geneXplain's Workflows

Gene set enrichment analysis (Affymetrix p... (1)

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This workflow is designed to perform Gene Set Enrichment Analysis, GSEA, as it is described at http://www.broadinstitute.org/gsea/index.jsp. As input, the normalized data with Affymetrix probeset IDs can be submitted.First, the input files are subjected to fold-change calculation. The table with probeset Ids and calculated fold change values is converted into a table with Ensembl Gene Ids. At the next step, the Ensembl genes are annotated with additional information, gene description and gene...

Created: 2013-10-29 | Last updated: 2015-04-17

Credits: geneXplain

Find master regulators in networks (GeneWays) (1)

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This workflow is designed to find master regulatory molecules upstream of an input list of genes. Input file is any gene or protein table.At the first step, the input table is converted into a table with Entrez Gene IDs.At the next step the Entrez genes are annotated with additional information, gene description and gene symbols.The annotated gene table is subjected to master regulator search in the GeneWays network. For each potential master regulator, FDR, Score, and Z-score are calculated....

Created: 2013-11-13 | Last updated: 2015-04-17

Credits: geneXplain

Analyze promoters (GTRD) (1)

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This workflow is designed to search for putative transcription factor binding sites, TFBS, on the promoters of an input gene set.As input, any gene or protein table can be submitted. The input table contains genes under study, and it is called “Yes” set.At the first step, the input table is converted into a table with Ensembl Gene IDs.At the next step, promoters are analyzed for potential cis-regulatory sites. Promoters in this workflow are defined as sequences from -1000 to +100 ...

Created: 2013-11-13 | Last updated: 2015-04-17

Credits: geneXplain

Analyze any DNA sequence for site enrichment (1)

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This workflow is designed to reveal TFBS  enrichment in any DNA sequence.  As input, any sequence collection in FASTA, EMBL or GeneBank format can be used. Yes and No sequence sets can be specified in the corresponding input fields.  As input, DNA sequences of any organisms and from any genome regions can be taken.At the first step Yes and No sequences are subjected to Site search on track analysis using the profile of positional weight matrices specified in the input form. The...

Created: 2013-11-13 | Last updated: 2015-04-17

Credits: geneXplain

Mapping to ontologies (Gene table) (1)

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This workflow is designed to classify an input gene set to several ontologies and to identify terms, hits for which are overrepresented in the input set. The input file can be any gene or protein table.At the first step, the input table is converted into a table with Ensembl Gene IDs.This table with Ensembl Gene Ids is subjected to functional classification, which is done in parallel by the following ontologies: GO biological processes, GO cellular components, GO molecular functions, Reactome...

Created: 2013-11-13 | Last updated: 2015-04-17

Credits: geneXplain

Compute differentially expressed genes (1)

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This workflow is designed to identify up-regulated, down-regulated and non-changed genes for experimental data with three and more data points for each experiment and control.  As input, normalized data with any types of IDs (Ensembl, gene symbols, EMBL, RefSeq) can be submitted.In the next step, p-values for up- and down-regulated probes are calculated for all probes using the “Up and Down Identification” analysis. This analysis applies Student’s T-test for p-value cal...

Created: 2013-11-13 | Last updated: 2015-04-17

Credits: geneXplain

ChIP-Seq - Identify and classify target genes (1)

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This workflow identifies and classifies target genes using positional information of peaks found by ChiP-Seq approach. As input, the peak regions in BED format, can be submitted. Actually, any dataset in BED format can be submitted as input track for this workflow.First, the track file is converted into a gene set using Track to gene set analysis. The Ensembl gene list is then annotated with additional information, gene descriptions and chromosomal location.The annotated Ensembl genes are sub...

Created: 2013-11-13 | Last updated: 2015-04-17

Credits: geneXplain

Analyze any DNA sequence, GeneBank (1)

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This workflow is designed to analyze a DNA sequence for potential binding sites. Sequences should be in GeneBank format.What is the geneXplain type?The geneXplain platform is an online toolbox for a broad range of bioinformatic and systems biology applications. It is developed by geneXplain GmbH. The technology behind the geneXplain platform is BioUML (www.biouml.org), which has been built, improved and supported for many years at the Institute of Systems Biology in Novosibirsk. The individua...

Created: 2013-11-13 | Last updated: 2015-04-17

Credits: geneXplain

Analyze any DNA sequence, Fasta (1)

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This workflow is designed to analyze a DNA sequence for potential binding sites. Sequences should be in Fasta format.What is the geneXplain type?The geneXplain platform is an online toolbox for a broad range of bioinformatic and systems biology applications. It is developed by geneXplain GmbH. The technology behind the geneXplain platform is BioUML (www.biouml.org), which has been built, improved and supported for many years at the Institute of Systems Biology in Novosibirsk. The individual w...

Created: 2013-11-13 | Last updated: 2015-04-17

Credits: geneXplain

Analyze any DNA sequence, EMBL (1)

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This workflow is designed to analyze a DNA sequence for potential binding sites. Sequences should be in EMBL format.What is the geneXplain type?The geneXplain platform is an online toolbox for a broad range of bioinformatic and systems biology applications. It is developed by geneXplain GmbH. The technology behind the geneXplain platform is BioUML (www.biouml.org), which has been built, improved and supported for many years at the Institute of Systems Biology in Novosibirsk. The individual wo...

Created: 2013-11-13 | Last updated: 2015-04-17

Credits: geneXplain