Perturbation
What happens when miR‑29 itself is changed? In primary human fibroblasts, miR‑29 is lowered or raised across three treatment cycles, and the effect is read in gene activity and in DNA methylation, always against time-matched controls.
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Each point is the average growth of the cells in one arm at one timepoint, relative to the start, with its standard error (SEM: how precisely the average is known across repeated runs). Lines that stay together mean treatment does not change how fast the cells multiply. This matters because if growth changed, every later difference could simply reflect faster- or slower-growing cultures; here it does not.
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Each point is the average reading of a transcriptomic clock — a statistical model that predicts age from gene expression, in model units, not calendar years — for one group at one timepoint, shown as the change from that arm's controls at T1. Points below the controls mean the clock reads lower with treatment; the shaded band is the SEM. This asks whether changing miR-29 moves expression-based age predictors, and in which direction.
The mimic baseline rests on three control samples.
Four FDR families are stored and they are not interchangeable. Showing {{fdrLabel}} — {{fdrNote}}
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Each bar shows whether a set of age-related genes tends to rise or fall over time when miR-29 is inhibited, compared with control. Bars to the right mean the set's genes tend to rise; bars to the left mean they tend to fall. For sets of genes that normally increase with age (‘UP’), falling is the opposite of ageing; for sets that normally decrease with age (‘DN’), rising is the opposite of ageing. The tag under each value says which way that bar points.
Each row repeats the signature test after leaving out one tissue at a time, so a reader can see whether any single tissue drives a result. Points that stay close together mean the result does not depend on one tissue. This is a robustness check, not a way of choosing signatures.
Activity is mean treatment minus mean own-arm control at the same timepoint — never a pooled reference across arms or timepoints. {{actDefinition}}
BH adjustment is within family, not across all 50 tests. {{famSizes}}
Each row is one transcription factor, pathway or regulator gene, and its two markers show how much its estimated activity shifts with the inhibitor and with the mimic, compared with each arm's own controls, with the sensitivity interval as a line. Markers right of zero mean higher activity with treatment, left of zero lower. This asks which regulators downstream of miR-29 change, and in which direction.
The two dials show the selected feature's activity shift with the inhibitor and with the mimic: the ring sweeps clockwise for an increase and counter-clockwise for a decrease, one full turn per 2.0 units. The dial shows size and direction only, so the interval and the p and q values are always printed beside it.
| Statistic | INH | MIM |
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Each bar counts the genes whose expression differs significantly between treated cells and their own controls at one timepoint, split into genes going up and genes going down. Taller bars mean more genes change at that timepoint. This shows when in the experiment the transcriptome responds most to each treatment.