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hagenaue / FrontalPole_Microarray

Reanalysis of public frontal pole (BA10) microarray data to accompany our qPCR project examining neurotransmission-related gene expression in the frontal pole in relationship to Bipolar Disorder and Schizophrenia.
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Outputting boxplots for top genes from Adriana's PCR dataset #6

Closed hagenaue closed 3 years ago

hagenaue commented 3 years ago

From both Maycox and Iwamoto:

Diagnosis boxplots for:

Genes: HTR2B DRD4 MAOB SST MAPK1 GPHN ABAT

Sample Code (to match the other boxplots in the paper): "SampleBoxplots.R" https://github.com/hagenaue/FrontalPole_Microarray/blob/main/SampleBoxplots.R

hagenaue commented 3 years ago

Iwamoto also has these additional diagnosis-related exploratory variables: LifetimeAlcohol LifetimeDrugs PsychoticFeature SmokingAtTimeOfDeath SuicideStatus

It would be useful to have diagnosis*exploratory variable boxplots for each of the top genes (listed above) for either: 1) each exploratory variable (i.e., via a loop), or 2) these exploratory variables that looked meaningful from Adriana's data:

SST vs. (basically everything) PsychoticFeature LifetimeAlcohol LifetimeDrugs SmokingAtTimeOfDeath SuicideStatus (maybe?)

MAPK1 vs. LifetimeDrugs LifetimeAlcohol (maybe) SuicideStatus (maybe)

MAOB vs. LifetimeDrugs SmokingAtTimeOfDeath

HTR2B vs. SuicideStatus (maybe) LifetimeDrugs

GPHN vs. LifetimeDrugs

DRD4 vs. PsychoticFeature LifetimeDrugs LifetimeAlcohol SuicideStatus

ABAT vs. LifetimeDrugs

hagenaue commented 3 years ago

More top genes to look at in relationship to diagnosis: DRD2 GAPDH HTR6 MAOA REEP5 TFRC AQP4 CALB1 GABBR2 GABRD GABRG1 GAD1 GFAP GJA1 GNAQ NSF PVALB S100B SLC1A2 SLC1A3 SLC6A1 SC6A11 SLC6A13 SLC38A1 TBP