Network-Based Disease Candidate Gene Prioritization: Towards Global Diffusion in Heterogeneous Association Networks
Joana P. Gonçalves,
INESC-ID Lisboa and IST –
Abstract:
Disease candidate gene prioritization addresses the association of genes with disease susceptibility. Network-based approaches have successfully exploited the connectivity of biological networks to compute a disease-relatedness score between candidate and known disease genes. Nonetheless, available strategies yield three major concerns: (1) most networks used rely exclusively on curated physical interactions, resulting in poor genome coverage and sparsity issues; (2) devised scores are often local and thus restrict the search to a limited neighborhood around known genes and ignore potentially informative indirect paths; (3) some methods disregard interaction confidence weights which could confer extra reliability.
Results: We hypothesized that capturing disease-relatedness at the interactome scale based on weighted gene associations integrated from heterogeneous sources is likely to outperform current methods lacking one of these features and proposed to combine a particular personalized ranking method with data from STRING. Our claim was confirmed in comparative leave-one-out cross-validation case studies assessing the impact of network density and coverage, score globality and confidence weights on the prioritization of candidate genes for 29 diseases. Finally, the proposed method was applied to Parkinson’s disease and proved effective to recover prior knowledge and unravel interesting genes which could be linked to several pathological mechanisms of the disease.
Date: 2011-Jan-28 Time: 14:00:00 Room: 336
For more information:
Upcoming Events
INESC Brussels HUB Winter Meeting 2023

This edition of the HUB Winter Meeting will be co-organised with Science Business and will take place on the 30 and 31 January, in Lisbon, at Instituto Superior Técnico, Department of Computer Science and Engineering.
Please see below a summary of the agenda, this will be updated on the INESC Brussels HUB website regularly (confirmed speakers and other relevant info). Places for onsite participation are limited so registration is mandatory. Online participants will be sent a ZOOM link for each specific session on the 27th January.
INESC Brussels HUB website: https://hub.inesc.pt/
Monday, 30 January
a) Digital Europe Programme & Chips Act: state of play and possibilities for INESC.
9h to 10h30 GMT
(Exclusive for INESC researchers and administrators).
b) Science Business: how can INESC tap into Science Business network, activities and communications tools.
(Exclusive for INESC researchers and administrators).
c) Networking Lunch (for all onsite participants).
d) Roundtable: From rhetoric to reality – Embedding international strategy in the DNA of research organisations.
(Closed-door, roundtable workshop, Chatham House rules, open to INESC researchers and administrators, external participants by invitation only).
e) Networking Dinner
(By invitation only – INESC researchers participating onsite in the event are elegible to join).
Tuesday, 31 January
f) Workshop: How they did it? Strategic positioning for structural success in Horizon Europe: a discussion of best practices.
(Exclusive for INESC researchers, administrators and international invited speakers).
g) The public consultation on European R&I Programmes: Towards FP10.
(Closed-door, roundtable workshop, Chatham House rules, open to INESC researchers and administrators, external participants by invitation only).
h) Networking Lunch (for all onsite participants).
i) Management Committee meeting (Directors and POB members)
The HUB Winter Meeting aims at bringing together researchers and administrators from the 5 INESC institutes, affiliated higher education institutions in Portugal and abroad, with key European and global players, to:
– Discuss key research and innovation issues at EU level.
– Inform institutional policy and strategy.
– Exchange best-practices about R&I management, career development and policy positioning.
– Promote, discuss and deliver vision, visibility, networking and impactful communication.
– Create, identify and deepen partnerships and collaboration opportunities for collaborative R&I.