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First paper
The focus for our first paper are cell type-specific QTLs for transcription and mRNA processing.
Outline and division of work (2014-05-21)
Todo list
- todo
Figures and Tables
Please create one subpage FgFirstPaper/FigureName per figure/table and put the underlying data there and an example plot. It will then be easy to make a polished set of plots from the underlying data.
Data and QC:
-- Table with number of samples per cohort and related statistics
- Table with general sequencing characteristics: average and range for
-- number of reads passing qc
-- number (percentage) of aligned reads
-- number (percentage) of aligned reads mapping to our annotated exons
-- number of detected genes (>0 count) per sample
- Graphs with:
-- GC distribution per biobank
-- RNA blood sampling age distribution per biobank
-- Genotype concordance per biobank
-- Heterozygosity per biobank
- Density plot of median Spearman correlations for genes and exons (Peter-Bram)
- MDS plot of Spearman correlations colored by GC such as this one (Peter-Bram)
- Significant correlations between PCs and sample characteristics
(Some of this can already be found at this page, this page, this page, and on normalization.)
QTLs general:
- The summary statistics table with the number of QTLs
- Table of the number of primary/secondary/tertiary effects. Details can be found on this page
- Histogram of genes with x independent QTLs
- Histogram of exons with x independent QTLs
- Venn diagram of gene-, transcript-, exon-level eQTLs overlap
- Replication results for GEUVADIS of gene level eQTLs and exon level eQTLs
- Replication in Array data (Westra et al, Wright et al (NTR+NESDA data)) (Dasha)
- Number of independent cis-effects after stepwise regression
- Distance to exon midpoint of top SNPs for exon/exon-ratio/polya QTLs
Gene eQTLs:
- distance top SNP relative to transcription start site
- distance top SNP relative to transcription end site
- Table of the number of cell-type specific effects. Details can be found on this page
- Top 10 TF binding sites enriched in global eQTL SNPs (Maarten)
- Top SNPs show a change in affinity for specific TF (Szymon)
- Interaction analysis (TF expression levels modify eQTL effect) overlapped with enriched TFs (Dasha and Maarten/Szymon?)
Exon eQTLs:
Exon-ratio QTLs:
- Distance of (top) SNP relative to exon start
- Classification of exons with exon-ratio QTLs (constitutive, cassette etc.)
- Overlap of QTL SNPs with donor/acceptor sites
- Enrichment of RNA-binding protein motifs (preliminary analysis)
- Example gene(s) (after overlapping with GWAS hits?)
Poly(A) QTLs:
- Distance of (top) SNP relative to polyadenylation site
- Overlap / enrichment of top SNP per poly(A) site with canonical and alternative poly(A) signals (Martijn)
- Example gene(s) (after overlapping with GWAS hits?)
Cell type-specific eQTLs and exon-ratio QTLs
- Table with number of Cell type-specific results for FDR 0.05 and 0.25 (Gene and exon ratio)
- TF binding and RNA binding protein analyses for cell-type specific eQTLs
Materials & Methods
Scripts and pipelines to deposit
Many things could (or already are) be deposited in GitHub or GitLab. It would be nice to have a page with a general overview of all scripts and pipelines.
Data to deposit
To be decided:
- Where to deposit? Molgenis site is nice for downstream results and browsing. Probably not for raw sequencing data.
- Primary data: fastq files, BAM files?
- Secondary data: expression/count files? Cell counts?
- For all QTL findings, what to deposit: all QTLs, only significant findings, or only the top hit per gene? All data, or just the SNP-probe pairs?
| Data | Location (on VM unless noted otherwise) |
|---|---|
| Gene eQTLs | /virdir/Backup/dzhernakova/LL+RS+CODAM+LLS_eqtls_genes_23062014/
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| Transcript eQTLs | /virdir/Backup/dzhernakova/LL+RS+CODAM+LLS_eqtls_transcr_01062014/
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| Exon eQTLs | /virdir/Backup/dzhernakova/LL+RS+CODAM+LLS_eqtls_meta-exons_28062014/
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| Basophil-specific gene-level QTLs (FDR 0.05) | /virdir/Backup/dzhernakova/LL+RS+CODAM+LLS_eqtls_genes_basophils_150714/
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| Eosinophil-specific gene-level QTLs (FDR 0.05) | /virdir/Backup/dzhernakova/LL+RS+CODAM+LLS_eqtls_genes_eosinophils_150714/
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| Lymphocyte-specific gene-level QTLs (FDR 0.05) | /virdir/Backup/dzhernakova/LL+RS+CODAM+LLS_eqtls_genes_lymphocytes_08062014/
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| Monocyte-specific gene-level QTLs (FDR 0.05) | /virdir/Backup/dzhernakova/LL+RS+CODAM+LLS_eqtls_genes_monocytes_150714/
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| Neutrophil-specific gene-level QTLs (FDR 0.05) | /virdir/Backup/dzhernakova/LL+RS+CODAM+LLS_eqtls_genes_neutrophils_150714/
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| [Basophil-specific gene-level QTLs (FDR 0.25)] | /virdir/Backup/dzhernakova/LL+RS+CODAM+LLS_eqtls_genes_basophils_fdr0.25_05082014
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| [Eosinophil-specific gene-level QTLs (FDR 0.25)] | /virdir/Backup/dzhernakova/LL+RS+CODAM+LLS_eqtls_genes_eosinophils_fdr0.25_05082014
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| [Lymphocyte-specific gene-level QTLs (FDR 0.25)] | /virdir/Backup/dzhernakova/LL+RS+CODAM+LLS_eqtls_genes_lymphocytes_fdr0.25_05082014
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| [Monocyte-specific gene-level QTLs (FDR 0.25)] | /virdir/Backup/dzhernakova/LL+RS+CODAM+LLS_eqtls_genes_monocytes_fdr0.25_05082014
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| [Neutrophil-specific gene-level QTLs (FDR 0.25)] | /virdir/Backup/dzhernakova/LL+RS+CODAM+LLS_eqtls_genes_neutrophils_fdr0.25_05082014
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| Exon-ratio QTLs | /virdir/Backup/RP3_data/exon-ratio-qtls/2014-07-23
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| Exon-ratio QTLs (secondary effects) | /virdir/Backup/RP3_data/exon-ratio-qtls/snps-present-in-all-datasets-secondary-2014-09-10
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| Exon-ratio QTLs (tertiary effects) | /virdir/Backup/RP3_data/exon-ratio-qtls/snps-present-in-all-datasets-tertiary-2014-09-10
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| Basophil-specific exon-ratio QTLs (FDR 0.05) | /virdir/Backup/RP3_data/exon-ratio-qtls/basophils-2014-08-16
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| Eosinophil-specific exon-ratio QTLs (FDR 0.05) | /virdir/Backup/RP3_data/exon-ratio-qtls/eosinophils-2014-08-16
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| Lymphocyte-specific exon-ratio QTLs (FDR 0.05) | /virdir/Backup/RP3_data/exon-ratio-qtls/lymphocytes-2014-08-16
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| Monocyte-specific exon-ratio QTLs (FDR 0.05) | /virdir/Backup/RP3_data/exon-ratio-qtls/monocytes-2014-08-16
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| Neutrophil-specific exon-ratio QTLs (FDR 0.05) | /virdir/Backup/RP3_data/exon-ratio-qtls/neutrophils-2014-08-16
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| Basophil-specific exon-ratio QTLs (FDR 0.25) | /virdir/Backup/RP3_data/exon-ratio-qtls/basophils-2014-09-03
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| Eosinophil-specific exon-ratio QTLs (FDR 0.25) | /virdir/Backup/RP3_data/exon-ratio-qtls/eosinophils-2014-09-03
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| Lymphocyte-specific exon-ratio QTLs (FDR 0.25) | /virdir/Backup/RP3_data/exon-ratio-qtls/lymphocytes-2014-09-03
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| Monocyte-specific exon-ratio QTLs (FDR 0.25) | /virdir/Backup/RP3_data/exon-ratio-qtls/monocytes-2014-09-03
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| Neutrophil-specific exon-ratio QTLs (FDR 0.25) | /virdir/Backup/RP3_data/exon-ratio-qtls/neutrophils-2014-09-03
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| Poly(A) QTLs | /virdir/Backup/RP3_data/polya-qtls/2014-06-20
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| Poly(A) QTLs (secondary effects) | /virdir/Backup/RP3_data/polya-qtls/snps-present-in-all-datasets-secondary-2014-09-29
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| Poly(A) QTLs (tertiary effects) | /virdir/Backup/RP3_data/polya-qtls/snps-present-in-all-datasets-tertiary-2014-09-30
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| Basophil-specific poly(A) QTLs (FDR 0.05) | /virdir/Backup/RP3_data/polya-qtls/basophils-2014-08-18
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| Eosinophil-specific poly(A) QTLs (FDR 0.05) | /virdir/Backup/RP3_data/polya-qtls/eosinophils-2014-08-19
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| Lymphocyte-specific poly(A) QTLs (FDR 0.05) | /virdir/Backup/RP3_data/polya-qtls/lymphocytes-2014-08-19
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| Monocyte-specific poly(A) QTLs (FDR 0.05) | /virdir/Backup/RP3_data/polya-qtls/monocytes-2014-08-19
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| Neutrophil-specific poly(A) QTLs (FDR 0.05) | /virdir/Backup/RP3_data/polya-qtls/neutrophils-2014-08-19
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| Basophil-specific poly(A) QTLs (FDR 0.25) | /virdir/Backup/RP3_data/polya-qtls/basophils-2014-09-04
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| Eosinophil-specific poly(A) QTLs (FDR 0.25) | /virdir/Backup/RP3_data/polya-qtls/eosinophils-2014-09-04
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| Lymphocyte-specific poly(A) QTLs (FDR 0.25) | /virdir/Backup/RP3_data/polya-qtls/lymphocytes-2014-09-04
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| Monocyte-specific poly(A) QTLs (FDR 0.25) | /virdir/Backup/RP3_data/polya-qtls/monocytes-2014-09-04
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| Neutrophil-specific poly(A) QTLs (FDR 0.25) | /virdir/Backup/RP3_data/polya-qtls/neutrophils-2014-09-04
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