ID Resolver
| Summary | ID Resolver is a tool for discriminating various types of data IDs. If you have any data IDs of unknown origin, please try it. Multiple IDs can be discriminated at a time. |
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| Data type | ID identifiers |
KAGIANA
| Summary | We have developed the KAGIANA tool, which allows a user to retrieve summary information obtained from selective databases and to access pages for a gene of interest in those databases. The tool is based on Microsoft Excel and provides several macro programs for gene expression analyses. It can assist plant biologists in accessing omics information for plant biology. The KAGIANA tool is freely available at http://pmnedo.kazusa.or.jp/kagiana/(cited from the original site). |
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| Data type | Gene expression |
KaPPA-View
| Summary | The web-based tool KaPPA-View was developed for representing quantitative data for individual transcripts and/or metabolites on plant metabolic pathway maps. The presentation of data in this manner facilitates a good grasp of the transcripts and metabolites, leading to hypotheses of gene function in the metabolic pathway being examined. (cited from CiNii http://ci.nii.ac.jp/naid/110004822705/)New Features of KaPPA-View4:1. A comprehensive review of the system was conducted, and the processing speed was improved dramatically compared to the previous versions.2. As well as Windows, Mac OS X is now fully supported and you can use all the features on it.3. The users can use their own metabolic pathway maps for the analyses.4. As a function for the system developers, KaPPA-View4 offers features to display data directly from external systems such as databases and applications.(cited from original site http://kpv.kazusa.or.jp/kpv4/information/overview_en.html ) |
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| Data type | Metabolite repression Gene expression |
KaPPA-View4 KEGG
| Summary | KaPPA-View4 is metabolic pathway database which is aimed to better understand metabolic regulation and to generate hypotheses from huge public available 'omics' data, i.e. transcriptome, metabolome, gene-to-gene co-expressions and metabolite-to-metabolite co-accumulations.KaPPA-View4 KEGG is one of the KaPPA-View4 version that has the pathway map data from the Kyoto Encylcopedia of Genes and Genomes (KEGG), and includes species infromation of animals, plants and microorganisms. Gene family maps generated from the "Genes and Proteins"classification of KEGG BRITE are also available. (cited from original site) |
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| Data type | Metabolite repression Pathway |
LAMP
| Summary | LAMP is a code for multiple testing correction. Given the relationships between transcription factors (TFs) and genes and gene expression levels, the code lists up statistically significant combinations of TFs. The LAMP algorithm calibrates the Family-Wise Error Rate (FWER) at the same level of Bonferroni correction. |
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| Data type | p-values of multiple testing correltions |
PMID-Extractor
| Summary | PMID-Extractor allows a user to obtain PubMed IDs (PMIDs) from PDF files or text format files of journal paper in your hand. From Digital Object Identifiers (DOIs, http://en.wikipedia.org/wiki/Digital_object_identifier) or text information (e.g. titles) in the first page of each files, To start using PubMedScan, a paper recommender, PMIDs are required to specify the users' interest. That is the main usage of PMID-Extractor. |
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| Data type | Journal |
PowerFT
| Summary | The peak detection and annotation tool for the analyses of metabolomics data obtained by chromatography - high resolution mass spectrometry(cited from original site).PowerFT is now available as a part of an integrated tool "PowerGet". |
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| Data type | mass spectrome data |
PubMedScan
| Summary | PubMedScan is a automatic paper recommendation system for newly published PubMed papers that are related to your interest. This system has the following features: 1) queries are given by a list of PMIDs to search for related articles rather than by keywords or phrases; 2) related papers are reported daily by E-mail and stored in the system; 3) the similarity score between two articles are, currently, scored by PubMed "Related articles" service; and 4) the system can be used through either Web (ver 2.0) or software for local installation (ver 1.1). The local version can be installed on a UNIX machine such as Linux and Macintosh. PHP, MySQL, Apache and Perl modules are required. This system is key-word free, therefore effective to compensate for the keyword search in surveying the papers.To collect the PMIDs of your interest easily from your PDF or text files, we also provide software "PMID-Exporactor". |
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| Data type | Articles registered in PubMed |
SAMURAI
| Summary | Gene expression networks have different gene components depending on the cell types. SAMURAI is a tool for finding such minimal functional units of genes called modules from large-scale gene expression data. Modules are searched against by an ultra fast and exhaustive biclustering method using a closed itemset mining algorithm.suspending for relocation. (confirmation on 2012/11/05) |
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| Data type | Gene expression |
SGCAL
| Summary | We have developed a web-based tool named SGCAL (Structural Glycomics CALculations). SGCAL is capable of building a 3D structure from oligosaccharide sequence information and of visualizing the calculated results and the experimental MS data, thereby supporting investigations on correlations between the structure of oligosaccharides and their fragmentation patterns. |
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| Data type | Sugar chain |