Introduction | Interface Manual

E3Miner

E3Miner is a text mining tool for ubiquitin-protein ligases (E3s). The tool is performed through the input of E3-related text.

USAGE: You can insert text or comma (,) separated PubMed IDs (PMIDs), and click the 'Mining' button. When a PMID is given, E3Miner makes online access to PubMed, and retrieves the corresponding title and abstract. Note that input text or PMIDs cannot begin with hyphen or comma (,). E3 data mined is structured as a table form, and you can also save the E3 data in text format through the 'Save Result' link. E3 data consist of the items as following. ('Heading' indicates the head in downloadable text data.)

Category	Data Description	Heading
E3	E3 names with UniProt ID (UPID), if exists. This data item also contains a source sentence in input text with other references that describe the same E3. The statistic information includes the number of reference articles and E3-interacting proteins, including substrates, E2s, and E1s.	ID
E3 Domain	E3 domain that binds to E2. The main E3 domains are RING, HECT, U-box, and PHD type. This item also contains source sentences for the mention of E3 domain.	DM
E3 Substrate	Target proteins of ubiquitin tagging by the corresponding E3. The data item contains source sentences, other references, and statistic information.	TP
Auto Ubiquitination	Auto-ubiquitinating activity of the E3. This item shows if the E3 ubiquitinates by itself (auto-/self-ubiquitination).	AU
Ubiquitination Type	Types of ubiquitination by the E3. The types can be classified into mono-/oligo-/poly-/multi-ubiquitination. The data item also contain its source sentences.	UT
Ubiquitination Site	Ubiquitin-binding motifs of the E3 substrate. The data item contain its source sentences.	US
E1	E1 enzymes that interact with the corresponding E2 and E3. The data item contains source sentences, other references, and statistic information.	E1
E2	E2 enzymes that interact with the corresponding E3. The item also contains source sentences, other references, and statistic information.	E2
DUB	Deubiquitinating enzymes with source sentences.	DE
Associated Protein	Proteins that interact with the E3. The proteins are imported from IntAct.	AP
GO Term	E3-related GO terms from UniProt. The evidence of GO terms can be found from GO site.	GU
GO Term	E3-related GO terms from user text. The GO terms are automatically tagged from sentences that mention the corresponding E3.	GO
Disease	E3-related disease names integrated from OMIM.	DS

EXAMPLE 1: Given the text of journal abstract (PMID:17646408), E3Miner extracts E3 names and identifies their UniProt IDs with relevant data, as shown below.

EXAMPLE 2: You can also see a video clip for an example usage of E3Miner, which mines data about the TRAF6 gene from the text (PMID:18042044), and then examines TRAF6-related substrates, functions, and diseases from the output by E3Miner.

Quick Search

Quick Search provides full-text search in all fields. This is always accessible through the search bar as shown below.

USAGE: You can type any keywords with 'AND' and 'OR' operators. If no operators are specified, then the keywords are treated as having the 'OR' operator. When using 'AND' and 'OR' together, the operator 'AND' has a higher precedence than 'OR'. Note that the keywords can be double-quoted for the exact match. In the results, each icon represents links as follows.
: E3DB entry
: Pathway Browser
: UniProt entry

EXAMPLE: Given the input 'mdm2 human', Quick Search returns E3 entries with 'mdm2 OR human' in all the available fields.
You can browse an entry by selecting an item from the search result, as shown below.

Advanced Search

Advanced Search provides text search by a combination of selected fields. This is accessible by the menu tab 'Advanced Search'.

USAGE: You can select a field in the 'drop-down' field box, and type any keywords with the 'AND' or 'OR' operators. After composing a combination of specified conditions, you can click the 'Search' button to search for E3 entries.
The following table shows all the fields provided by Advanced Search.

Field Name	Description	Example
UniProt ID	Search for E3 entries by UniProt ID	MDM2_HUMAN
E3 Protein Name	Search for E3 entries by protein name	hdm2
E3 Gene Name	Search for E3 entries by gene name	mdm2
Domain Name	Search for E3 entries by domain name	RING
Ubiquitin Structure	Search for E3 entries by types of ubiquitin structure	polyubiquitination
Target Protein	Search for E3 entries by names of target proteins	p53
E1 Enzyme	Search for E3 entries by names of E1 enzyme involved in pathways	UBE1
E2 Enzyme	Search for E3 entries by names of E2 enzyme involved in pathways	UbcH5A
DUB Enzyme	Search for E3 entries by names of DUB enzyme involved in pathways	HAUSP
GO Term	Search for E3 entries by E3-related GO terms	ubiquitin-protein ligase activity
Disease	Search for E3 entries by E3-related disease names	papilloma

EXAMPLE: To search for "RING domain E3 protein that is related to human papilloma", you can input 'human' in the organism field, 'papilloma' in the disease field, and 'ring' in the E3 domain field. Then, you can get the results as shown below.

Pathway Browser

Pathway Browser is a graphic tool to view the ubiquitination pathways of a particular E3.

USAGE: You can see the ubiquitination pathway from E1 to E2, E3, and the target protein. You can control the distance of protein interactions in pathways by the "Zoom In" Zoom In or "Zoom Out" buttons. The "Zoom In" button enables you to see more detailed protein interactions, and the "Zoom Out" button to see less detailed ones. In Pathway Browser, rectangles and their connections indicate proteins and ubiquitinating relations, respectively. The color of a rectangle indicates E1, E2, E3, and the target protein, as follows.

  E1
  E2
  E3
  Target Protein

You can click any protein rectangle to view a ubiquitination pathway. For each rectangle, you can browse protein information by clicking the blue-colored or red-colored little boxes on the rightmost side of the protein rectangle. The blue-colored little box is linked to the corresponding entry in UniProt, and the red-colored little box to the entry in E3DB.