Step-wise instruction
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Construction of model
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1.
Input sequences in
FASTA
format/pre-aligned MSF
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2.
Multiple alignment via clustalW
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3.
Construct model by Hmmer2.0 package
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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 (2fldmg8m2f
in example).
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Data retrieval
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Users retrieve result by account
number in “My Result “session
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Data access
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Sections of Result Access
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a.
access the
raw data and classification
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View all:
the raw output from HMMER, which could be used in other cross ref.
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GO clustering:
By GO, user annotates
TF-regulated targets and has an insight in biological function of predicted transcriptome.
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l Select one/more categories
(molecular function/biological process/cellular
component) for further analysis
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Examples of gene clustering by level
3 biological process
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User could click blue box for detail
information of the grouped genes
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b.
Field searching:
Retrieving
results by |
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i.
Gene name/descriptions ex: FGF, growth fact |
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ii.
Gene Ontology term/Key words ex: growth, metabolism
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c.
ENSG searching:
Retrieving
subset of results
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by known ENSG ID (list) ex: ENSG00000129991
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d.
AFFY ID searching:
Retrieving
subset of results |
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by
known AFFYMETRIX microarray ID (list) ex:
205742_at
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Typical output
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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.
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