Gene expression in primate liver during viral hemorrhagic fever

doi:10.1186/1743-422X-6-20

Virology Journal

Volume 6

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Djavani M
Crasta OR
Zhang Y
Zapata JC
Sobral B
Lechner MG
Bryant J
Davis H
Salvato MS

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Crasta OR
Zhang Y
Zapata JC
Sobral B
Lechner MG
Bryant J
Davis H
Salvato MS
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Gene expression in primate liver during viral hemorrhagic fever

Mahmoud Djavani¹ , Oswald R Crasta² , Yan Zhang² , Juan Carlos Zapata¹ , Bruno Sobral² , Melissa G Lechner³ , Joseph Bryant¹ , Harry Davis¹ and Maria S Salvato¹

¹Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD 21201, USA

²Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, VA 24061, USA

³University of Southern California, Keck School of Medicine, Los Angeles, CA 90089, USA

author email corresponding author email

Virology Journal 2009, 6:20doi:10.1186/1743-422X-6-20


Published:	12 February 2009

Additional files

Additional File 1:

Cluster analysis of differentially-expressed genes. Cluster analysis of differentially expressed genes representing 4482 probe sets from uninfected or LCMV-infected liver samples filtered by having p < 0.05 and at least 20 percent of present call. Each row represents the indicated gene. Each column corresponds to the experimental liver sample as listed at the top. Red indicates an up-regulation of gene expression and green indicates a down-regulation of expression in rhesus macaque liver. The origin of each sample is described in Table 1.

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Additional File 2:

Lists genes from the Venn diagram of Figure 1 in the form of 2751 probe sets. "Pre" means they were expressed in the pre-viremic stage (day 1–3) in blood, but not in liver.

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Additional File 3:

Lists genes from the Venn diagram of Figure 1in the form of 500 probe sets. "Pre" means they were expressed in the pre-viremic stage (day 1–3) in both blood and liver.

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Additional File 4:

Lists genes from the Venn diagram of Figure 1in the form of 2033 probe sets. "Pre" means they were expressed in the pre-viremic stage (day 1–3) in liver, but not in blood.

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Additional File 5:

Lists genes from the Venn diagram of Figure 1 in the form of 3136 probe sets. "Vir" means they were expressed in the viremic stage (day 4–7) in blood, but not in liver.

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Additional File 6:

Lists genes from the Venn diagram of Figure 1in the form of 963 probe sets. "Vir" means they were expressed in the viremic stage (day 4–7) in blood and liver.

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Additional File 7:

Lists genes from the Venn diagram of Figure 1in the form of 1722 probe sets. "Vir" means they were expressed in the viremic stage (day 4–7) in liver, but not in blood.

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Additional File 8:

List of differentially-expressed genes in LCMV-infected liver. This list of human probe sets identified in hybridization of rhesus macaque liver cRNA includes those transcripts differentially expressed with respect to uninfected (uninf) control samples (n = 4484), or those transcripts differentially expressed with respect to samples from monkeys that were LCMV-infected but not diseased (nodis). These were identified as differentially expressed using LIMMA analysis. WE1 refers to 4 liver samples taken day 1 to day 3 after infection (pre-viremic stage). WE2 refers to 5 liver samples taken day 4 to day 7 after infection (viremic stage), and WE3 refers to 2 liver samples taken day 11 and day 12 after infection (terminal stage). WEx vs uninf refers to virulent samples being compared to data from 3 uninfected samples. WEx vs nodis refers to virulent samples being compared to data from 6 infected but not diseases samples. Samples are more fully described in Table 1 of the manuscript. Mean fold changes were calculated using a division of log (2)-normalized expression values between experimental sample and uninfected control as described in Materials & Methods. False discovery rate of the pair-wise comparisons were calculated using p-values from LIMMA. Significantly regulated genes were selected using a 2-fold cut-off and a false discovery rate of < 0.05.

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Additional File 9:

Pathway gene expression in LCMV-WE-infected macaque liver tissues. Significantly affected pathway gene expression in LCMV-WE-infected macaque liver tissues. KEGG software was used to identify groupings of genes with pathways based on published data. False discovery rate of the pair-wise comparisons were calculated using p-values from LIMMA. Significantly regulated genes were selected using a 2-fold cut-off and a false discovery rate of < 0.05.

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