I've been playing around with the EBI Gene Expression Atlas (GXA). It has an API. So, for example, I can retrieve data about the human gene SRI in JSON format using this URI:

http://www.ebi.ac.uk:80/gxa/api/vx?geneIs=ENSG00000075142&format=json

I wrote some R code to fetch/parse the JSON into a data frame:

library(RCurl)
library(rjson)
library(plyr)

j2df <- function(l) {
  e <- lapply(l$results[[1]]$expressions, function(x) {
    ef  <- x$ef
    efv <- x$efv
    updn <- sapply(x$experiments, function(y) {
      y$updn
    })
    pval <- sapply(x$experiments, function(y) {
      y$pvalue
    })
    accn <- sapply(x$experiments, function(y) {
      y$experimentAccession
    })
    list(ef = ef, efv = efv, accn = accn, updn = updn, pvalue = pval)
  }
              )
  e <- ldply(e, as.data.frame)
  return(e)
}

# fetch the JSON
j <- fromJSON(getURL("http://www.ebi.ac.uk:80/gxa/api/vx?geneIs=ENSG00000075142&format=json"))
# convert to data frame
sri <- j2df(j)

When I examine the first few rows, I see:

head(sri)
         ef   efv      accn updn pvalue
1 cell_line   1A2 E-MTAB-37 DOWN  0.000
2 cell_line 22Rv1 E-MTAB-37   UP  0.003
3 cell_line 22Rv1 E-MTAB-37 DOWN  0.019
4 cell_line  5637 E-MTAB-37   UP  0.000
5 cell_line  647V E-MTAB-37   UP  0.009
6 cell_line  769P E-MTAB-37   UP  0.000

According to rows 2 and 3, the same gene (SRI) in the same experiment (E-MTAB-37) is both up-regulated (p = 0.003) and down-regulated (p = 0.019) in cell line 22Rv1, as compared with mean expression from all cell lines. At least, that is my understanding of UP and DOWN as defined in the GXA documentation.

Am I missing something obvious? Or are the data returned by the GXA API simply nonsense?