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Supplementary Data for Detecting Spatial Dependency in Gene Expression

dataset
posted on 14.01.2020 by Naihui Zhou, Iddo Friedberg, Mark Kaiser
Intermediate results using the IMR90 and GM12878 cell lines for detection of spatial dependency in quantitative gene expression in the 3D genome.
Generated using https://github.com/ashleyzhou972/bioMRF.

Glossary:
- PhiMRF data: input data needed for PhiMRF, adjacency matrix and count matrix, in rds format.
- PhiMRF results: output data from PhiMRF, list of posterior distributions, in rds format.
- See https://github.com/ashleyzhou972/PhiMRF for details


Note: GM12878_10kb_inter.tar.gz is split into parts due to upload size restriction
Join the parts back using the cat command:
```
cat GM12878_10kb_inter.parta*>GM12878_10kb_inter.tar.gz
```

Directory:

-- | IMR90_10kb_rnaseq.tar.gz
-- | -- | ENCFF353SBP.tsv : Raw RNA-seq quantification file from ENCODE
-- | -- | ENCFF496RIW.tsv : Raw RNA-seq quantification file from ENCODE
-- | -- | rnaseq_ENCFF353SBP.txt : Processed RNA-seq file
-- | -- | rnaseq_ENCFF496RIW.txt : Processed RNA-seq file
-- | -- | gene_names : Folder of gene names saved in rds format, by chromosome

-- | IMR90_10kb_intra.tar.gz
-- | -- | norm : Folder of normalized HiC counts mapped to gene, by chromosome
-- | -- | genepairs : Folder of normalized HiC count collapsed by gene pair, by chromosome
-- | -- | info : Folder of network info saved in rds format, by chromosome
-- | -- | linear : Folder of PhiMRF data saved in rds format, for linear gene networks, by chromosome
-- | -- | data : Folder of PhiMRF data saved in rds format, for linear gene networks, by chromosome
-- | -- | results : Folder of PhiMRF results, for four summary statistics, by chromosome

-- | IMR90_10kb_inter.tar.gz
-- | -- | norm : Folder of normalized HiC counts mapped to gene, by chromosome pair
-- | -- | genepairs : Folder of normalized HiC count collapsed by gene pair, by chromosome pair
-- | -- | info : Folder of network info saved in rds format, by chromosome pair
-- | -- | data : Folder of PhiMRF data saved in rds format, by chromosome pair
-- | -- | results : Folder of PhiMRF results, by chromosome pair

-- | IMR90_10kb_wholeGenome.tar.gz
-- | -- | all_data : Folder of PhiMRF data saved in rds format, for the combined (intra- and inter-) data of the whole genome

-- | IMR90_10kb_TADs.tar.gz
-- | -- | data
-- | -- | -- | all_edges : Folder of PhiMRF data saved in rds format, for TAD genes, by chromosome
-- | -- | -- | intra_edges : Folder of PhiMRF data saved in rds format, for TAD genes, and intra-TAD edges, by chromosome
-- | -- | -- | inter_edges : Folder of PhiMRF data saved in rds format, for TAD genes, and inter-TAD edges, by chromosome
-- | -- | results
-- | -- | -- | all_edges : Folder of PhiMRF results, for TAD genes, by chromosome
-- | -- | -- | intra_edges : Folder of PhiMRF results, for TAD genes, and intra-TAD edges, by chromosome
-- | -- | -- | inter_edges : Folder of PhiMRF results, for TAD genes, and inter-TAD edges, by chromosome

-- | IMR90_10kb_functional.tar.gz
-- | -- | data
-- | -- | -- | GO:0000122_False_data : Folder of PhiMRF data saved in rds format, for genes annotated with GO:0000122, not propagated
-- | -- | -- | ... (18 folders ommited)
-- | -- | -- | GO:0045944_False_data : Folder of PhiMRF data saved in rds format, for genes annotated with GO:0045944, not propagated
-- | -- | results
-- | -- | -- | ret_GO:0000122_False.rds : PhiMRF results, for genes annotated with GO:0000122, not propagated
-- | -- | -- | ... (18 files ommited)
-- | -- | -- | ret_GO:0045944_False.rds : PhiMRF results, for genes annotated with GO:0045944, not propagated

-- | IMR90_10kb_sheets.tar.gz
-- | -- | intra_all_mean_table3.csv : Parameter estimates (mean, 95% credible interval), using mean as summary, by chromosome
-- | -- | intra_all_max_table3.csv : Parameter estimates (mean, 95% credible interval), using max as summary, by chromosome
-- | -- | intra_all_median_table3.csv : Parameter estimates (mean, 95\% credible interval), using median as summary, by chromosome
-- | -- | intra_all_min_table3.csv : Parameter estimates (mean, 95% credible interval), using min as summary, by chromosome
-- | -- | linear_all_table3.csv : Parameter estimates (mean, 95% credible interval), of all linear networks, by chromosome
-- | -- | inter_pair_all_table3.csv : Parameter estimates (mean, 95\% credible interval), by chromosome pair
-- | -- | TADs_eta_table.csv : Parameter estimates (mean, 95\% credible interval) of TAD genes, by chromosome
-- | -- | TADs_intra_eta_table.csv : Parameter estimates (mean, 95\% credible interval) of TAD genes, and intra-TAD edges, by chromosome
-- | -- | TADs_inter_eta_table.csv : Parameter estimates (mean, 95\% credible interval) of TAD genes, and inter-TAD edges, by chromosome
-- | -- | functional_nopropagate_all_table3.csv : Parameter estimates (mean, 95\% credible interval) of functional genes

-- | GM12878_10kb_rnaseq.tar.gz
-- | -- | ENCFF680ZFZ.tsv : Raw RNA-seq quantification file from ENCODE
-- | -- | ENCFF781YWT : Raw RNA-seq quantification file from ENCODE
-- | -- | rnaseq_ENCFF680ZFZ.txt : Processed RNA-seq file
-- | -- | rnaseq_ENCFF781YWT.txt : Processed RNA-seq file
-- | -- | gene_names : Folder of gene names saved in rds format, by chromosome

-- | GM12878_10kb_intra.tar.gz
-- | -- | norm : Folder of normalized HiC counts mapped to gene, by chromosome
-- | -- | genepairs : Folder of normalized HiC count collapsed by gene pair, by chromosome
-- | -- | info : Folder of network info saved in rds format, by chromosome
-- | -- | linear : Folder of PhiMRF data saved in rds format, for linear gene networks, by chromosome
-- | -- | data : Folder of PhiMRF data saved in rds format, for linear gene networks, by chromosome
-- | -- | results : Folder of PhiMRF results, for four summary statistics, by chromosome

-- | GM12878_10kb_inter.tar.gz
-- | -- | norm : Folder of normalized HiC counts mapped to gene, by chromosome pair
-- | -- | genepairs : Folder of normalized HiC count collapsed by gene pair, by chromosome pair
-- | -- | info: Folder of network info saved in rds format, by chromosome pair
-- | -- | data Folder of PhiMRF data saved in rds format, by chromosome pair
-- | -- | results: Folder of PhiMRF results, by chromosome pair

-- | GM12878_10kb_wholeGenome.tar.gz
-- | -- | all_data : Folder of PhiMRF data saved in rds format, for the combined (intra- and inter-) data of the whole genome

-- | GM12878_10kb_sheets.tar.gz
-- | -- | intra_all_table3.csv : Parameter estimates (mean, 95% credible interval), using mean as summary, by chromosome
-- | -- | linear_all_table3.csv : Parameter estimates (mean, 95% credible interval), of all linear networks, by chromosome
-- | -- | inter_pair_all_table3.csv : Parameter estimates (mean, 95\% credible interval), by chromosome pair

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