Gene Expression Commons: An Open Platform for Absolute Gene Expression Profiling

Abstract

Gene expression profiling using microarrays has been limited to comparisons of gene expression between small numbers of samples within individual experiments. However, the unknown and variable sensitivities of each probeset have rendered the absolute expression of any given gene nearly impossible to estimate. We have overcome this limitation by using a very large number (>10,000) of varied microarray data as a common reference, so that statistical attributes of each probeset, such as the dynamic range and threshold between low and high expression, can be reliably discovered through meta-analysis. This strategy is implemented in a web-based platform named “Gene Expression Commons” (https://gexc.stanford.edu/) which contains data of 39 distinct highly purified mouse hematopoietic stem/progenitor/differentiated cell populations covering almost the entire hematopoietic system. Since the Gene Expression Commons is designed as an open platform, investigators can explore the expression level of any gene, search by expression patterns of interest, submit their own microarray data, and design their own working models representing biological relationship among samples.

Annexin A8 controls leukocyte recruitment to activated endothelial cells via cell surface delivery of CD63

“…8d). AnxA8 is not expressed in murine leukocytes 24 , and we found that surface levels of the P-selectin counterligand P-selectin glycoprotein ligand-1 (PSGL-1), which is constitutively expressed on neutrophils, were unchanged in the anxA8 KO mice (Fig. 8e).…”

Endogenous dendritic cells from the tumor microenvironment support T-ALL growth via IGF1R activation

“…Genome-wide expression analysis was performed on T-ALL cells and DC subsets sorted from LN3 thymic tumors using Affymetrix GeneChip Mouse Genome 430 2.0 Arrays (n = 3, LN3 tumor Sirpα + DCs and Sirpα − DCs; n = 3, T-ALL cells). We have previously reported expression profiling of WT thymic DCs and thymocytes (32,60) [Gene Expression Omnibus (GEO) accession nos. GSE34723 and GSE56928]; 1 μg of total RNA from 3 × 10 4 sorted tumor-associated Sirpα + DCs, Sirpα − DCs, or T-ALL cells was amplified, labeled, and hybridized according to the manufacturer's specifications.…”

“…Tumor-associated Sirpα + DCs expressed higher levels of Pdgfc and Igf1 than Sirpα − DCs. Expression data from tumor-associated and WT thymic DC subsets, T-ALL cells, and WT thymocyte subsets are provided in a searchable model within Gene Expression Commons (https:// gexc.stanford.edu/models/1118/genes) (32).…”

Identification and characterization of an injury-induced skeletal progenitor

“…Representative genes involved in cell survival, osteogenesis, chondrogenesis, and angiogenesis were analyzed (Fig. 5A) using the Gene Expression Commons (Materials and Methods) (21). Analysis included BCSPs isolated from uninjured femora at postnatal days 3 (P3, u-BCSP) and 56 (P56, u-BCSP) and from calluses at postfracture days 3 (D3) and 7 (D7).…”

“…Scanned data were exported to DCHIP software for normalization. Raw microarray data were submitted to Gene Expression Commons (https://gexc.stanford.edu/) (21), where data normalization was computed against the Common Reference, a large collection (n = 11,939) of publicly available microarray data from the National Center for Biotechnology Information Gene Expression Omnibus. Metaanalysis of the Common Reference also provides the dynamic range of each probe set on the array.…”