wellslab/HTR_Transcriptome

HTR Transcriptome (Thesis chapter)

HTR_Transcriptome

Data

• https://human.brain-map.org/static/download
• https://gtexportal.org/home/tissueSummaryPage

Analysis Based on

• https://jokergoo.github.io/ComplexHeatmap-reference/book/index.html for heatmaps
• https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4937821/ for data pre-processing and DEG
• https://f1000research.com/articles/9-1444 for design matrix
• http://genomicsclass.github.io/book/ for statistics

File name: GTEX_subsetting

Code function:

splitting the GTEX data into system-specific data sets

Location in Results:

Classifying the HTRs by Shared Pattern of Expression (Thesis Chapter Two: Materials and Methods)

File name: GTEX_propersampling

Code function:

making a small data set with 25 randomly selected sample from each tissue

Location in Results:

Classifying the HTRs by Shared Pattern of Expression (Thesis Chapter Two: Materials and Methods)

File name: GTEX_filtering

Code function:

setting the threshold for detection

Location in Results:

Classifying the HTRs by Shared Pattern of Expression (Thesis Chapter Two: Materials and Methods)

File name: GTEX_detection_data

Code function:

creating the probabilityXtissue matrix for HTR detection percentage

Location in Results:

HTRs Can be Grouped by Tissue Distribution (Thesis Chapter Four: The Specialised Expression Patterns of HTRs: A Family of Diverse Roles in Tissues)

File name: GTEX_detection

Code function:

making heatmaps using the percentage of reproducible detection calculated before

Location in Results:

HTRs Can be Grouped by Tissue Distribution (Thesis Chapter Four: The Specialised Expression Patterns of HTRs: A Family of Diverse Roles in Tissues)

File name: GTEX_htr_df_build

Code function:

shorten the dataframe just to have the HTR genes

Location in Results:

HTRs Can be Grouped by Tissue Distribution (Thesis Chapter Four: The Specialised Expression Patterns of HTRs: A Family of Diverse Roles in Tissues)

File name: AllenBrain_filtering

Code function:

evaluation the threshold of expression detection

Location in Results:

Classifying the HTRs in Brain by Relative Abundance of Expression (Thesis Chapter Two: Materials and Methods)

File name: AllenBrain_compare_donor

Code function:

compare the two donors to see if they can be treated as replicates

Location in Results:

Classifying the HTRs in Brain by Relative Abundance of Expression (Thesis Chapter Two: Materials and Methods)

File name: AllenBrain_qc

Code function:

go through quality-control checkpoints

Location in Results:

Classifying the HTRs in Brain by Relative Abundance of Expression (Thesis Chapter Two: Materials and Methods)

File name: AllenBrain_abundance

Code function:

look at the relative abundance of the HTR in brain tissues

Location in Results:

Five Patterns of HTR Expression Exists in the Brain (Thesis Chapter Four: The Specialised Expression Patterns of HTRs: A Family of Diverse Roles in Tissues)

File name: AllenBrain_lm

Code function:

fit the data to the linear model, look for variability across tissues, account for donor variability

Location in Results:

Five Patterns of HTR Expression Exists in the Brain (Thesis Chapter Four: The Specialised Expression Patterns of HTRs: A Family of Diverse Roles in Tissues)