"Algumas ferramentas para
pesquisar a história dos genes participantes de um fenômeno"
J. Miguel Ortega, miguel@ufmg.br, Lab. Biodados
UFMG
1. Informação já disponível em bases secundárias
a.
KEGG
disease:
H00031 (Breast
cancer)
b.
KEGG Pathways:
Pathways in
cancer & Transcriptional
misregulation in cancer
c.
OMIM entry #114480:
BREAST CANCER
2. Como criar um pathway
com a ferramenta de mineração PESCADOR
a. Query PubMed with:
breast cancer - mais
de 200 mil resumos
b.
Save the PubMed ID list -
Send to: (o) File, Format: PMID List
c.
Choose training set - select informative abstracts
manually or copy from KEGG
d.
Open MedLineRanker
e.
Prepare the form as below and press “Rank it”
The query
topic (the training set) is defined by:
· the
following list of PMIDs
paste the trainning set in the
box
The reference (the background set)
is defined by:
· the
following list of PMIDs
paste the saved PMID List in the Box
The abstracts to be ranked (the
test set) are defined by:
· the
background set
f.
Either select/copy after p-value or submit all (up to 1000) to PESCADOR
g.
Add customized concepts (splicing) in: Load below the biological concepts to be checked for
h.
Save PESCADOR ID = Your request ID is 1328022653
i.
See the Reports from NLProt
and from LAITOR
j.
Manually
inspect the results!