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Neuropathology and miRNA expression

Neuropathology in the posterior cingulate cortex, as measured by Braak stage, CERAD score, and NIA-Reagan score, present as hubs with miRNA spokes for those species whose expression correlated (rho).

Fruchterman Reingold colored by hubs

ForceAtlas 2 colored by hubs

MultiGravity ForceAtlas 2 colored by hubs

Yifan-Hu proportional colored by hubs

Subject characteristics and miRNA expression

Subject characteristics, age at death and biological sex, are hubs and miRNA are spokes where expression correlated (rho).

ForceAtlas 2 + Fruchterman Reingold colored by hubs

Cognitive test performance and miRNA expression

Performance on cognitive test battery as individual tests or composite domain scores as hubs with miRNA spokes where expression level correlates (rho).

Yifan-Hu colored by positive/negative correlation

Yifan-Hu colored by hubs

Fruchterman Reingold colored by hub

Fruchterman Reingold colored by positive/negative correlation

Fruchterman Reingold colored by hubs

Fruchterman Reingold colored by hubs

ForceAtlas 2 + Fruchterman Reingold colored by positive/negative correlation

Fruchterman Reingold colored by hubs and positive/negative correlation

Fruchterman Reingold colored by hubs and positive/negative correlation

Fruchterman Reingold colored by hubs and positive/negative correlation

mRNA expression and miRNA expression

mRNA and miRNA with expression significantly associated with Braak stage and evidence in literature or databases for regulatory (functional) or mechanical interaction.

Fruchterman Reingold colored by increased/decreased miRNA expression relative to Braak stage

Fruchterman Reingold colored by increased/decreased mRNA expression relative to Braak stage

Fruchterman Reingold colored by increased/decreased mRNA and miRNA expression relative to Braak stage

Fruchterman Reingold colored by increased/decreased miRNA expression relative to Braak stage

Fruchterman Reingold colored by increased/decreased miRNA expression relative to Braak stage

Yifan Hu colored by increased/decreased miRNA expression relative to Braak stage

Network plots are useful for pattern detection and visualization of large amounts of data. The data used to make the plots is user-defined and directly related to the layout. The color is applied after layout and may or may not correspond to layout appearance. The above plots were made using Gephi which employs force-directed, magnetic, or gravitational rules of attraction. In my experience these plots correspond to agglomerative hierarchical clustering without imputing a distance formula on the data outside of the algorithm used within Gephi. While network plots (and graphical learning) can be useful in data analysis, they are sometimes just the most comprehensive way of presenting data. This is the current use. As such, I present layouts associated with different algorithms and each plot is labeled by the algorithm. In these plots, correlation (rho) was used to define strength of attraction. For some algorithm physical distance on image has meaning (force atlas) and for some it does not (Fructerman-Reingold). Further information on the data used can be found in the publication.

Note on networks