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ANAP FAQs
How to quick start?
Please refer to the "Video Tutorial" or "User Guide".
Where has the raw data for ANAP come from and what is the level of accuracy?
All the ANAP raw data were collected from the PSICQUIC Registry at the EBI.
These data are widely used in many key projects.
These include: Cytoscape, IntAct, Reactome, Taverna and etc., which are
described in Aranda et al (2011) PSICQUIC and PSISCORE: accessing and
scoring molecular interactions. Nature methods 8: 528-529.
How much data is included in ANAP V1.0?
ANAP V1.0 was updated on November 17, 2011, and currently includes:
*11 protein interaction databases
*73 species, such as cow, mouse which show protein interactions with
Arabidopsis
*Data generated from 89 unique interaction detection methods.
*6,161 unique literature citations.
*15,208 unique identifiers (including 11931 TAIR IDs).
*201,699 unique protein interactions.
Does ANAP integrate the newest Arabidopsis Protein interaction data?
Yes, we not only used the current data collected from the PSICQUIC
Registry, but have also incorporated data from the newest research papers.
For example, data has been included from the paper "Evidence for Network
Evolution in an Arabidopsis Interactome Map" by "Arabidopsis Interactome
Mapping Consortium" published in Science, 29 JULY 2011. However, if
you find that we have missed some useful data, please let us know!
How often does ANAP update?
Generally, we update ANAP each 3 months; we have recently established
a semi-automatic update program for efficient, accurate updates.
What input identifier formats does it support?
ANAP supports TAIR IDs and UniProt IDs. However, we recommend that you
use TAIR IDs in the search, because the network nodes are shown with TAIR
IDs. If you have identifiers that are not TAIR IDs or UniProt IDs, please convert
them to TAIR IDs or UniProt IDs (see below).
I have some identifiers not from TAIR or UniProt, what shall I do?
You can use the online convert tool. We suggest you use bioDBnet or UniProt
ID Mapping.
Why use "Source Database", or "Interaction Detection Method" as the node
relationship?
There are a total of 7 fields in ANAP data, including the node "Name molecule
A", "Name molecule B", and also, "Interaction Detection Method", "PubMed
Identifier", "Species molecule A", "Species molecule B", "Source Database".
The edge links, which connect the nodes together, are based upon the evidence
in ANAP. These links can be presented by Interaction Detection Method or
Source Database. By selecting one of these the network is presented showing
the links based upon the database or the experimental procedure used.
What output file formats does ANAP generate?
ANAP can generate several network data formats including "SIF", "GRAPHML",
"XGMML", and network graph format include "PNG", "PDF", and "SVG". ANAP
can also generate the network interaction data in table form containing the
evidence supporting the interactions.
How many input identifiers does ANAP support?
Currently, we can support searches with up to 500 input identifiers, however
searches of this size are very large and will generate a huge resultant network.
In general, if you put in 500 input identifiers, it is likely that a network with
about 6,000 nodes and 50,000 edges will be generated. Because the network
is so large, the internet browser cannot view the network (Note: This is not a
shortcoming of ANAP, rather it depends on the internet browser). The ANAP
results page will show a message "The network is too large. Please import into
Cytoscape to see the network using the SIF file of "Source Database", or
"Interaction Detection Method!" you can download the ANAP generated
network data to do this.
If you want to query more than 500 input identifiers, please contact the author
directly.
What happens if my input generates a very large number of nodes?
If your input identifies more than 30 nodes, it may generate a huge network
with of a total of >1000 nodes and 3000 edges. For example, the input
"AT1G01060 AT1G01210 AT1G01470 AT1G01510 AT1G01560 AT1G01610
AT1G01640 AT1G02090 AT1G02120 AT1G02160 AT1G02170 AT1G02280
AT1G02390 AT1G02450 AT1G02680 AT1G02780 AT1G02920 AT1G03370
AT1G04330 AT1G04550 AT1G04810 AT1G04860 AT1G05690 AT1G06520
AT1G06590 AT1G06720 AT1G07000 AT1G07660 AT1G07820 AT1G07920"
generates a network with 1,468 nodes and 3,278 edges.
Although you can view the generated network with your browser,
we recommend that you download the "SIF", "GRAPHML" or "XGMML" data
and use Cytoscape to view the network.
Why can I not download the network data (SIF, GRAPHML, XGMML) or
graph (PNG, PDF, SVG) when the ANAP results page shows the message
"The network is too large. Please import into Cytoscape to see the network
using SIF file of Source Database, or Interaction Detection Method!" ?
This is because the internet browser cannot generate the network because it is
so large, therefore there are no relevant network data and graphs, however
ANAP generates the SIF file of "Source Database" and "Interaction
Detection Method" for use with Cytoscape. In this case only these two files
(which also include the Evidence data) are generated from the query.
Why are the edge colours of the network not displayed in the legend?
There is no need to list the edge colour legend in the network graph because
each edge displays a text hint when you mouse-over the edge, (this edge text
hint is highlighted in bigger font). Also if the edge relationship is "Interaction
detection method", it has 89 unique colours and there is not enough space to
place it with the generated network graph. However, if you want to check the
colour of the legend, you can find two lists of the edge colour legend included
in the "Source Database" and the "Interaction Detection Method".
Does ANAP support Rice Protein interaction data analysis?
We currently do not support Rice Protein interaction data analysis in ANAP
V1.0, however we hope to incorporate this in future releases.
If one interaction data is not the same as in the original database (like STRING),
what happens?
Occasionally this may happen because the PSICQUIC update occurs after
changes to individual databases, however this will happen less and less in the
future because PSICQUIC has established interfaces to several individual
databases (such as IntAct) and will therefore update at the same time as these
databases. If you find this kind of problem, please contact us, we will check
and try to update that record.
What is the license for ANAP?
There is no license requirement for any use of ANAP, which means anyone can
use ANAP free of charge.
What is it written in?
It is written in a combination of HTML, Shell, AWK, PHP and JavaScript.
What internet browser supports the use of ANAP?
We recommend the use of Firefox or Safari browsers.
We have tested Firefox, Safari, Internet Explorer (IE), Chrome and Opera.
Firefox.
*Safari and IE work well on all of ANAP's functions.
*When using Firefox, if you want to link to "AVT", "1001 Genomes",
"UniProtKB", "KEGG" or "EnsemblGenomes" of one node, click and hold on the
right button of the mouse to choose the link.
*When using Safari or IE, click on the right button of the mouse to choose the
relevant link.
*Chrome and Opera can work well on all functions, except the links to "AVT",
"1001 Genomes", "UniProtKB", "KEGG" and "EnsemblGenomes".
What is the difference between direct and indirect interaction?
If protein A and B, and also B and C have direct interactions, then A and C
indirectly interact.
Taking AT2G17033 as an example; a small network containing AT2G17033
and other five interaction proteins (AT3G23700, AT2G03160, AT5G42190,
AT1G60940 and AT1G75950) is generated. All have direct interactions with
AT2G17033, whilst two of these five proteins have indirect interactions.
You can use the "Depth Search" function to find the indirect interactions of the
input query.