Annotation Viewer Help
FANTOM data for our mouse clones is available through the FANTOM annotation viewer.Annotation view window
Annotation data search
FANTOM qualifier
Annotation view window
The annotation viewer window consists of three frames. The top (summary) frame is to show a sequence ID, links to RIKEN, NTT software, and pages containing the nucleotide sequence or the deduced amino acid sequence. The middle (annotation) frame is to table annotation results which include RIKEN definition (see: list of qualifiers). The bottom (reference) frame is to graphically display precomputed sequence similarity and motif search results. For example, in FASTA search, the top black thin line and numbers above the line represent a sequence and nucleotide numbers of a cDNA clone, respectively, the middle red line represents CDS predicted by DECODER program, and the bottom blue thin line, blue-colored box, and the number in the blue-colored box represent non-homology region, homology region, and % identity of homology, respectively. The result of alignment for homology search can also be browsed by following the link ('align').Annotation data Search
Annotation data for mouse clones can be seen through "FANTOM search". You can search clones by following way.ID search
Keyword search
Pfam Domain search
TIGER Cellular Role search
ID Search
Each entry has many kinds of IDs. Users can search for entries by the following IDs.- Sequence ID (seqid)
- A unique number assigned to each RIKEN full-length cDNA sequences.
- FANTOM ID (fantomid)
- A unique code assigned to each cluster (see clustering concept), in which redudant sequences are gathered, and non-clustered (singleton) sequence. Each cluster has a representative sequence.
- Clone ID (cloneid)
- A unique code assigned to each cDNA clones collected in RIKEN.
- DDBJ Accession (accession)
- DDBJ Accession number assigned to each full-length cDNA sequence that is not assembled with public EST databases.
- MGI Accession
- Accession number assigned by MGI, Jackson Lab.
Keyword search
Users can search for entries by the keywords of following qualifiers.riken_def
riken_def_suppl
gene_symbol
note
gene_ontology_C
gene_ontology_P
gene_ontology_F
Qualifiers to select
Check boxes for qualifiers to be searched. If multiple qualifiers are selected, the system will retrieve entries containing keywords (satisfying conditions) in any of selected qualifiers.
note: GO IDs can be used for keywords (e.g. GO:0004364)Basic keyword search
If you would like to search for entries that contain a specific word, you may write the word in the first text box.
Keyword searches are executed case-insensitively, which means that the keywords 'RNA' and 'rna' are regarded as the same.'And' keyword search
If you write multiple words in the box, the system searches for entries that containing all words.
'Not' keyword search
If you wish to searches for entries that contain specific words and DON'T contain other specific words, you should attach the minus('-') character before the word not to be contained.
'Or' keyword search
If you would like to search for entries that one of specific words, you should write each word in each box.
You can combine 'and', 'or' and 'not' searches.Non-redundant sequences
If you checked the checkbox labeled `Non-redundant cDNA sequences only', keyword search will be executed against representative sequences in clusters and singleton sequences.Pfam domain search
Users can search for entries with results of estwisedb (this program is in Wise2 package) against Pfam database.
Pfam domain name search
If you have already been known Pfam name to retrieve, you can input the name in the textbox. The name is case-sensitive, which means that the system distinguish between capital letter and small letter.
Pfam domain list
If you don't know Pfam name, you can show a list of all Pfam names matched to sequences in FANTOM data set.
Non-redundant sequences
If you check the checkbox or select link labeled `only non-redundant cDNA sequences', you can show only entries that are representative sequences in clusters or singleton sequences.Cellular role search
Users can search for entries with results of TIGR cellular role prediction by homology searches against EGAD HT database.
Cellular role list
When you click a link in the cellular role search, a list of main role is shown, each role has a link to show a list of entries that are categorized in the role. If a role has sub roles, it has also a link to show a list of sub roles.
Non-redundant sequences
If you click a link labeled 'only non-redundant cDNA sequences', you can show only entries that are representative sequences in clusters or singleton sequences.
Qualifiers in FANTOM
- riken_def = riken definition
- The brief annotation for describing and defining functions of cDNAs constructed in RIKEN (RIKEN cDNAs); minimal annotation for RIKEN cDNAs.
- riken_def_suppl = riken definition supplement
- Description to supplement the riken definition when RIKEN cDNAs can not be sufficiently described only by the riken definition.
- gene_ontology
- Biological process, Molecular Function, and/or Cellular Component attributed to RIKEN cDNAs based on the classification, established by the GENE ONTOLOGY CONSORTIUM, of genes' attributes. Each Category consists of restricted vocabularies.
- organ
- Organ(s) from which each full-length cDNA clone's corresponding EST(s) in RIKEN cDNA library(s) was obtained. The first character(s) is Library ID defined by RIKEN. The integer in parentheses is the number of EST clone(s) obtained in the organ.
- note
- Additional information that can not be described by any qualifiers should be input in this qualifier. Any words used in this qualifier can be retrieved by keyword search.
- comment
- Any comment concerning the clone can be provided using this qualifier. This qualifier is NOT subjected to keyword search.