Supplemental data: TRANSPLANTATION

Gene-expression profiles and age of donor kidney biopsies obtained before transplantation distinguish medium term graft function

Alexander Kainz1, Paul Perco1,2, Bernd Mayer2,3, Afschin Soleiman4, Rudolf Steininger5, Gert Mayer6, Christa Mitterbauer1, Christoph Schwarz1, Timothy Meyer7, and Rainer Oberbauer1

1 - Department of Nephrology, KH Elisabethinen Linz, and Medical University of Vienna
2 - Institute of Theoretical Chemistry, University of Vienna
3 - emergentec biodevelopment GmbH, Vienna
4 - Department of Pathology, Medical Universtiy of Vienna
5 - Department of Transplant Surgery, Medical University of Vienna
6 - Department of Nephrology, Medical University of Innsbruck
7 - Department of Nephrology, Stanford University


TABLES
FIGURES
Table 1 Table 1

Demographic data of kidney donors and recipients. Data are given as median and interquartile range.

BCAR ... biopsy confirmed acute rejection
GFR ... glomerular filtration rate estimated using the abbreviated MDRD formula
CIT ... cold ischemia time
DM ... diabetes mellitus
h_GFR ... normal allograft function, calculated GFR > 45 ml/min/1.73 m2
l_GFR ... higher impaired allograft function, calculated GFR < 45 ml/min/1.73 m2

Figure 1 Figure 1

The dendrogram derived by unsupervised hierarchical clustering of differentially expressed genes between the groups l_GFR (calculated GFR < 45ml/min/1.73 m2) and h_GFR (calculated GFR ≥ 45ml/min/1.73 m2). The cosine correlation and complete linkage were used as distance measure and linkage rule in the hierarchical cluster algorithm, respectively. Red spots indicate abundantly expressed transcripts, whereas green spots indicate transcripts expressed on low level when compared to the reference RNA. GenBank accession numbers and Gene Symbols are used for labeling the cDNA clones.
Table 2 Table 2

Representation of the differentially expressed genes between groups l_GFR (low GFR) and h_GFR (high GFR). Genes are categorized based on GO terms and PANTHER classifications and are ranked by difference of mean expression between the two groups under study. Values represent ratios of sample to standard reference expression on a log2 scale.

 Figure 2 Figure 2

Protein-protein interaction networks of up-regulated genes of group h_GFR (calculated GFR ≥ 45 ml/min/1.73 m2) and group l_GFR are given in figures 2A and 2B, respectively. Black boxes indicate differentially regulated proteins between the two groups; grey boxes represent proteins identified by the nearest neighbor expansion method. Proteins up-regulated in group l_GFR showed a high connectivity on the level of protein-protein interactions thus indicating concerted interaction. (C) The index of aggregation (IA; y-axis) in dependence of the number of proteins used for constructing protein interaction networks (x-axis). The IA of genes up-regulated in group l_GFR (calculated GFR < 45 ml/min/1.73 m2) is significantly above the IA of randomly selected lists. The thick black line represents mean IAs of randomly selected gene lists. Dotted lines represent two standard deviations of these distributions.
Webtable 1A
Webtable 1B		 Webtable 1A B

RT-PCR validation of microarray experiments for BF, CR2, GRK5 and STAT1.

A. Retrospective validation.

B. Prospective validation

    


Original data according to the MIAME guidelines

(MIAME Checklist)

ARRAY experiment image
(jpg-file ~ 1.3 MB each)		 raw data
(gz=tab-delimited txt-file ~ 7.1 MB each)
l_GFR123 l_GFR123_sher232.jpg l_GFR123_sher232.gz
l_GFR138 l_GFR138_sher240.jpg l_GFR138_sher240.gz
l_GFR147 l_GFR147_sher190.jpg l_GFR147_sher190.gz
l_GFR162 l_GFR162_sher228.jpg l_GFR162_sher228.gz
l_GFR167 l_GFR167_shem205.jpg l_GFR167_shem205.gz
l_GFR190 l_GFR190_sher209.jpg l_GFR190_sher209.gz
l_GFR195 l_GFR195_shem253.jpg l_GFR195_shem253.gz
l_GFR206 l_GFR206_sher182.jpg l_GFR206_sher182.gz
l_GFR207 l_GFR207_sher188.jpg l_GFR207_sher188.gz
l_GFR216 l_GFR216_sher238.jpg l_GFR216_sher238.gz
l_GFR229 l_GFR229_sher231.jpg l_GFR229_sher231.gz
l_GFR232 l_GFR232_sher221.jpg l_GFR232_sher221.gz
l_GFR255 l_GFR255_sher244.jpg l_GFR255_sher244.gz
l_GFR258 l_GFR258_sher245.jpg l_GFR258_sher245.gz
l_GFR260 l_GFR260_shem252.jpg l_GFR260_shem252.gz
l_GFR262 l_GFR262_shem254.jpg l_GFR262_shem254.gz
h_GFR121 h_GFR121_shem251.jpg h_GFR121_shem251.gz
h_GFR130 h_GFR130_sher180.jpg h_GFR130_sher180.gz
h_GFR153 h_GFR153_sher211.jpg h_GFR153_sher211.gz
h_GFR155 h_GFR155_sher189.jpg h_GFR155_sher189.gz
h_GFR156 h_GFR156_sher208.jpg h_GFR156_sher208.gz
h_GFR160 h_GFR160_sher210.jpg h_GFR160_sher210.gz
h_GFR169 h_GFR169_sher239.jpg h_GFR169_sher239.gz
h_GFR172 h_GFR172_sher198.jpg h_GFR172_sher198.gz
h_GFR200 h_GFR200_sher230.jpg h_GFR200_sher230.gz
h_GFR201 h_GFR201_shem206.jpg h_GFR201_shem206.gz
h_GFR211 h_GFR211_sher246.jpg h_GFR211_sher246.gz
h_GFR213 h_GFR213_sher222.jpg h_GFR213_sher222.gz
h_GFR214 h_GFR214_sher241.jpg h_GFR214_sher241.gz
h_GFR227 h_GFR227_sher242.jpg h_GFR227_sher242.gz
h_GFR244 h_GFR244_sher243.jpg h_GFR244_sher243.gz