- Annotation of proteins in clusters
Collection of queries to retrieve all available annotation for proteins
in particular MCL or OrthoMCL clusters. Annotation includes protein sub-cellular
localisation predicted using PSort and Wolf-PSort, prediction of secretory proteins
using SignalP, Pfam motifs identified for each protein, Gene Ontology annotation and
KEGG pathways the proteins are involved in. Clusters can be specified either by
their identifier or in terms of their contents, such as a particular protein or proteins
with a particular annotation, such as a specific sub-cellular localisation.
- Cellular localisation analysis
Queries in this category can be used to retrieve the sub-cellular
localisation for a particular protein, or retrieve proteins with the same
sub-cellular localisation as a given protein. Furthermore, all proteins with
a given localisation can be retrieved. Localisations have been predicted using
PSort and Wolf-PSort.
- Essential yeast
genes cluster analysis
Queries to retrieve Mcl Clusters containing proteins of a given
genome and proteins of (non) essential yeast genes.
- Essential yeast
genes orthology analysis
This group of queries analyses clusters containing a given genome
and proteins of (non) essential yeast genes in terms of the number of
genomes present in those clusters.
- EST analysis
Collection of general EST analyses. Information available include
group/hierarchy structure of ESTs and genes as well as number of
homologs of genes in all genomes (in the database).
- Functional annotation analysis
Queries to retrieve Gene Ontology annotation or Pfam motifs for a given protein.
Furthermore, all proteins with a particular GO annotation or Pfam motif can
be retrieved.
- Genomic analysis
Collection of queries for general genomic analyses.
- Mcl Cluster analysis
Queries in this group provide a general analysis of the MCL
clusters in the database. Clusters containing proteins of a given
genome, or a group of genomes, such as plant pathogens or filamentous
fungi, can be retrieved. Furthermore, clusters that contain more or
less than a given percentage of proteins of a given genome can also be
obtained.
- OrthoMcl Cluster analysis
Queries in this group provide a general analysis of the OrthoMCL
clusters in the database. Clusters containing proteins of a given
genome, or a group of genomes, such as plant pathogens or filamentous
fungi, can be retrieved. Furthermore, clusters that contain more or
less than a given percentage of proteins of a given genome can also be
obtained.
- Pathway analysis
Queries to retrieve Enzyme annotation for a given protein or the pathways it
is involved in. Furthermore, all proteins with a particular Enzyme annotation or
those involved in a particular pathway can be retrieved.
- Redundancy analysis
The queries in this group analyse MCL and OrthoMCL clusters containing proteins of a
given genome in terms of the number of proteins of that given genome
present.
- Secretome analysis
Queries in this category can be used to retrieve the SignalP prediction, i.e.,
whether it's been predicted to be secretory or non-secretory. Furthermore, all
secretory or non-secretory proteins for a given genome can be retrieved.
- Transcript abundance
Collection of queries for transcript abundance analyses. These
queries are able help in identification of genes that may be highly
expressed in a particular growth conditions. Information of these
genes and conditions can also be retrieved.