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The goal of this tool is to provide the user, to decide
which experiments will be crossed, between the experiment
and the respective biological/technical replicate. The
output is shown in a table format containing the gene name,
categories and %(up,down,inside) of sampled genes in the
chip.
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The goal of this tool is to provide the user to select an
hybridized experiment, that have already been normalized,
calculated the log ratio and crossed against your respective
biological/technical replicate. The dif. expr. genes are
shown according to the HTSelf method. The output exhibit the
raw average expression profile (without log) between the
experiment and your replicate, indicating if the genes are
High(Up) or Low(down) expressed
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This tool displays a list of all available experiments
hybridized in the project, and allows the user to select one
or more experiments and generate a list of differentially
expressed genes or no variation in the levels of
transcripts, resulting in an expression profile (up / down /
inside) in each of the selected experiments, with their
categories. The user need to set up the parameters for the
analysis, as the cutoff (% up / down / inside), the type of
expression (up/down or inside) and can add filters as: Gene
Names, Annotation or by Categories.
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Tool developed with the principle of mathematical Model of
Venn diagrams. The tool integrated to the database
containing statistical results from microarray experiments,
enables the user to create as many groups as required for
their analysis, each group may incorporate an infinite
number of experiments. The tool enables you to perform the
selection of differentially expressed genes for each group
of experiment, setting up a cutoff, and providing the final
result of genes that are common/specific among each group
individually.
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The goal of this tool is to generate a table that can be
used for cluster analysis of genes by expression level. To
generate the resulting table the user selects the
experiments selected, sets the cutoff (%), the type of
expression profile (up / down or inside) and choose the
output format for the ratios of each experiment, which can
generate the result with the ratio of the experiment and the
replication of each gene separately, or an average between
the experiment and its replica (biological / technical).
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Identification of genes differentially expressed by Pearson
correlation method to calculate the significance level of
correlation between three or more experiments, with
implementation of the normalization of genes by Mean
Centering, Median Centering or Z-score to eliminate possible
variations between hybridizations with crossing with method
list of genes HTSelf modified.
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Method developed for the analysis of gene expression by
intensity (by channel), a gene is expressed if its level of
expression and most of its replicas are significantly above
the background, and to reduce false positives we can filter
by their replicates in both technical / biological . To
determine if an oligo is significantly expressed, it uses a
method based on a criterion to quantify the signal error.
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Tool that allow us to analyze the enrichment in databases.
This tool uses the software to search for enrichment in
GeneMerge databases locally developed. Our current version
of the tool allows you to search for enrichment in :
Functional Category, Gene Ontology, Metabolic Pathways from
KEGG, Metabolic Pathways from PlantCyc and KEGG Enzymatic
Annotation.
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Expression patterns derived from tissue pair-wise
comparisons. The expression ratios from each tissue against
pool hybridizations were used to calculate "virtual ratios"
between each pair of tissues. The patterns derived were
clustered. The results from the tissue against pool
hybridizations are shown in the last 12 columns. The green
areas denote lower expression in the tissue indicated than
in the others (<0.5x), red areas show higher expression
(>2x), and yellow indicates that the expression is similar
in both tissues being compared. White areas correspond to
data excluded from the analysis due to low quality
hybridization in some experiments (data from Papini-Terzi et
al., 2005).
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Search Microarray Design Information
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Tool to search experiment details.
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A new algorithm to compare metabolic pathway activities from
gene expression profiles, identifying differences in the
pathways activity between different conditions. Using the
significatively expressed genes from expression analysis,
and their expression profiles, for each experiment
condition. The program allow hierarchical clustering and
spearman/pearson/kendall correlations to compare the
pathways activity between different conditions
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Web interface to use Pathview R Tool.
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Correspondence between multiple gene structure annotations of the SP80-3280 gene space assembly.
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Tool to search Rnaseq Analysis.
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Tool to search Rnaseq cross experiments.
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Tool to search Rnaseq Description.
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Metabolomics
Tool developed to explore metabolic profiles of different tissues, varieties and species, and the relative intensities of these metabolites.
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Tool developed to explore metabolic data exploring regular expression.
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Tool developed to explore cross metabolic description about samples of control and treatment.
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Tool developed to explore cross metabolic data.
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Web interface to use Pathview R Tool.
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Sugarcane Genome BACs - R570
Sugarcane BACs - SP80-3280
Sugarcane Genome - SP80-3280
Search Downstream-Upstream Genome regions
Search Downstream-Upstream BAC regions
Search Motifs in Downstream-Upstream Genome regions
Search Motifs in Downstream-Upstream BAC regions
Search of Cloning Information in Transgenic Plant Data &
analysis
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Transcript Search by name, part of name, oligo name, EST name
or annotation. The search tool returns a hyperlink transcript
list for more detailed information, for each selected
transcript.
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The tool allow the user to search by specific or all Ortholog
Sugarcane transcripts with other Grasses.
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Search by a list of Genes, Full-lenghts, ESTs, and Oligo Probe and get protein and/or nucleotide FASTA.
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Search tool for the blast alignment results by gene and
annotation, filtering by multiple criteria.
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Search by SAS sequence and show the gene assembly composition.
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Search of Cloning Information in RT-PCR data & analysis
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Tool to update SAS annotation
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Insert or update SAS annotation by file upload (tab-delimited
separation)
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Search by list of SAS name and recover gene categories and
annotation
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Search by SAS name or gene function or Access by the tree of
catalogues.
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Search Metabolic PathWay (under
development)
Search by one or more SAS names to recover the respective
Metabolic Pathways.
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View all publication
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Tool to Insert data and analysis for publications such as:
- Journal and paper description - qRT-PCR figures - List of Differentially Expressed Genes - Clustering results (HeatMap and SOM Self-Organizing Maps). |
The collection and descriptions of the data objects and items
in the data Model
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Tool to Insert data and analysis for publications such as:
- Journal and paper description - qRT-PCR figures - List of Differentially Expressed Genes - Clustering results (HeatMap and SOM Self-Organizing Maps). |
Examples and explanation about our tools.
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Examples and explanation about our tools.
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Tool to insert / update data about physiology of plants
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Tool to select physiology crossing and visualize data
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