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eQTL browser files

Location at JHPCE: /dcl01/lieber/ajaffe/lab/brainseq_phase2/browser.

This directory has all the files for creating the eQTL browser. As stated in the log file the files and their number of lines are:

      396584 BrainSeqPhaseII_clean_expression_development_exon.txt
       24653 BrainSeqPhaseII_clean_expression_development_gene.txt
      297182 BrainSeqPhaseII_clean_expression_development_jxn.txt
       92733 BrainSeqPhaseII_clean_expression_development_tx.txt
      396584 BrainSeqPhaseII_clean_expression_eqtl_dlpfc_exon.txt
       24653 BrainSeqPhaseII_clean_expression_eqtl_dlpfc_gene.txt
      297182 BrainSeqPhaseII_clean_expression_eqtl_dlpfc_jxn.txt
       92733 BrainSeqPhaseII_clean_expression_eqtl_dlpfc_tx.txt
      396584 BrainSeqPhaseII_clean_expression_eqtl_hippo_exon.txt
       24653 BrainSeqPhaseII_clean_expression_eqtl_hippo_gene.txt
      297182 BrainSeqPhaseII_clean_expression_eqtl_hippo_jxn.txt
       92733 BrainSeqPhaseII_clean_expression_eqtl_hippo_tx.txt
      396584 BrainSeqPhaseII_clean_expression_eqtl_interaction_exon.txt
       24653 BrainSeqPhaseII_clean_expression_eqtl_interaction_gene.txt
      297182 BrainSeqPhaseII_clean_expression_eqtl_interaction_jxn.txt
       92733 BrainSeqPhaseII_clean_expression_eqtl_interaction_tx.txt
      396584 BrainSeqPhaseII_clean_expression_regionspecific_adult_exon.txt
       24653 BrainSeqPhaseII_clean_expression_regionspecific_adult_gene.txt
      297182 BrainSeqPhaseII_clean_expression_regionspecific_adult_jxn.txt
       92733 BrainSeqPhaseII_clean_expression_regionspecific_adult_tx.txt
      396584 BrainSeqPhaseII_clean_expression_regionspecific_prenatal_exon.txt
       24653 BrainSeqPhaseII_clean_expression_regionspecific_prenatal_gene.txt
      297182 BrainSeqPhaseII_clean_expression_regionspecific_prenatal_jxn.txt
       92733 BrainSeqPhaseII_clean_expression_regionspecific_prenatal_tx.txt
      396584 BrainSeqPhaseII_clean_expression_sczd_casecontrol_dlpfc_exon.txt
       24653 BrainSeqPhaseII_clean_expression_sczd_casecontrol_dlpfc_gene.txt
      297182 BrainSeqPhaseII_clean_expression_sczd_casecontrol_dlpfc_jxn.txt
       92733 BrainSeqPhaseII_clean_expression_sczd_casecontrol_dlpfc_tx.txt
      396584 BrainSeqPhaseII_clean_expression_sczd_casecontrol_hippo_exon.txt
       24653 BrainSeqPhaseII_clean_expression_sczd_casecontrol_hippo_gene.txt
      297182 BrainSeqPhaseII_clean_expression_sczd_casecontrol_hippo_jxn.txt
       92733 BrainSeqPhaseII_clean_expression_sczd_casecontrol_hippo_tx.txt
      396584 BrainSeqPhaseII_clean_expression_sczd_casecontrol_interaction_exon.txt
       24653 BrainSeqPhaseII_clean_expression_sczd_casecontrol_interaction_gene.txt
      297182 BrainSeqPhaseII_clean_expression_sczd_casecontrol_interaction_jxn.txt
       92733 BrainSeqPhaseII_clean_expression_sczd_casecontrol_interaction_tx.txt
    28863540 BrainSeqPhaseII_eQTL_dlpfc_full.txt
     3698269 BrainSeqPhaseII_eQTL_dlpfc_raggr.txt
   758634578 BrainSeqPhaseII_eQTL_dlpfc_replication_GTEx.txt
    22603132 BrainSeqPhaseII_eQTL_hippo_full.txt
     3698269 BrainSeqPhaseII_eQTL_hippo_raggr.txt
   758634578 BrainSeqPhaseII_eQTL_hippo_replication_GTEx.txt
     1776812 BrainSeqPhaseII_eQTL_interaction_full.txt
   398556091 BrainSeqPhaseII_eQTL_interaction_replication_GTEx.txt
      396584 BrainSeqPhaseII_feature_annotation_exon.txt
       24653 BrainSeqPhaseII_feature_annotation_gene.txt
      297182 BrainSeqPhaseII_feature_annotation_jxn.txt
       92733 BrainSeqPhaseII_feature_annotation_tx.txt
         902 BrainSeqPhaseII_sample_metadata.txt
     7023861 BrainSeqPhaseII_snp_annotation.txt
     7023861 BrainSeqPhaseII_snp_genotype.txt

Sample information

         902 BrainSeqPhaseII_sample_metadata.txt

Includes many columns, but some of the more useful ones are:

  • SAMPLE_ID: actual file ID
  • RNum: internal LIBD RNA sequencing ID
  • BrNum: internal LIBD brain (subject) ID
  • Region: either HIPPO or DLPFC
  • Dx: either Control or SCZD
  • Age: numeric age in years
  • DLFPC_HIPPO_correlation_* (* can be geneRpkm, exonRpkm, jxnRp10m or txTpm): HIPPO vs DLPFC correlation across the corresponding feature (only 265 subjects). Values are stored only for the Region == DLPFC entries.
  • analysis_regionspecific_adult: logical, TRUE if the sample was used for the HIPPO vs DLPFC region analysis with adult controls.
  • analysis_regionspecific_prenatal: similar to the previous one, but for prenatal age.
  • analysis_development: logical, TRUE if the same was used for the analysis across development (age); they are only controls.
  • analysis_sczd_casecontrol_dlpfc: logical, TRUE if used for the SCZD vs control DE analysis for the DLPFC region.
  • analysis_sczd_casecontrol_hippo: logical, TRUE if used for the SCZD vs control DE analysis for the HIPPO region.
  • analysis_sczd_casecontrol_interaction: logical, TRUE if used for the SCZD vs control and brain region interaction DE analysis across DLPFC and HIPPO.
  • analysis_eqtl_dlpfc: logical, TRUE if used for the eQTL analysis with DLFPC samples.
  • analysis_eqtl_hippo: logical, TRUE if used for the eQTL analysis with HIPPO samples.
  • analysis_eqtl_interaction: logical, TRUE if used for the eQTL and brain region interaction analysis.

SNP information

     7023861 BrainSeqPhaseII_snp_annotation.txt

Columns:

  1. snp: snp ID
  2. chr_hg38: chromosome in hg38 coordinates
  3. pos_hg38: position in hg38 coordinates
  4. chr_hg19: similar to chr_hg38 but in hg19 coordinates
  5. pos_hg19: hg19 position.
  6. cm
  7. counted: allele quantified
  8. alt: alternative allele
  9. type
  10. newref: new reference allele (use this); this is the non-effect (major) allele
  11. newcount: new counted allele (use this); this is the effect (minor) allele
  12. name: snp rs number (use this)
  13. rsnumguess: guessed snp name

This file is available for download here.

Genotype information

Columns are the subjects labeled by the BrNum from the sample metadata. Rows are the SNPs with labels corresponding to the snp column from the SNP information table. Entries are 0, 1, 2 or NA.

Expression feature info

      396584 BrainSeqPhaseII_feature_annotation_exon.txt
       24653 BrainSeqPhaseII_feature_annotation_gene.txt
      297182 BrainSeqPhaseII_feature_annotation_jxn.txt
       92733 BrainSeqPhaseII_feature_annotation_tx.txt

Each files includes the annotation for each feature type. Since each feature is a bit different, each files has different columns. Some common ones are:

  • seqnames: chromosome
  • start: start position of the feature
  • end: end position
  • strand: strand of the feature
  • feature_id: this matches the id used for the eQTL result tables.
  • Symbol (gene_name for tx): symbol of the gene the feature corresponds to
  • Class (except for tx): classification for the feature, this really only matters for jxn where the exon-exon junction could be un-annotated (novel), in Gencode, etc.
  • gencodeID (gene, exon), gencodeGeneID (jxn), gene_id (tx): Gencode gene ID.

eQTL result tables

 28863540 BrainSeqPhaseII_eQTL_dlpfc_full.txt
  3698269 BrainSeqPhaseII_eQTL_dlpfc_raggr.txt
 22603132 BrainSeqPhaseII_eQTL_hippo_full.txt
  3698269 BrainSeqPhaseII_eQTL_hippo_raggr.txt
 22603132 BrainSeqPhaseII_eQTL_interaction_full.txt

Each of these tables has the following columns:

  1. snp: snp ID, matches the snp column from the SNP information file (BrainSeqPhaseII_snp_annotation.txt).
  2. feature_id: feature ID, matches the feature_id column of the expression feature files.
  3. statistic: eQTL t-statistic
  4. pvalue: nominal p-value
  5. FDR: FDR adjusted p-value
  6. beta: eQTL beta coefficient. If you want the SE, you can compute it using beta / statistic.
  7. Type: feature type in lower-case. This matches the expression feature files, for example gene for BrainSeqPhaseII_feature_annotation_gene.txt.

The 5 eQTL tables correspond to the following types of eQTLs:

  • DLPFC using all the genome (dlpfc_full), so the samples with TRUE under the analysis_eqtl_dlpfc column from the sample info table. Shows only results with a nominal p-value <0.001.
  • HIPPO using all the genome (hippo_full), so the samples with TRUE under the analysis_eqtl_hippo column from the sample info table. Shows only results with a nominal p-value <0.001.
  • Brain region and eQTL interaction across all the genome (interation_full), so the samples with TRUE under the analysis_eqtl_interaction column from the sample info table. Shows only results with a nominal p-value <0.001.
  • Sub-analysis using only the PGC2 SNPs and neighboring SNPs identified with rAggr (9,736 SNPs) for DLFPC (dlpfc_raggr). Given the smaller number of SNPs considered, the FDR is different compared to dlpfc_full. Shows all associations (so no nominal p-value filter).
  • Sub-analysis using only the PGC2 SNPs and neighboring SNPs identified with rAggr (9,736 SNPs) for HIPPO (hippo_raggr). Given the smaller number of SNPs considered, the FDR is different compared to hippo_full. Shows all associations (so no nominal p-value filter).

We considered as significant associations those that had a FDR < 0.01.

A subset of the *full.txt results are available at SupplementaryTable15_eQTL.tar.gz which has the results with FDR < 1%. If you are interested in the complete unfiltered list of eQTL associations please let us know.

GTEx eQTL replication tables

We also have 3 more tables that include all associations (no nominal p-value filter) between any of the features that had a significant eQTL in the 5 main analyses against any of the SNPs involved in those analyses. Note that some values are NA in these tables (likely to them not being observed in the GTEx samples).

758634578 BrainSeqPhaseII_eQTL_dlpfc_replication_GTEx.txt
758634578 BrainSeqPhaseII_eQTL_hippo_replication_GTEx.txt
398556091 BrainSeqPhaseII_eQTL_interaction_replication_GTEx.txt

The nominal p-value can be reported for replication purposes.

Cleaned (residualized) expression tables

The tables contained the expression values for making boxplots or other types of graphs. The expression values are already normalized (RPKM: gene/exon, RP10M: jxn, TPM: tx) and log2 scaled (log2(x + 0.5)) with covariates for the corresponding analysis removed. Samples can be identified using the analysis_* columns from the sample table. The column names are the RNum from the sample metadata table and the rows correspond to the feature_id (as in the same order as the feature annotation tables).

HIPPO or DLPFC eQTLs

Can be visualized as 3 boxplots, one per allele type, for example CC, AC and AA.

Sample visualization

396584 BrainSeqPhaseII_clean_expression_eqtl_dlpfc_exon.txt
 24653 BrainSeqPhaseII_clean_expression_eqtl_dlpfc_gene.txt
297182 BrainSeqPhaseII_clean_expression_eqtl_dlpfc_jxn.txt
 92733 BrainSeqPhaseII_clean_expression_eqtl_dlpfc_tx.txt
396584 BrainSeqPhaseII_clean_expression_eqtl_hippo_exon.txt
 24653 BrainSeqPhaseII_clean_expression_eqtl_hippo_gene.txt
297182 BrainSeqPhaseII_clean_expression_eqtl_hippo_jxn.txt
 92733 BrainSeqPhaseII_clean_expression_eqtl_hippo_tx.txt

DLPFC and HIPPO interaction eQTLs

Can be visualized as 6 (3 x 2) boxplots, one per allele type, for example CC, AC and AA for each brain region. Brain region can be extracted from the sample metadata column.

Sample visualization

396584 BrainSeqPhaseII_clean_expression_eqtl_interaction_exon.txt
 24653 BrainSeqPhaseII_clean_expression_eqtl_interaction_gene.txt
297182 BrainSeqPhaseII_clean_expression_eqtl_interaction_jxn.txt
 92733 BrainSeqPhaseII_clean_expression_eqtl_interaction_tx.txt

DLPFC vs HIPPO differential expression (adult, prenatal)

Can be visualized as 2 boxplots, one per brain region. R colors:

  • DLPFC: 'dark orange'
  • HIPPO: 'skyblue3'

Sample visualization

396584 BrainSeqPhaseII_clean_expression_regionspecific_adult_exon.txt
 24653 BrainSeqPhaseII_clean_expression_regionspecific_adult_gene.txt
297182 BrainSeqPhaseII_clean_expression_regionspecific_adult_jxn.txt
 92733 BrainSeqPhaseII_clean_expression_regionspecific_adult_tx.txt
396584 BrainSeqPhaseII_clean_expression_regionspecific_prenatal_exon.txt
 24653 BrainSeqPhaseII_clean_expression_regionspecific_prenatal_gene.txt
297182 BrainSeqPhaseII_clean_expression_regionspecific_prenatal_jxn.txt
 92733 BrainSeqPhaseII_clean_expression_regionspecific_prenatal_tx.txt

Note that the analysis was done using limma-voom with log2(CPM + 0.5) instead of log2(RPKM + 1) for genes/exons or log2(RP10M + 1) for jxns.

Development differential expression

Can be visualized as a scatterplot of expression versus time split by the age linear spline cutoffs (age in years: 0, 1, 10, 20 and 50). Age below 0 (prenatal) can be transformed from years to the PCW scale using the function round(range(age) * 52 + 40, 0). R colors:

  • DLPFC: 'dark orange'
  • HIPPO: 'skyblue3'

Sample visualization

396584 BrainSeqPhaseII_clean_expression_development_exon.txt
 24653 BrainSeqPhaseII_clean_expression_development_gene.txt
297182 BrainSeqPhaseII_clean_expression_development_jxn.txt
 92733 BrainSeqPhaseII_clean_expression_development_tx.txt

Note that the analysis was done using limma-voom with log2(CPM + 0.5) instead of log2(RPKM + 1) for genes/exons or log2(RP10M + 1) for jxns.

SCZD vs control differential expression (DLPFC, HIPPO)

Can be visualized as 2 boxplots, one for SCZD cases and one for controls. R colors:

  • SCZD case: 'aquamarine4'
  • control: 'orchid4'

Sample visualization

396584 BrainSeqPhaseII_clean_expression_sczd_casecontrol_dlpfc_exon.txt
 24653 BrainSeqPhaseII_clean_expression_sczd_casecontrol_dlpfc_gene.txt
297182 BrainSeqPhaseII_clean_expression_sczd_casecontrol_dlpfc_jxn.txt
 92733 BrainSeqPhaseII_clean_expression_sczd_casecontrol_dlpfc_tx.txt
396584 BrainSeqPhaseII_clean_expression_sczd_casecontrol_hippo_exon.txt
 24653 BrainSeqPhaseII_clean_expression_sczd_casecontrol_hippo_gene.txt
297182 BrainSeqPhaseII_clean_expression_sczd_casecontrol_hippo_jxn.txt
 92733 BrainSeqPhaseII_clean_expression_sczd_casecontrol_hippo_tx.txt

Note that the analysis was done using limma-voom with log2(CPM + 0.5) instead of log2(RPKM + 1) for genes/exons or log2(RP10M + 1) for jxns.

SCZD vs control and brain region interaction differential expression

Can be visualized as 4 boxplots, one for SCZD cases and one for controls for each brain region. R colors:

  • SCZD case: 'aquamarine4' (box)
  • control: 'orchid4' (box)
  • DLPFC: 'dark orange' (dots)
  • HIPPO: 'skyblue3' (dots)

Sample visualization

396584 BrainSeqPhaseII_clean_expression_sczd_casecontrol_interaction_exon.txt
 24653 BrainSeqPhaseII_clean_expression_sczd_casecontrol_interaction_gene.txt
297182 BrainSeqPhaseII_clean_expression_sczd_casecontrol_interaction_jxn.txt
 92733 BrainSeqPhaseII_clean_expression_sczd_casecontrol_interaction_tx.txt

Note that the analysis was done using limma-voom with log2(CPM + 0.5) instead of log2(RPKM + 1) for genes/exons or log2(RP10M + 1) for jxns.

Correlation

The DLFPC_HIPPO_correlation_* values from the sample metadata table (remember that they are only listed for the DLPFC samples, although the values for the HIPPO ones would be identical for the 265 subjects used in this analysis) can be visualized as 2 boxplots, one for SCZD cases and one for controls. R colors:

  • SCZD case: 'aquamarine4'
  • control: 'orchid4'

Sample visualization (although this one doesn't have the right colors)