Table of Contents

  1. Overview
  2. Main Features and Workflows
    1. Creating a new pathway
    2. Opening an existing pathway
    3. Searching for pathways
      1. Search by gene symbol
      2. Search by gene identifier
      3. Browsing search results
    4. Displaying experimental data
  3. Editing and Viewing Pathways
    1. Manipulating objects
      1. Placing new objects
      2. Selecting objects
      3. Moving objects
      4. Changing the size of objects
      5. Deleting objects
      6. Editing object properties
      7. Grouping objects
      8. Aligning, scaling and stacking objects
      9. Changing line and arrow type
      10. Using Molecular Interaction Map styles
      11. Changing the drawing order
      12. Copy and paste
    2. Annotating pathways
      1. Creating links between biological entities
      2. Creating links between lines
      3. Adding Literature References
      4. Adding Comments
      5. Changing general pathway information
    3. Manipulating pathways
      1. Zoom
      2. Import and export pathways
        1. Import/export between PathVisio and GenMAPP
        2. Export DataNode list
        3. Export to Eu.Gene
        4. Export to graphics formats
  4. Using experimental data in PathVisio
    1. Preparing raw data for PathVisio
    2. Creating an expression dataset
    3. Creating color sets
      1. Threshold color set
      2. Gradient color sets
  5. Retrieving Pathways and Databases
    1. Retrieving pathways
    2. Retrieving synonym databases
    3. Available synonym databases
    4. Supported database systems
  6. Pathway Statistics
    1. Running statistical analysis
    2. Results
        1. positive (r)
        2. measured (n)
        3. total
        4. %
        5. Z Score
  7. Other Features
    1. Setting Preferences
      1. Display
      2. Directories
      3. Files
      4. Database
    2. Keyboard shortcuts
  8. Tutorials

Retrieving Pathways and Databases

Retrieving pathways

Pathways in gpml format can be downloaded directly from  WikiPathways, either as individual files or in  batch mode.

After downloading either individual pathways or pathway archives, place the files in the PathVisio\pathways folder in your user directory (e.g C:\Documents and Settings\Username\Pathvisio-Data\pathways on windows XP). This is the default folder where !Pathvisio looks for pathway files. You can also choose to store pathway files in any other directory on your computer. In this case, you may also want to change the PathVisio default location for pathways. See Setting Preferences for details on how to change preferences.

Retrieving synonym databases

Gene Databases provide PathVisio with cross references between gene identifiers in pathways and other database identifiers. Databases are downloaded and installed locally for use with PathVisio. Links to databases can be found at  PathVisio website. Download and unzip databases to the Pathvisio-Data\gene databases directory in your user directory on your computer. You can also choose to store databases in any other directory on your computer. In this case, you may also want to change the PathVisio default location for databases. See Setting Preferences for details on how to change preferences. NOTE: Gene databases can take up a lot of disc space. For the human gene database you need at least 400 Mb of free disk space.

Available synonym databases

Our synonym databases contain the latest information from  Ensembl. A synonym database for any species that is in Ensembl can be generated. If you would like to have a PathVisio synonym database for another species that is present in Ensembl, please contact us.

Supported database systems

Each public database supported in PathVisio synonym databases has a specific system code that is used to identify which system a particular identifier belongs to. The following list displays the proper system codes for PathVisio:

System codes for genes and proteins:

System CodeSystem NameSample ID and LinkOut
A  TAIR  AT1G35255
Ag  Agilent A_24_P98555
Bg  BioGrid  59420
C Cint
Cc  CCDS  CCDS43989 ***
D  SGD (S. cerevisiae)  CUP1-2
E EC (Enzyme Code)  2.7.1.71
Ec Ecoli
Em  EMBL  AL030996
En  Ensembl  ENSG00000139618 ***
EnHs?  Ensembl Human  ENSG00000139618
EnMm?  Ensembl Mouse  ENSMUSG00000017167
EnRn?  Ensembl Rat  ENSRNOG00000016648
EnDm?  Ensembl Fruitfly  FBgn0032956
EnDr?  Ensembl Zebrafish  ENSDARG00000024771
EnCe?  Ensembl Celegans  Y42H9B.1
EnSc?  Ensembl Scerevisiae  YGR147C
F  FlyBase  FBgn0031208
G  GenBank
Ge  CodeLink GE86325
Gg  Gramene GenesDB  GR:0060184
Gl  Gramene Literature  6200
Gm  Gramene Pathway PROTEIN-KINASE-RXN
Gp GenPept AAH72400
H  HUGO  25068
Hs HsGene
I  InterPro
Il  Illumina ILMN_5668
Ip IPI  IPI00020529
Ir  IRGSP Gene  Os12g0561000
L  Entrez Gene  1232
M  MGI (M. musculus)  MGI:2687328
Mb  miRBase  MI0000808
Mg  MaizeGDB  acc1
N  NASC Gene ATMG00960-TAIR-G
Nw  NuGO Wiki  Copper
Ob  Oryzabase  468
Om  OMIM  608981
Os  Rice Ensembl Gene  LOC_Os04g54800
Pd  PDB  2Z17
Pf  Pfam
Pl  PlantGDB PUT-157a-Vitis_vinifera-37378
Q  RefSeq  NM_001054966
R  RGD (R. norvegicus)  1587276
Rf  Rfam  RF00066
S  Uniprot/TrEMBL  P57770
Sn  dbSNP
T  Gene Ontology  GO:0005634
Ti  J. Craig Venter Institute (formerly TIGR) 12012.t00308
U  UniGene  Hs.553708
Uc  UCSC Genome Browser  uc001tyh.1
W  WormBase  T24D1.1
Wc  Wheat Gene Catalog (Grain Genes)  341
Wn  Wheat Gene Names (Grain Genes)  5S-Rrna-D1_(Triticum)
Wr  Wheat Gene References (Grain Genes)  WGS-95-1333
X  Affymetrix Probe Set ID  1851_s_at ***
Z  ZFIN  ZDB-GENE-041118-11
O Other, for use with a custom database

System codes for metabolites:

System CodeSystem NameSample ID and LinkOut
Ca Chemical Abstracts (CAS)
Ce  ChEBI
Ch  HMDB
Cp  PubChem
Cs  Chemspider

*** Organism name is also required as a variable in url for linkout