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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.
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
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.
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.
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).
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.
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.
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.
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).
Search Microarray Design Information
Tool to search experiment details.
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
Tool to search experiment details.
Tool to search experiment details.
Tool to search experiment details.
Tool to search experiment details.

Metabolomics

Tool to search experiment details.
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Genome Browse
Sugarcane Genome BACs - R570 Go
Sugarcane BACs - SP80-3280 Go
Sugarcane Genome - SP80-3280 Go

Search of Cloning Information in Transgenic Plant Data & analysis
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.
The tool allow the user to search by specific or all Ortholog Sugarcane transcripts with other Grasses.
Search by a list of Genes or Full-Length Genes, and show protein and or Nucleotide Sequences.
Search tool for the blast alignment results by gene and annotation, filtering by multiple criteria.
Search of Cloning Information in RT-PCR data & analysis
Search by list of SAS name and recover gene categories and annotation
Search by SAS name or gene function or Access by the tree of catalogues.
Search Metabolic PathWay (under development)
Search by one or more SAS names to recover the respective Metabolic Pathways.
Blast

Blast2Seq

View all publication
The collection and descriptions of the data objects and items in the data model
Home | General Coordinator: Glaucia Souza, Biochemistry Department,
University of São Paulo
This platform is continuously under development.