A measure of agreement across numerous conditions : Assessing when changes in network structures are tissue-specific
Cáceres, Alejandro (Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública)
González, Juan Ramón (Universitat Autònoma de Barcelona. Departament de Matemàtiques)

Fecha:	2019
Resumen:	Background: There is great interest to study how gene pathways change their structure across different tissues. The assessment of inter-study reliability of pathway changes across tissues can inform on the fraction of tissues with specific functional changes in network structure. However, there is a lack of agreement measures among studies that independently observe how a group of observations change across conditions. We, therefore, propose λ, a new inter-study reliability measure that determines the consistency to distinguish observations by condition. Results: We derived λ's distributional characteristics, determine its reliability properties and compared it with Cohen's κ. We studied the co-expression structure of 287 gene pathways across four brain regions in two transcriptomic studies and applied λ to assess the inter-study reliability of the pathways' brain-regional changes. Brain-related pathways showed highest λ; the top value was for the nicotine addiction pathway whose structure was reliably distinguishable among regions with dopaminergic projections. Conclusion: Our results offer novel substantial evidence that changes in network structure across tissues can be inferred independently of samples, algorithms and experiments (RNA-sequencing or microarrays). Reliability measures, such as λ, can inform on the tissues where changes in a network's structure are likely functional. An R package is available at https://github. com/isglobal-brge/lambda.
Ayudas:	Ministerio de Ciencia e Innovación MTM2015-68140-R
Nota:	Altres ajuts: Red Española de Supercomputación BCV-2016-3-0002
Derechos:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Lengua:	Anglès
Documento:	Article ; recerca ; Versió publicada
Materia:	Brain ; Transcriptome ; Co-expression networks ; Reliability ; Coehn'skappa ; GTEx ; RNA-sequencing ; Addiction ; Nicotine
Publicado en:	BMC genomics, Vol. 20 (January 2019) , art. 26, ISSN 1471-2164

DOI: 10.1186/s12864-018-5340-3
PMID: 30626339

13 p, 1.7 MB

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