| | 1 | = First paper = |
| | 2 | |
| | 3 | The focus for our first paper are cell type-specific QTLs for transcription and mRNA processing. |
| | 4 | |
| | 5 | [https://docs.google.com/document/d/1HoLmhJD0L2nmPF8Xr9jotm-wF1h7UWPj35YCug0tio4/edit Outline and division of work (2014-05-21)] |
| | 6 | |
| | 7 | |
| | 8 | == Todo list == |
| | 9 | |
| | 10 | - todo |
| | 11 | |
| | 12 | |
| | 13 | == Figures and Tables == |
| | 14 | |
| | 15 | 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. |
| | 16 | |
| | 17 | '''Data and QC:''' |
| | 18 | -- [wiki:FgFirstPaper/table_with_number_of_samples_per_cohort_and_related_statistics Table with number of samples per cohort and related statistics] [[BR]] |
| | 19 | - [wiki:FgFirstPaper/table_with_general_sequencing_characteristics Table with general sequencing characteristics: average and range for][[BR]] |
| | 20 | -- [wiki:FgFirstPaper/qc_and_alignment_stats number of reads passing qc][[BR]] |
| | 21 | -- [wiki:FgFirstPaper/qc_and_alignment_stats number (percentage) of aligned reads][[BR]] |
| | 22 | -- [wiki:FgFirstPaper/qc_and_alignment_stats number (percentage) of aligned reads mapping to our annotated exons][[BR]] |
| | 23 | -- number of detected genes (>0 count) per sample[[BR]] |
| | 24 | - Graphs with:[[BR]] |
| | 25 | -- [wiki:FgFirstPaper/gc_distribution_per_biobank GC distribution per biobank][[BR]] |
| | 26 | -- [wiki:FgFirstPaper/RNA_blood_sampling_age_distribution_per_biobank_plot RNA blood sampling age distribution per biobank][[BR]] |
| | 27 | -- [wiki:FgFirstPaper/genotype_concordance_plots Genotype concordance per biobank][[BR]] |
| | 28 | -- [wiki:FgFirstPaper/genotype_concordance_plots Heterozygosity per biobank] [[BR]] |
| | 29 | - Density plot of median Spearman correlations for genes and exons (Peter-Bram)[[BR]] |
| | 30 | - MDS plot of Spearman correlations colored by GC such as [raw-attachment:mdsplot_exon_filt_colored_gc.pdf:wiki:FgGeneExonTranscriptCounts this one] (Peter-Bram)[[BR]] |
| | 31 | - [wiki:FgFirstPaper/PCs_phenotypes_correlations Significant correlations between PCs and sample characteristics] [[BR]] |
| | 32 | (Some of this can already be found at [wiki:FgGeneExonTranscriptCounts this page], [wiki:FgPrimeBias this page], [wiki:FgQualityControl/FgQualityControlRun1 this page], and on normalization.) |
| | 33 | |
| | 34 | |
| | 35 | '''QTLs general:''' |
| | 36 | - [wiki:FgQTL/cis/QTL_numbers The summary statistics table with the number of QTLs] |
| | 37 | - [raw-attachment:run1_eQTLs_numbers.xlsx:wiki:FgQTL/cis/gene-eQTL Table of the number of primary/secondary/tertiary effects]. Details can be found on [wiki:FgQTL/cis/gene-eQTL this] page |
| | 38 | - [wiki:FgFirstPaper/histogram_numCisEffects Histogram of genes with x independent QTLs] |
| | 39 | - [wiki:FgFirstPaper/histogram_numCisEffects_exons Histogram of exons with x independent QTLs] |
| | 40 | - [wiki:FgFirstPaper/venn_eQTL_overlap Venn diagram of gene-, transcript-, exon-level eQTLs overlap] |
| | 41 | - Replication results for GEUVADIS of [wiki:FgQTL/cis/gene-eQTL gene level eQTLs] and [wiki:FgQTL/cis/exon-eQTL exon level eQTLs] |
| | 42 | - Replication in Array data ([wiki:FgQTL/cis/gene-eQTL Westra et al], Wright et al (NTR+NESDA data)) (Dasha) |
| | 43 | - [wiki:FgFirstPaper/EffectLevels Number of independent cis-effects after stepwise regression] |
| | 44 | - [wiki:FgFirstPaper/QTLDistanceToExon Distance to exon midpoint of top SNPs for exon/exon-ratio/polya QTLs] |
| | 45 | |
| | 46 | |
| | 47 | '''Gene eQTLs:''' |
| | 48 | - [wiki:FgFirstPaper/geneEqtls_distanceToTSS distance top SNP relative to transcription start site] |
| | 49 | - [wiki:FgFirstPaper/geneEqtls_distanceToTES distance top SNP relative to transcription end site] |
| | 50 | - [raw-attachment:run1_eQTLs_numbers.xlsx:wiki:FgQTL/celltype Table of the number of cell-type specific effects]. Details can be found on [wiki:FgQTL/celltype this] page |
| | 51 | - [wiki:FgFirstPaper/Enriched_TF_Binding_Sites Top 10 TF binding sites enriched in global eQTL SNPs (Maarten)][[BR]] |
| | 52 | - Top SNPs show a change in affinity for specific TF (Szymon) |
| | 53 | - Interaction analysis (TF expression levels modify eQTL effect) overlapped with enriched TFs (Dasha and Maarten/Szymon) |
| | 54 | |
| | 55 | '''Exon eQTLs:''' |
| | 56 | - [wiki:FgFirstPaper/exonEqtls_distanceToMidExon distance top SNP relative to exon mid point] |
| | 57 | |
| | 58 | '''Exon-ratio QTLs:''' |
| | 59 | - [wiki:FgFirstPaper/ExonRatioQTLDistanceToExon Distance of (top) SNP relative to exon start] |
| | 60 | - [wiki:FgFirstPaper/ExonRatioExonClassification Classification of exons with exon-ratio QTLs (constitutive, cassette etc.)] |
| | 61 | - [wiki:FgFirstPaper/ExonRatioAcceptorDonorOverlap Overlap of QTL SNPs with donor/acceptor sites] |
| | 62 | - Enrichment of RNA-binding protein motifs ([wiki:FgQTL/exon-ratio/motifs preliminary analysis]) |
| | 63 | - Example gene(s) (after overlapping with GWAS hits?) |
| | 64 | |
| | 65 | '''Poly(A) QTLs:''' |
| | 66 | - [wiki:FgFirstPaper/PolyAQTLDistanceToSite Distance of (top) SNP relative to polyadenylation site] |
| | 67 | - Overlap / enrichment of top SNP per poly(A) site with canonical and alternative poly(A) signals (Martijn) |
| | 68 | - Example gene(s) (after overlapping with GWAS hits?) |
| | 69 | |
| | 70 | '''Cell type-specific eQTLs and exon-ratio QTLs''' |
| | 71 | - Table with number of Cell type-specific results for FDR 0.05 and 0.25 (Gene and exon ratio) |
| | 72 | - TF binding and RNA binding protein analyses for cell-type specific eQTLs |
| | 73 | |
| | 74 | |
| | 75 | == Materials & Methods == |
| | 76 | |
| | 77 | [https://docs.google.com/document/d/1l1livkojjX2ajbTxaotQO0DoSxZ31xR3XfXVzqQPJuI/edit Google Docs] |
| | 78 | |
| | 79 | |
| | 80 | == Scripts and pipelines to deposit == |
| | 81 | |
| | 82 | 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. |
| | 83 | |
| | 84 | - [https://git.lumc.nl/groups/rp3 RP3 on GitLab] |
| | 85 | - [https://github.com/molgenis/systemsgenetics/tree/master/eqtl-mapping-pipeline QTL mapping pipeline] |
| | 86 | |
| | 87 | |
| | 88 | == Data to deposit == |
| | 89 | |
| | 90 | To be decided: |
| | 91 | |
| | 92 | - Where to deposit? Molgenis site is nice for downstream results and browsing. Probably not for raw sequencing data. |
| | 93 | - Primary data: fastq files, BAM files? |
| | 94 | - Secondary data: expression/count files? Cell counts? |
| | 95 | - 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? |
| | 96 | |
| | 97 | ||= Data =||= Location (on VM unless noted otherwise) =|| |
| | 98 | || [wiki:FgQTL/cis/gene-eQTL Gene eQTLs] || `/virdir/Backup/dzhernakova/LL+RS+CODAM+LLS_eqtls_genes_23062014/` || |
| | 99 | || [wiki:FgQTL/cis/transcript-eQTL Transcript eQTLs] || `/virdir/Backup/dzhernakova/LL+RS+CODAM+LLS_eqtls_transcr_01062014/` || |
| | 100 | || [wiki:FgQTL/cis/exon-eQTL Exon eQTLs] || `/virdir/Backup/dzhernakova/LL+RS+CODAM+LLS_eqtls_meta-exons_28062014/` || |
| | 101 | || [wiki:FgQTL/celltype Basophil-specific gene-level QTLs (FDR 0.05)] || `/virdir/Backup/dzhernakova/LL+RS+CODAM+LLS_eqtls_genes_basophils_150714/` || |
| | 102 | || [wiki:FgQTL/celltype Eosinophil-specific gene-level QTLs (FDR 0.05)] || `/virdir/Backup/dzhernakova/LL+RS+CODAM+LLS_eqtls_genes_eosinophils_150714/` || |
| | 103 | || [wiki:FgQTL/celltype Lymphocyte-specific gene-level QTLs (FDR 0.05)] || `/virdir/Backup/dzhernakova/LL+RS+CODAM+LLS_eqtls_genes_lymphocytes_08062014/` || |
| | 104 | || [wiki:FgQTL/celltype Monocyte-specific gene-level QTLs (FDR 0.05)] || `/virdir/Backup/dzhernakova/LL+RS+CODAM+LLS_eqtls_genes_monocytes_150714/` || |
| | 105 | || [wiki:FgQTL/celltype Neutrophil-specific gene-level QTLs (FDR 0.05)] || `/virdir/Backup/dzhernakova/LL+RS+CODAM+LLS_eqtls_genes_neutrophils_150714/` || |
| | 106 | || [Basophil-specific gene-level QTLs (FDR 0.25)] || `/virdir/Backup/dzhernakova/LL+RS+CODAM+LLS_eqtls_genes_basophils_fdr0.25_05082014` || |
| | 107 | || [Eosinophil-specific gene-level QTLs (FDR 0.25)] || `/virdir/Backup/dzhernakova/LL+RS+CODAM+LLS_eqtls_genes_eosinophils_fdr0.25_05082014` || |
| | 108 | || [Lymphocyte-specific gene-level QTLs (FDR 0.25)] || `/virdir/Backup/dzhernakova/LL+RS+CODAM+LLS_eqtls_genes_lymphocytes_fdr0.25_05082014` || |
| | 109 | || [Monocyte-specific gene-level QTLs (FDR 0.25)] || `/virdir/Backup/dzhernakova/LL+RS+CODAM+LLS_eqtls_genes_monocytes_fdr0.25_05082014` || |
| | 110 | || [Neutrophil-specific gene-level QTLs (FDR 0.25)] || `/virdir/Backup/dzhernakova/LL+RS+CODAM+LLS_eqtls_genes_neutrophils_fdr0.25_05082014` || |
| | 111 | || [wiki:FgQTL/exon-ratio#a2014-07-23exonratioQTLs Exon-ratio QTLs] || `/virdir/Backup/RP3_data/exon-ratio-qtls/2014-07-23` || |
| | 112 | || Exon-ratio QTLs (secondary effects) || `/virdir/Backup/RP3_data/exon-ratio-qtls/snps-present-in-all-datasets-secondary-2014-09-10` || |
| | 113 | || Exon-ratio QTLs (tertiary effects) || `/virdir/Backup/RP3_data/exon-ratio-qtls/snps-present-in-all-datasets-tertiary-2014-09-10` || |
| | 114 | || [wiki:FgQTL/exon-ratio#a2014-08-16celltypespecificexonratioQTLs Basophil-specific exon-ratio QTLs (FDR 0.05)] || `/virdir/Backup/RP3_data/exon-ratio-qtls/basophils-2014-08-16` || |
| | 115 | || [wiki:FgQTL/exon-ratio#a2014-08-16celltypespecificexonratioQTLs Eosinophil-specific exon-ratio QTLs (FDR 0.05)] || `/virdir/Backup/RP3_data/exon-ratio-qtls/eosinophils-2014-08-16` || |
| | 116 | || [wiki:FgQTL/exon-ratio#a2014-08-16celltypespecificexonratioQTLs Lymphocyte-specific exon-ratio QTLs (FDR 0.05)] || `/virdir/Backup/RP3_data/exon-ratio-qtls/lymphocytes-2014-08-16` || |
| | 117 | || [wiki:FgQTL/exon-ratio#a2014-08-16celltypespecificexonratioQTLs Monocyte-specific exon-ratio QTLs (FDR 0.05)] || `/virdir/Backup/RP3_data/exon-ratio-qtls/monocytes-2014-08-16` || |
| | 118 | || [wiki:FgQTL/exon-ratio#a2014-08-16celltypespecificexonratioQTLs Neutrophil-specific exon-ratio QTLs (FDR 0.05)] || `/virdir/Backup/RP3_data/exon-ratio-qtls/neutrophils-2014-08-16` || |
| | 119 | || [wiki:FgQTL/exon-ratio#a2014-09-03celltypespecificexonratioQTLs Basophil-specific exon-ratio QTLs (FDR 0.25)] || `/virdir/Backup/RP3_data/exon-ratio-qtls/basophils-2014-09-03` || |
| | 120 | || [wiki:FgQTL/exon-ratio#a2014-09-03celltypespecificexonratioQTLs Eosinophil-specific exon-ratio QTLs (FDR 0.25)] || `/virdir/Backup/RP3_data/exon-ratio-qtls/eosinophils-2014-09-03` || |
| | 121 | || [wiki:FgQTL/exon-ratio#a2014-09-03celltypespecificexonratioQTLs Lymphocyte-specific exon-ratio QTLs (FDR 0.25)] || `/virdir/Backup/RP3_data/exon-ratio-qtls/lymphocytes-2014-09-03` || |
| | 122 | || [wiki:FgQTL/exon-ratio#a2014-09-03celltypespecificexonratioQTLs Monocyte-specific exon-ratio QTLs (FDR 0.25)] || `/virdir/Backup/RP3_data/exon-ratio-qtls/monocytes-2014-09-03` || |
| | 123 | || [wiki:FgQTL/exon-ratio#a2014-09-03celltypespecificexonratioQTLs Neutrophil-specific exon-ratio QTLs (FDR 0.25)] || `/virdir/Backup/RP3_data/exon-ratio-qtls/neutrophils-2014-09-03` || |
| | 124 | || [wiki:FgQTL/apa#a2014-06-20polyaQTLs250kbwindow Poly(A) QTLs] || `/virdir/Backup/RP3_data/polya-qtls/2014-06-20` || |
| | 125 | || Poly(A) QTLs (secondary effects) || `/virdir/Backup/RP3_data/polya-qtls/snps-present-in-all-datasets-secondary-2014-09-29` || |
| | 126 | || Poly(A) QTLs (tertiary effects) || `/virdir/Backup/RP3_data/polya-qtls/snps-present-in-all-datasets-tertiary-2014-09-30` || |
| | 127 | || [wiki:FgQTL/apa#a2014-08-19celltypespecificpolyaQTLs250kbwindow Basophil-specific poly(A) QTLs (FDR 0.05)] || `/virdir/Backup/RP3_data/polya-qtls/basophils-2014-08-18` || |
| | 128 | || [wiki:FgQTL/apa#a2014-08-19celltypespecificpolyaQTLs250kbwindow Eosinophil-specific poly(A) QTLs (FDR 0.05)] || `/virdir/Backup/RP3_data/polya-qtls/eosinophils-2014-08-19` || |
| | 129 | || [wiki:FgQTL/apa#a2014-08-19celltypespecificpolyaQTLs250kbwindow Lymphocyte-specific poly(A) QTLs (FDR 0.05)] || `/virdir/Backup/RP3_data/polya-qtls/lymphocytes-2014-08-19` || |
| | 130 | || [wiki:FgQTL/apa#a2014-08-19celltypespecificpolyaQTLs250kbwindow Monocyte-specific poly(A) QTLs (FDR 0.05)] || `/virdir/Backup/RP3_data/polya-qtls/monocytes-2014-08-19` || |
| | 131 | || [wiki:FgQTL/apa#a2014-08-19celltypespecificpolyaQTLs250kbwindow Neutrophil-specific poly(A) QTLs (FDR 0.05)] || `/virdir/Backup/RP3_data/polya-qtls/neutrophils-2014-08-19` || |
| | 132 | || [wiki:FgQTL/apa#a2014-09-04celltypespecificpolyaQTLs250kbwindow Basophil-specific poly(A) QTLs (FDR 0.25)] || `/virdir/Backup/RP3_data/polya-qtls/basophils-2014-09-04` || |
| | 133 | || [wiki:FgQTL/apa#a2014-09-04celltypespecificpolyaQTLs250kbwindow Eosinophil-specific poly(A) QTLs (FDR 0.25)] || `/virdir/Backup/RP3_data/polya-qtls/eosinophils-2014-09-04` || |
| | 134 | || [wiki:FgQTL/apa#a2014-09-04celltypespecificpolyaQTLs250kbwindow Lymphocyte-specific poly(A) QTLs (FDR 0.25)] || `/virdir/Backup/RP3_data/polya-qtls/lymphocytes-2014-09-04` || |
| | 135 | || [wiki:FgQTL/apa#a2014-09-04celltypespecificpolyaQTLs250kbwindow Monocyte-specific poly(A) QTLs (FDR 0.25)] || `/virdir/Backup/RP3_data/polya-qtls/monocytes-2014-09-04` || |
| | 136 | || [wiki:FgQTL/apa#a2014-09-04celltypespecificpolyaQTLs250kbwindow Neutrophil-specific poly(A) QTLs (FDR 0.25)] || `/virdir/Backup/RP3_data/polya-qtls/neutrophils-2014-09-04` || |
