Center for Bioinformatics
Oxidoreductases | Transferases | Hydrolases | Lyases | Isomerases | Ligases
How to use RLEdb:

1.Query and search database

   Text search of rate-limiting enzymes and transcription factors

   Batch retrieve a list of genes in database

   References related query

   Blast all sequences of rate-limiting enzymes and their interacting genes

   Blast transcription factors in database and find target enzymes

2.Browse database

   By organisms or enzyme code (Comparation rate-limiting roles in different organisms)

   By regulatory type

   Browse all data from different features including chromosome localization, subcellular localization and tissue expression

   Color marking of all the rate-limiting enzymes in each KEGG pathway map

3.Enzyme and gene pages

   Information of enzyme pages

   Information of gene pages

4.Data download and feedback to us

   Download page

   Your contribution


Topic 1: Query and search database [ top ]

Three main dataset are searchable. The first is all rate-limiting enzymes and their related genes; Second is all the transcriptional factors; and the last one is all the genes including rate-limiting enzyme genes and their interacting genes. To access the three dataset, text search(Query menu) and sequence-based blast(Blast menu) are provided.

1) Text search of rate-limiting enzymes and transcription factors [ top ]

Text search information in database mainly include three steps: select a database from Query menu; select fields; input your insteresting keyword.

Select a database [ top ]

For the first step, the query of rate-limiting enzymes on enzyme level is shown on Query --> enzyme page. You can also retrieve them on gene level by gene name or gene description (on Query --> Gene page). The overall layout of the page is similar for both, however, it differs in the default columns that are displayed.

Another text search page is specific for transcription factors in database from Query --> TFs page.

Select fields and input keywords [ top ]

Searchable fields are selected from the dropdown menu. The items vary according to database selected, since each database contains different information. In enzyme page, it allow users to search enzyme code, enzyme name, pathway, comment and different regulatory types [see curation page]. Enzyme code will be exact match search, other searchable fields will be substring searches (as if preceded and followed by wild cards).

Take query for "1.1.1.1" in enzyme page as an example, you can either a) choose "Enzyme number " as query type and then input "1.1.1.1", three enzymes from Human, Rat and Mouse will be shown in result page. or b) choose "Name" as query type and then input the office name "alcohol dehydrogenase". The same result page can be reached here.

Search supports the logical 'And', 'Or', and 'Not' operators. For instance, to retrieve phosphorylation regulated "alcohol dehydrogenase", enter "alcohol dehydrogenase" for "name" field and select the OR operator, and then input "phosphorylation" for "regulation" field. Similar, to retrieve transcription factor regulated "alcohol dehydrogenase", enter "alcohol dehydrogenase" for "name" field and select the OR operator, and then input "transcriptional factor " for "regulation" field.


2) Batch retrieve a list of genes in database [ top ]

To access all the genes including rate-limiting enzyme genes and their interacting genes, batch retrieve are provided in Query --> batch page.

3) References related query [ top ]

To assistant user to discover more rate-limiting enzyme and their regulatory information, all the 15688 references and 46656 generif records are searchable in Query --> Literature page and Generif page .

For example, user could discover more detail about the relation between SREBP transcription factor family with all the rate-limiting enzymes from generif search as following:

For example, user could try detail about the relation between SREBP transcription factor family with all the rate-limiting enzymes from rate-limiting relevant sentences search as following:

4) Blast all sequences of rate-limiting enzymes and their interacting genes [ top ]

To do sequence-based search for all the genes including rate-limiting enzyme genes and their interacting genes, please access Blast --> enzyme page.

5) Blast transcription factors in database and find target enzymes [ top ]

To blast all the transcription factors in our database, please access Blast--> TFs page. From the result page, you could link to your insteresting transcriptional factors page in our database.




Topic 2: Browse database

1) By organisms or enzyme code (Comparation rate-limiting roles in different organisms) [ top ]

From Browser--> Organism page, user could compare the different rate-limiting role in five common model organisms including Human, Rat, Mouse, Yeast and E.coli straightforwardly.

2) By regulatory type [ top ]

From Browser--> Regulatory type page, user could easily browse rate-limiting enzymes which are regulated by different regulatory types such as regulated by transcription factors, phosphorylation ect.

3) Browse all data from different features including chromosome localization, subcellular localization and tissue expression [ top ]

From Browser--> classification page, users could browse all the annotation in a hierarchical style including pathway, subcellular localization and regulatory type. For human rate-limiting enzymes, addtional hierarchy browsing for chromosome localization and tissue expression are provided.

4) Color marking of all the rate-limiting enzymes in each KEGG pathway map [ top ]

From Browser--> pathway page, users could access all the relevant KEGG maps color-marked by all the repoted rate-limiting enzymes from different organisms.

The maps are look like this:

Follow the links in red, user could reach corresponding gene pages of rate-limiting enzyme.




Topic 3: Enzyme page [ top ]

Information are represented on five different types of pages including enzyme view, gene view, uniprot view, all gene view, hprd view and transcription factor view. Enzyme pages record all curated information from literatures including rate-limiting role descriptions, regulatory description and their corresponding transcription factors. From enzyme page, user could link to their corresponding gene pages, uniprot pages, hprd pages and transcription factor pages.

Enzyme page are like the following:

The gene page is like the following:

Follow the links to iHOP, the summary result of text mining will be like this:




Topic 4: Data download and feedback [ top ]

You could freely download our data for academic researchers, but not for profit purposes. Please access Data--> Download page.

We also hope you could help us to improve our database.

If you have any suggestion to add new comment to records in current RLEdb or to revise wrong information in current RLEdb or to suggest new rate-limiting enzymes or habout RLEdb website or Others, please access Data--> Contribution page.



  Copyright 2009, Center for Bioinformatics 
  Last Modified: 2009-03-24  
  Design by Zhao Min