l Construction of model
1. Input sequences in FASTA format/pre-aligned MSF
2. Multiple alignment via clustalW
3. Construct model by Hmmer2.0 package
The threshold in step 3 can be adjusted by user. The default setting is derived from the lowest score of hmmsearch with input sequences. There are three databases (Human, Mouse and Rat) can be used for hmmsearch. A notice will be sent to by email, after the whole process is finished. User can access the results using this account number (2fldmg
8m2f in example).
l Data retrieval
Users retrieve result by account number in “My Result “session
l Data access
Sections of Result Access a. access the raw data and classification
View all: the raw output from HMMER, which could be used in other cross ref.
By GO, user annotates TF-regulated targets and has an insight in biological function of predicted transcriptome.
l Select one/more categories (molecular function/biological process/cellular
component) for further analysis
l Examples of gene clustering by level 3 biological process
User could click blue box for detail information of the grouped genes
b. Field searching: Retrieving results by i. Gene name/descriptions ex: FGF, growth fact ii. Gene Ontology term/Key words ex: growth, metabolism
c. ENSG searching: Retrieving subset of results
by known ENSG ID (list) ex: ENSG00000129991
d. AFFY ID searching: Retrieving subset of results
by known AFFYMETRIX microarray ID (list) ex: 205742_at
ENSG ID: the gene ID in ensemble database
Gene: HUGO ID
Gene description: full name of gene
ENST: the transcript IDs of the corresponding promoter sequence
Score: the bit score of found TF site in the promoter
Hit seq: the sequence of found TF site
Position: the position of found TF site related to transcription start site (TSS)
Orientation: the orientation of found TF site related to TSS.
GO characterization: the Gene Ontology classification of this gene in three categories.
InterPro characterization: the protein domain/family of the gene in interpro DB.