Data Summary

 Data Depository and Summary Page for seeQTL

Processed genotype and expression data:

genotype_expression_data.tar.gz (gzip text matrix format, 300MB)

genotype_expression_data.7z (7zip text matrix format, 250MB)

eQTLs of meta-analysis (consensus eQTLs) from HapMap human lymphoblastoid cell lines (sample summary):

HapMap cis eQTL consensus, HapMap trans eQTL consensus

eQTLs of human brain from Myers et al:

Myers European brain cis eQTL, Myers European brain trans eQTL

Processed RNA-seq data:

Montgomery et al 2010 Mapped RNA-seq data with read count (Montgomery)

Pickrell et al 2010 Mapped RNA-seq data with read count (Yale, Argonne)

Principal Component Analysis:

PCs of genotype data for each dataset

HapMap genotype samples:

Consensus genotype of HapMap3 of Release 3 (HapMap FTP website)

Please cite the following reference if you used the processed genotype data, processed expression data and eQTLs in your study:

Xia, K., Shabalin, A.A., Huang, S., Madar, V., Zhou, Y.H., Wang, W., Zou, F., Sun, W., Sullivan, P.F. and Wright FA. (2011) seeQTL: A searchable database for human eQTLs. Bioinformatics. (2012) 28(3): 451-452

The summarized table of eQTLs in each dataset:

Datasets

Sample
Size

# of
Genes

# of
cis-eQTL (q<0.1)

# of
trans-eQTL (q<0.1)

Reference

Stranger_CEU

56

16,925

9,228

11,793

Stranger
et al 2007

Stranger_YRI

57

16,925

6,497

11,166

Stranger
et al 2007

Stranger_CHB_JPT

85

16,925

33,507

16,580

Stranger
et al 2007

Price_CEU/Spielman_CEU

56

8,696

921

1,311

Price et al
2008

Price_YRI

56

8,696

794

3,077

Price et al
2008

Choy_CEU

53

13,094

2,667

2,578

Choy
et al 2008

Choy_YRI

51

13,094

628

1,704

Choy
et al 2008

Choy_CHB_JPT

66

13,094

2,229

3,799

Choy
et al 2008

Spielman_CHB_JPT

75

8,696

3,317

3,543

Spielman et al 2007

Montgomery1RNAseq_CEU

55

20,861

1,899

6,339

Montgomery et al 2010

Montgomery2_CEU

107

16,624

18,747

19,952

Montgomery et al 2010

PickrellRNAseq_YRI

52

20,861

627

6,714

Pickrell
et al 2010

Myers European brain

186

16,819

2,586

23,280

Myers et al
2007

Zeller European monoctye

1,490

37,808

73,363

6,913

Zeller et al 2010

HapMap eQTL
consensus

N/A

20,881

51,924

16,699

All
HapMap samples