1. A meta-analysis of expression signatures in glomerular disease
Sam H. Tryggvason, Jing Guo, Masatoshi Nukui, Jenny Norlin, Börje Haraldsson, Hans Jörnvall, Karl Tryggvason, Liqun He 
Kidney International 
Volume 84, Issue 3, Pages (September 2013)
DOI: /ki
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2. Figure 1
Summary of Kyoto Encyclopedia of Genes and Genome (KEGG) pathway analysis. (a1) Pathways that are identified by most data sets. For illustration, 10 out of 16 data sets associate the differential expression with ‘colorectal cancer’. (a2) The distribution of commonly identified pathways within 16 data sets, including different time points. For example, only one pathway (‘colorectal cancer’ in a1) is detected by 10 data sets, 16 pathways are detected by 9 data sets, etc. Similarly, b1 lists pathways that are identified by most diabetic nephropathy data sets, and b2 demonstrates the distribution of commonly identified pathways within six diabetic nephropathy (DN) data sets, including different time points. CAM, cell adhesion molecule; ECM, extracellular matrix; TCA, tricarboxylic acid.
Kidney International  , DOI: ( /ki )
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3. Figure 2
Illustration of transcriptome profile changes during disease progression. (a) Cells, tissues, and organs undergo series of stages (t0–t5) during disease progression. In normal healthy state (t0), all genes/proteins in pathways or networks are normally regulated (transparent circles). As the disease process is initiated (t1), only minor changes occur in the transcriptome or proteome. As the disease progresses (t2–t5), more genes and proteins are involved and upregulated or downregulated (green and red circles) in pathways and networks. Each stage of the cell can be associated with a specific transcriptome or proteome profile. With a detailed analysis of the transcriptome or proteome expression changes during disease progression, the pathomechanical pathways and networks can be visualized. (b) The glomerular transcriptome was analyzed at three different time points during progression of adriamycin-induced nephrosis in mice.31 Day 0, before administration of adriamycin, day 4, when proteinuria had developed but abnormal histology was not apparent by light microscopy, day 7, when proteinuria was at maximum and electron microscopy analyses revealed foot process effacement without glomerular basement membrane changes, and day 14, when the proteinuria had diminished, but histological analyses showed familial focal segmental glomerulosclerosis changes in about 5–8% of the glomeruli. Such expression signatures show promise for the development of new diagnostic methods identifying molecular pathways and expression signatures for different types of early and advanced glomerular disease.
Kidney International  , DOI: ( /ki )
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4. Figure 3
Work flow of meta-analysis process. All data sets are analyzed in the same protocol. Each data set is preprocessed including quality check and normalization, before doing the SAM (significant analysis of microarray) and Kyoto Encyclopedia of Genes and Genome (KEGG) pathway analysis. Differentially expressed genes are integrated from SAM using universal threshold false discovery rate (FDR)<0.2 and, similarly, significant associated pathways are detected by threshold BH<0.1.
Kidney International  , DOI: ( /ki )
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