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Correlated gene expression supports synchronous activity in brain networks

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Science  12 Jun 2015:
Vol. 348, Issue 6240, pp. 1241-1244
DOI: 10.1126/science.1255905

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  • distance is not everything - reply to the 'mind the distance' eLetter
    • Jonas Richiardi, University of Geneva
    • Other Contributors:
      • Andre Altmann, University College London
      • Michael Greicius, Stanford University

    A detailed reply to the eLetter by Pantazatos and Li has been posted at https://doi.org/10.1101/132746, showing that our original results stand. We provide a short summary here for convenience.

    To a first approximation, all connectivity, like all politics, is local and these two features -- nearness and connectivity -- are challenging to disentangle. Evidence abounds that the majority of connectivity is local, but this critical attribute of functional anatomy is perhaps most efficiently conveyed in a macaque tracer study by Markov et al (2012, see in particular Figure 7). Thus, in undertaking our analysis, we were well aware that spatial nearness is correlated with connectivity, which we addressed using a measure of "fine" tissue-tissue similarity derived from an ontological atlas provided by the Allen Institute. The peer-reviewers at Science were also aware of this confound and insisted on an additional level of tissue-tissue similarity correction which our analysis survives (note that Data File S1 of our paper also included information about "coarse" tissue classes (field coarse_tissue_class)).

    The commenters suggest that the tissue-tissue similarity correction we applied is inadequate and point out that in the brain samples we used there remains a significant linear correlation between Euclidean distance and correlated gene expression between brain regions. The r-value for this correlation i...

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    Competing Interests: None declared.
  • Mind the distance: high within-network strength fraction is entirely attributable to spatial proximity and is unrelated to resting-state brain networks
    • Spiro Pantazatos, Research Scientist/Assistant Professor of Clinical Neurobiology, New York State Psychiatric Institute/Columbia University
    • Other Contributors:
      • Xinyi Li, Masters Candidate, Columbia University Depart of Biomedical Informatics

    This is a novel and very interesting study. However, the authors do not adequately control for spatial proximity, which, contrary to the authors’ claims in the original article, accounts entirely for high within-network strength fraction according to our recent replication/reanalysis of these same data. Furthermore, “null networks”, (i.e. contiguous clusters with center coordinates randomly placed throughout cortex), also have significantly high strength fractions, indicating that high within-network strength fraction is not related to resting-state networks identified by fMRI.

    Here is a link to the full technical commentary and replication/reanalysis write-up with additional supplementary discussion: http://biorxiv.org/content/early/2016/10/04/079202

    And here is a link to the replication/reanalysis code on Github: https://github.com/spiropan/ABA_functional_networks

    The lead authors are aware of these findings and concerns (I notified them via personal email in March, 2016) and they have let me know they plan to respond. I have submitted the commentary for peer review to Frontiers in Neuroscience. If accepted, they have the option to publish a formal rebuttal/response letter there, and/or respond in the comments section here.

    Commentary Abstract

    A recent report claims that functional brain networks defined wit...

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    Competing Interests: None declared.