ARC Centre of Excellence for Plant Energy Biology

Pre-release edition

Data for "Expressologs" (Toronto: Patel, et al. 2012: DOI: 10.1111/j.1365-313X.2012.05055.x) have been imported for homologous genes in Arabidopsis thaliana as determined by the authors' choice of OrthoMCL v1.4 software. From their official website:

"...we have computed the most likely expressolog (expression homolog) for most genes across 7 plant species (including maize), based expression profile similarity in the gene expression developmental atlases available for these species..."

The authors' data download format differs from their official Expressolog viewer, so please note:

  • The authors' choice of OrthoMCL for homology gives different results than the InParanoid and Gramene orthology shown elsewhere in Rice DB.
  • The Expressolog paper defines only one "Expressolog" per gene per pair of correlated species, on the basis of maximum positive Spearman's rank correlation coefficient (SCC) between two tissues considered "equivalent". However, Rice DB shows a larger amount of data, specifically the correlation coefficients for all homologous gene probes in the authors' database.
  • In the authors' graphical viewer, the ranking of homologous genes is done with an apparently arbitrary choice of gene probe, and in particular not necessarily the average or maximum RNA probe correlation for that gene. Therefore, some highly-correlated probes are not considered to be Expressologs. In contrast, Rice DB shows all known probes so you can make your own judgement.
  • The authors' data are per-gene (not per transcript variant) in contrast to Rice DB is based on loci point numbers. Each point number in one gene will have identical Expressolog results even if the splice variants are actually dissimilar.
  • SCC data are only available for the authors' algorithmically-matched "equivalent tissues" (e.g., "carpels from stage 12 flowers of Arabidopsis being equivalent to rice ovaries"). This is different from the curated tissue equivalence used elsewhere in Rice DB's RNA expression data. The authors' note that "expression similarities are to be used at the users discretion, due to difficulties in comparisons of monocots and dicots".
Usage When Searching Rice DB Usage Viewing Rice DB Results
  • Expressolog columns can be requested when searching.
  • Expressolog-related data are shown in search summaries.
  • Expressolog-related data are shown in flat file pages.
Example: show expressologs for LOC_Os01g21960.1
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System Information

Transcript of last update

Took 1 second, 469 millis starting Wed, 20 Jun 2012 06:52:21 GMT:
Using /var/folders/75/983jwhw537q11ck7b_b0zwf80000gn/T/RiceDB/Expressologs_
Using db.local/downloaded/Expressologs_
Fetching Expressolog data from UToronto via JSON REST
Batch size = 30
Downloading via HTTP JSON REST
Interpreting probe prioritisation
Calculating display order