* pI: 6.03

* mw: 50.695

* proteinLength: 446

* Gene

** Coordinates:  410 → 1,750

** Phenotypes of a mutant
essential [Pubmed|12682299]
Description
AAA ATPase, replication initiation protein
Isoelectric point
6.03
Protein length
446 aa
Gene
Coordinates
410 → 1,750
Phenotypes of a mutant
  • essential [Pubmed|12682299]
  • In this markup system, all section titles starts with a asterisk " * ", the primary section title with one " * " while the secondary section title with two " * ".

    Content of the section can be placed either right behind the title, or under the title. A new line in the edit box corresponds to a bullet point when parsed.

    A universal template is provided for gene's page in SubtiWiki. Information can be added to intended section.

    Note:

    A space is needed between " * " and the title, as well as between " : " and the content.

    Editing table

    NameSyntaxParsedHot key
    gene [[gene|dnaA]]
    [[gene|ptsH|Hpr]]
    [gene|6740108089F13116F200C15F35C2E7561E990FEB|dnaA]
    [gene|29B793660E4D30C0656248F3EF403FEF76FB9025|Hpr]
    ctrl + shift + g
    protein [[protein|dnaA]]
    [[protein|ptsH|Hpr]]
    [protein|6740108089F13116F200C15F35C2E7561E990FEB|DnaA]
    [protein|29B793660E4D30C0656248F3EF403FEF76FB9025|Hpr]
    ctrl + shift + p
    SubtiWiki [SW|Ribosome] [SW|Ribosome] ctrl + shift + a
    PDB [PDB|2Z4R] [PDB|2Z4R] None
    PUBMED [Pubmed|23909787,22286949] [Pubmed|23909787,22286949] ctrl + shift + c
    REGULON [[regulon|dnaA]]
    [[regulon|T-box]]
    [regulon|6740108089F13116F200C15F35C2E7561E990FEB|dnaA]
    [regulon|T-box|T-box]
    None
    External url [https://www.google.de/ Google] [https://www.google.de/ Google] None
    I(i) <i>italic text</i> italic text None
    B(b) <b>bold text</b> bold text None
    X2(down) X<sub>2</sub> X2 None
    X2(up) X<sup>2</sup> X2 None
    Citation <pubmed>23909787,22286949</pubmed> Citation in green box None

    Edit a gene

    In this version of SubtiWiki, the editing page of a gene provides portals of all editing interface concerning this gene.

    Section nameDescription
    GeneGeneral information about this gene, transcribed RNA, and translated protein (if exists).
    InteractionsInformation of protein-protein interactions.
    Translational regulationsregulation which happens at translational level, transcriptional regulation please go to "Operons" section
    Operonall operons this gene is in, transcriptional regulation data stored here.
    Protein Complexesfunctional protein complexes, still under construction, but you are welcome to add in data already.
    Additional information on regulonIf this protein is a regulator, some information about this protein as regulation can be added here, such as the reference papers or etc.

    3. Regulation browser

    What is radius, and zoom?

    In the new regulation browser, a sub network centering the target gene is displayed. Radius is informally defined as 'how many steps it take from the target gene into the regulatory network'. Formally speaking, radius is the maximal distance between any gene in this sub network to target gene.

    The zoom button in the settings panel controls the radius.

    What is coverage?

    It is the ratio of genes in this sub network over all genes in B.subtilis subsp 168

    How can I get the underlying data?

    Right click on the white area in the regulation browser. A pop up menu provides the link to export the data as csv, export the network as image, and export the network in NetVis supported format.

    What is NetVis?

    NetVis is a simple cross-platform network visualizer. It can be seen as the offline version of regulation browser. It uses the same visualization engine and from regulation browser network can be exported and viewed later locally.

    Pathway browser Expression browser Interaction browser Regulation browser Genome browser

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