Journal: Scientific Reports

Article Title: Identifying chromatin features that regulate gene expression distribution

doi: 10.1038/s41598-020-77638-2

Figure Lengend Snippet: Identification of key transcription factors associated with reporter expression levels and noises using multivariate linear regression analysis. ( A ) View of the barcode 29 locus on chromosome 1. Genome coordinate of each barcode was obtained from conducting TRIP experiment. Six examples of normalized ChIP-seq signal profile of transcription factor surrounding the integration site of the barcode 29 were visualized for a domain of 50 kb. ( B ) The heatmap showing the correlation between the enrichment of transcription factors and reporter expression mean and noise. Transcription factors with Spearman's rank-order correlation coefficient of more than 0.2 were selected from over 200 tested transcription factors. ( C , D ) To understand the relationship between the enrichment of TF and the expression levels ( C ) and noise ( D ) of reporter in an integrative way, we selected transcription factors showing a significant correlation in ( B ) to fit multivariate linear regression model. Features with a significant level above the threshold or dashed line (p < 0.05) contributed significantly to the model. ( E ) A Venn diagram listing transcription factors contributing to reporter expression mean (green) and noise (red).

Article Snippet: The analysis of statistical significance was done using standard multivariate regression analysis (using the Matlab command fitlm).

Techniques: Expressing, ChIP-sequencing

Journal: Scientific Reports

Article Title: Identifying chromatin features that regulate gene expression distribution

doi: 10.1038/s41598-020-77638-2

Figure Lengend Snippet: Distance to specific chromatin states influences expression mean and variance ( A ) Nearest distance from the barcode location to each chromatin state segmented by ChromHMM method was calculated. ( B ) The correlation plot between distance to specific chromatin state and reporter expression mean or noise. ( C ) A multivariate linear regression model was used to determine significant chromatin states influencing reporter expression mean and noise. Panels show the student t statistics and p-values of each coefficient in the model for expression mean (top) and noise (bottom). Chromatin states are color-coded.

Article Snippet: The analysis of statistical significance was done using standard multivariate regression analysis (using the Matlab command fitlm).

Techniques: Expressing

Journal: Scientific Reports

Article Title: Similar contrast sensitivity functions measured using psychophysics and optokinetic nystagmus

doi: 10.1038/srep34514

Figure Lengend Snippet: ( a ) The mean total distance moved by the eye of one observer that was consistent with OKN in the stimulus direction, for 16 drifting noise trials across five spatial frequencies, and eight velocities. Note substantially more OKN consistent motion at lower SFs. ( b ) As ( a ) but showing the total proportion of eye movements consistent with OKN in the stimulus direction (C θ ). ( c ) The optimum velocity (derived from log-Gaussian fits to 6 observers similar to ( b )) as a function of SF. ( d ) As for ( c ) but showing the amplitude of the log-Gaussian fit (a measure of signal-to-noise ratio) which does not show a strong dependence on SF, within observer.

Article Snippet: Patterns were two-dimensional Gaussian noise (made with the randn command in Matlab), filtered to be isotropic and spatial-frequency (SF) band-pass ( ).

Techniques: Derivative Assay