Upstreamer: Fetch upstream sequences using gene identifiers:    [ Help ]

• Organism: Homo Sapiens (human) Mus Musculus (mouse) Rattus Norvegicus (rat)
• Desired upstream length: 500 1000 1500 2000 2500 3000 3500 4000 4500 5000 base pairs.
• Gene Identifier type: Genbank Accession Number Clone ID Entrez Gene ID (Locuslink) Ensembl Gene ID Probe ID microRNA Based ID
• Array Identifier: Not ProbeId ---------- Human - Affymetrix HuGene Mouse - Affymetrix MoGene Rat - Affymetrix RaGene ---------- Human - Affymetrix HG-U133 Plus 2 Mouse - Affymetrix Mouse 430_2 Rat - Affymetrix Rat 230_2 ---------- Human - Affymetrix HG-U133A Human - Affymetrix HG-U133A_2 Human - Affymetrix HG-U133B Mouse - Affymetrix Mouse 430A_2 Mouse - Affymetrix Mouse 430A Mouse - Affymetrix Mouse 430B Rat - Affymetrix RAE230A Rat - Affymetrix RAE230B ---------- Human, Mouse, Rat - Agilent WholeGenome Human - Agilent cgh44b ---------- Human - Illumina HumanWG6v1 Human - Illumina HumanWG6v2 Human - Illumina HumanWG6v3 Mouse - Illumina MouseWG6v1 Mouse - Illumina MouseWG6v2
• Upload plain text file of type Gene Identifiers list Upstream sequences (FASTA format)    (NOT Word/RTF/Excel/PDF/HTML/ZIP files)
  [ File Format ]

TF Retriever: Find Transcription Factor binding sequences (TREs) on gene upstream sequences:    [ Help ]

• TRE finding program: Match (TRANSFAC Public) Match (TRANSFAC Professional v 2009.4)
• Login information for this web based TRE finding program:
• TRANSFAC Public: Free registration at www.gene-regulation.com
• TRANSFAC Pro: Purchase License at www.biobase-international.com
• Username:
• Password:


• MATCH filter option: Minimize False Positives
  
• MATCH Profile options: Vertebrates non redundant Minimize False Positives ---- Below will work for DBI users only ---- NFkB minimize False Positive NFkB minimize sum of False Positives and Negatives
• Core similarity threshold: 1.00 0.95 0.90
•   Find TREs on complementary strand?