=== qrtpcr_human_tissues.tbl.txt.bz2
##ColumnVariables[Primer_Name] = name of the qRT-PCR primer
##ColumnVariables[Entrez] = Entrez Gene ID of the primer target
##ColumnVariables[Symbol] = Entrez Gene Symbol of the primer target
##ColumnVariables[Adipose] = normalized copy number of the expression in Adipose, where higher copy number indicates higher expression
##ColumnVariables[Adrenal_Gland] = normalized copy number of the expression in Adrenal_Gland, where higher copy number indicates higher expression
##ColumnVariables[Bone_Marrow] = normalized copy number of the expression in Bone_Marrow, where higher copy number indicates higher expression
##ColumnVariables[Breast] = normalized copy number of the expression in Breast, where higher copy number indicates higher expression
##ColumnVariables[Cerebellum] = normalized copy number of the expression in Cerebellum, where higher copy number indicates higher expression
##ColumnVariables[Fetal_Brain] = normalized copy number of the expression in Fetal_Brain, where higher copy number indicates higher expression
##ColumnVariables[Fetal_Liver] = normalized copy number of the expression in Fetal_Liver, where higher copy number indicates higher expression
##ColumnVariables[Fetal_Lung] = normalized copy number of the expression in Fetal_Lung, where higher copy number indicates higher expression
##ColumnVariables[Frontal_Cortex] = normalized copy number of the expression in Frontal_Cortex, where higher copy number indicates higher expression
##ColumnVariables[Heart] = normalized copy number of the expression in Heart, where higher copy number indicates higher expression
##ColumnVariables[Kidney] = normalized copy number of the expression in Kidney, where higher copy number indicates higher expression
##ColumnVariables[Liver] = normalized copy number of the expression in Liver, where higher copy number indicates higher expression
##ColumnVariables[Lung] = normalized copy number of the expression in Lung, where higher copy number indicates higher expression
##ColumnVariables[Lymph_Node] = normalized copy number of the expression in Lymph_Node, where higher copy number indicates higher expression
##ColumnVariables[Occipital_Cortex] = normalized copy number of the expression in Occipital_Cortex, where higher copy number indicates higher expression
##ColumnVariables[Ovary] = normalized copy number of the expression in Ovary, where higher copy number indicates higher expression
##ColumnVariables[Pancreas] = normalized copy number of the expression in Pancreas, where higher copy number indicates higher expression
##ColumnVariables[Parietal_Cortex] = normalized copy number of the expression in Parietal_Cortex, where higher copy number indicates higher expression
##ColumnVariables[Placenta] = normalized copy number of the expression in Placenta, where higher copy number indicates higher expression
##ColumnVariables[Prostate] = normalized copy number of the expression in Prostate, where higher copy number indicates higher expression
##ColumnVariables[Salivary_Gland] = normalized copy number of the expression in Salivary_Gland, where higher copy number indicates higher expression
##ColumnVariables[Skeletal_Muscle] = normalized copy number of the expression in Skeletal_Muscle, where higher copy number indicates higher expression
##ColumnVariables[Skin] = normalized copy number of the expression in Skin, where higher copy number indicates higher expression
##ColumnVariables[Smooth_Muscle] = normalized copy number of the expression in Smooth_Muscle, where higher copy number indicates higher expression
##ColumnVariables[Spinal_Cord] = normalized copy number of the expression in Spinal_Cord, where higher copy number indicates higher expression
##ColumnVariables[Spleen] = normalized copy number of the expression in Spleen, where higher copy number indicates higher expression
##ColumnVariables[Testis] = normalized copy number of the expression in Testis, where higher copy number indicates higher expression
##ColumnVariables[Thymus] = normalized copy number of the expression in Thymus, where higher copy number indicates higher expression
##ColumnVariables[Thyroid] = normalized copy number of the expression in Thyroid, where higher copy number indicates higher expression
##ColumnVariables[Trachea] = normalized copy number of the expression in Trachea, where higher copy number indicates higher expression
##ColumnVariables[Uterus] = normalized copy number of the expression in Uterus, where higher copy number indicates higher expression
##ColumnVariables[Whole_Brain] = normalized copy number of the expression in Whole_Brain, where higher copy number indicates higher expression
##ColumnVariables[THP-1] = normalized copy number of the expression in THP-1, where higher copy number indicates higher expression
##ColumnVariables[THP-1+PMA] = normalized copy number of the expression in THP-1 after stimulation with PMA, where higher copy number indicates higher expression
# this file is converted from Table S5 of Cell 140(5):744-752
=== qrtpcr_pma_timecourse.tbl.txt.bz2
##ColumnVariables[id] = primer name
##ColumnVariables[chrom] = The name of the chromosome
##ColumnVariables[start] = The starting position of the cluster in the chromosome. The first base in a chromosome is numbered 1 (conventional 1-based coordinate system)
##ColumnVariables[end] = The ending position of the feature in the chromosome
##ColumnVariables[FWD] = forward primer sequnece
##ColumnVariables[REV] = reverse primer sequence
##ColumnVariables[EntrezGene_id] = EntrezGene ID
##ColumnVariables[EntrezGene_symbol] = gene symbol of the EntrezGene
##ColumnVariables[EntrezGene_synonyms] = synonyms of the EntrezGene
##ColumnVariables[status] = mapping status of the primer pair onto the genome and EntrezGene
##ColumnVariables[norm.RIKEN1_PMA_0h] = normalized copy number at PMA_0h of the biological replicate RIKEN1
##ColumnVariables[norm.RIKEN1_PMA_1h] = normalized copy number at PMA_1h of the biological replicate RIKEN1
##ColumnVariables[norm.RIKEN1_PMA_2h] = normalized copy number at PMA_2h of the biological replicate RIKEN1
##ColumnVariables[norm.RIKEN1_PMA_4h] = normalized copy number at PMA_4h of the biological replicate RIKEN1
##ColumnVariables[norm.RIKEN1_PMA_6h] = normalized copy number at PMA_6h of the biological replicate RIKEN1
##ColumnVariables[norm.RIKEN1_PMA_12h] = normalized copy number at PMA_12h of the biological replicate RIKEN1
##ColumnVariables[norm.RIKEN1_PMA_24h] = normalized copy number at PMA_24h of the biological replicate RIKEN1
##ColumnVariables[norm.RIKEN1_PMA_48h] = normalized copy number at PMA_48h of the biological replicate RIKEN1
##ColumnVariables[norm.RIKEN1_PMA_72h] = normalized copy number at PMA_72h of the biological replicate RIKEN1
##ColumnVariables[norm.RIKEN1_PMA_96h] = normalized copy number at PMA_96h of the biological replicate RIKEN1
##ColumnVariables[raw.RIKEN1_PMA_0h] = Ct value at PMA_0h of the biological replicate RIKEN1
##ColumnVariables[raw.RIKEN1_PMA_1h] = Ct value at PMA_1h of the biological replicate RIKEN1
##ColumnVariables[raw.RIKEN1_PMA_2h] = Ct value at PMA_2h of the biological replicate RIKEN1
##ColumnVariables[raw.RIKEN1_PMA_4h] = Ct value at PMA_4h of the biological replicate RIKEN1
##ColumnVariables[raw.RIKEN1_PMA_6h] = Ct value at PMA_6h of the biological replicate RIKEN1
##ColumnVariables[raw.RIKEN1_PMA_12h] = Ct value at PMA_12h of the biological replicate RIKEN1
##ColumnVariables[raw.RIKEN1_PMA_24h] = Ct value at PMA_24h of the biological replicate RIKEN1
##ColumnVariables[raw.RIKEN1_PMA_48h] = Ct value at PMA_48h of the biological replicate RIKEN1
##ColumnVariables[raw.RIKEN1_PMA_72h] = Ct value at PMA_72h of the biological replicate RIKEN1
##ColumnVariables[raw.RIKEN1_PMA_96h] = Ct value at PMA_96h of the biological replicate RIKEN1
##ColumnVariables[norm.RIKEN3_PMA_0h] = normalized copy number at PMA_0h of the biological replicate RIKEN3
##ColumnVariables[norm.RIKEN3_PMA_1h] = normalized copy number at PMA_1h of the biological replicate RIKEN3
##ColumnVariables[norm.RIKEN3_PMA_2h] = normalized copy number at PMA_2h of the biological replicate RIKEN3
##ColumnVariables[norm.RIKEN3_PMA_4h] = normalized copy number at PMA_4h of the biological replicate RIKEN3
##ColumnVariables[norm.RIKEN3_PMA_6h] = normalized copy number at PMA_6h of the biological replicate RIKEN3
##ColumnVariables[norm.RIKEN3_PMA_12h] = normalized copy number at PMA_12h of the biological replicate RIKEN3
##ColumnVariables[norm.RIKEN3_PMA_24h] = normalized copy number at PMA_24h of the biological replicate RIKEN3
##ColumnVariables[norm.RIKEN3_PMA_48h] = normalized copy number at PMA_48h of the biological replicate RIKEN3
##ColumnVariables[norm.RIKEN3_PMA_72h] = normalized copy number at PMA_72h of the biological replicate RIKEN3
##ColumnVariables[norm.RIKEN3_PMA_96h] = normalized copy number at PMA_96h of the biological replicate RIKEN3
##ColumnVariables[raw.RIKEN3_PMA_0h] = Ct value at PMA_0h of the biological replicate RIKEN3
##ColumnVariables[raw.RIKEN3_PMA_1h] = Ct value at PMA_1h of the biological replicate RIKEN3
##ColumnVariables[raw.RIKEN3_PMA_2h] = Ct value at PMA_2h of the biological replicate RIKEN3
##ColumnVariables[raw.RIKEN3_PMA_4h] = Ct value at PMA_4h of the biological replicate RIKEN3
##ColumnVariables[raw.RIKEN3_PMA_6h] = Ct value at PMA_6h of the biological replicate RIKEN3
##ColumnVariables[raw.RIKEN3_PMA_12h] = Ct value at PMA_12h of the biological replicate RIKEN3
##ColumnVariables[raw.RIKEN3_PMA_24h] = Ct value at PMA_24h of the biological replicate RIKEN3
##ColumnVariables[raw.RIKEN3_PMA_48h] = Ct value at PMA_48h of the biological replicate RIKEN3
##ColumnVariables[raw.RIKEN3_PMA_72h] = Ct value at PMA_72h of the biological replicate RIKEN3
##ColumnVariables[raw.RIKEN3_PMA_96h] = Ct value at PMA_96h of the biological replicate RIKEN3
# 
# 
# ---------------
# Normalization 
# ---------------
# 
# 1. Copy number conversion for each gene
# 
# We calculated copy numbers by using coefficients (slope and intercept)
# of standard curves which were obtained by using genomic DNA.
# 
#   raw copy number = 10 ^ { ( raw Ct value - intercept ) / slope }
# 
# 
# 2. Invariant Set (IS)
# 
# We looked for genes that retained their ordering across two experimental
# samples and considered this subset a rank invariant set. 
# (Because copy number below 40 is not reliable, we didnt include any
# invariant gene that has copy number < 40 in a invariant set.)
# 
# We found rank invariant sets for each possible pairwise combination of
# experimental samples within a time course and then took the intersection
# of all the invariant sets. 
# 
# 3. Scaling for each sample 
# 
# We scaled all copy numbers in each sample by the geometric average of
# copy number of the genes in the final invariant set. 
# The scale factor used is a ratio of the 2 geometric averages of copy numbers. 
# 
# For sample t, 
#   the scale factor = {geometric average expression of IS in control sample} / {geometric average expression of IS in sample t}
# 
# For gene g in sample t, 
#   normalized copy number = {copy number of gene g in sample t} * {the scale factor of sample t} 
# 
# The control sample here is PMA_0_hour
#