4.2 Locus view

H-InvDB provides annotation items in graphical and text-based table views for each HIX (H-Invitational cluster) in Locus view.

The text based views for Locus view can be selected by the pull-down menu at the top of Locus view within four data format listed below;

• Flat file
• XML file
• DDBJ format file
• Nucleotide fasta file (Locus genome sequence)

Fig. 4.2.1 Summary view of H-InvDB Locus view

The graphical view of Locus view consists of following sections (tabs) including listed annotation.

No.	TAB name	SECTION name
1	Gene structure	Gene structure information
2	Function	Gene function information
3	Alternative splicing	Alternative splicing (AS) information
4	Expression	Gene expression information
5	Disease	Disease/pathology information
6	Member	Cluster member (s)

1) Gene structure information [Gene structure tab]

Provides annotation items below and related links;

• H-Inv cluster ID
• Genomic location
• Related links (Ensembl, RefSeq, EntrezGene, GeneCards, H-GOLD)

Fig. 4.2.2 H-InvDB Locus view: Gene structure information

2) Gene function information [Function tab]

Provides annotation items below and related links;

• Gene symbol/name
• Gene family/group
• Definition
• Coding potential
• Related links (Ensembl, RefSeq, EntrezGene, GeneCards, H-GOLD)

3) Alternative splicing (AS) information [AS tab]

Provides annotation items below and related links;

• Pattern of alternative splicing isoforms
• Position of alternative splicing isoforms
• Alternative splicing isoform H-Inv ID(s)
• Related links to H-DBAS

Fig. 4.2.3 H-InvDB Locus view: Alternative splicing (AS) information

4) Gene expression information [Expression tab]

Provides annotation items below and related links;

• Tissue-specific expression
• Tissue-specific expression data were analyzed by H-Invitational original pipeline. We determined the expression to be tissue specific when the iAFLP (JBIRC) expression of a certain cluster was larger than 50% in one or two in 10 tissue categories.
• Probe mapping information

Fig. 4.2.4 H-InvDB Locus view: Gene expression information

5) Disease/pathology information [Disease tab]

Provides two kinds of disease related information related to HIX: known disease-related genes and co-localized orphan pathology with the name of the disease and OMIM ID;

• Disease relation
• Related information in OMIM
• Co-localized orphan diseases
• Disease related mutation (MutationView)

Fig. 4.2.5 H-InvDB Locus view: Disease/pathology information

6) Cluster member (s) [Member tab]

Provides annotation items below and related links for all the cluster members.