EcoGene

You can help EcoliWiki by editing the content of this page. For information about obtaining editing privileges, see E._coli_Wiki:Membership

EcoGene
Who:	proprietor
What:	short description
Where:	EcoGene
Updates
Upcoming events	link to event calendar, if applicable
Web Services

About EcoGene

Ecogene contains genomic and proteomic information about E.coli K12 MG1655.

Using EcoGene

Searching

Once you type in your gene of interest, Ecogene brings up several tidbits of information about that gene including, but not limited to synonyms and other identifiers, the gene name mnemonics (which are good to know), functions, and genomic location. Also, Ecogene also allows you to view other ORFs within a set distance from your gene. You can also get DNA and protein sequences and MW. A unique aspect of this database is that you also get a bibliography of the gene.

Input	Output
Gene Name (DNA, RNA, or pseudo gene) Synonym Gene Product EcoGene number (EG) ECK number SWISS-PROT number Genbank number (gi) Blattner lab number (b) CGSC number Genomic Address Gene Description	Primary Gene Name EG number ECK number b number Sequence Gene Name Mnemonic Alternate Gene Symbols Sequence Description Protein Sequence Protein length and MW Gene Quality Genomic Address (right end, left end, direction, and minute(%)) EcoMap (10 kb neighbor genes) Link out Resources (AmiGO, CMR, COG, ColiBASE, Colibri, Doodle, ECCE, ECDC, EchoBASE, EcoCyc, GenBank, GenExpDB, GenomeReviews, GenProtEC, GTOP, KEGG, ModBase, NiceZyme, pfam, ProDom, ProtoNet, SWISS-2D, TF Binding Sites, TIGR-CMR, TIGRHmm, Uniprot) ASAP CGSC GenoBase RegulonDB SWISS-PROT PDB Links
Title, author, or reference ID	Title, authors, year, journal, vol, pages, Pudmed ID, Gene Links
Enzyme(s) and Genomic Adress	Restriction Map

Analysis

• Find the neighboring genes to the initially identified set

Yes. EcoMap (10 kb neighboring genes)

• Find/design primers for a certain gene

No.

• Find all the clones/KOs for those genes

Yes. Link to CGSC and GenoBase

• Find commonalities in function in the genes that are up or down-regulated in a given experiment

No.

• Find genes with similar behavior across sets of different experiments (see Hughes et al 2000)

No.

• Given a gene name, find all the available info about this gene (motif, clones, mutants and relevant construction information, e.g., for making the mutants or the clones)

No.

• For a gene, segment of DNA, operon/regulons, pathway , find all the available information

No.

Usage examples

Add links to additional pages describing success stories here.

Discussion

Trackbacks

This feature is not yet functional

• $4$5: [$2 $1]

References

Rudd, K.E., EcoGene: a genome sequence database for Escherichia coli K-12, Nucleic Acids Res., 28:60-64, 2000

External Links

EcoGene