Celsius: a community resource for Affymetrix microarray data

Day, Allen; Carlson, Marc; Dong, Jun; O’Connor, Brian D.; Nelson, Stanley F.

doi:10.1186/gb-2007-8-6-r112

Cited by 60 publications

(62 citation statements)

References 37 publications

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“…Data from the Celsius database, a unique resource encompassing many Affymetrix microarrays, confirms high coexpression of probe sets representing these four hubs (Fig. 3B) (26). Although three of these hubs are of unknown function, ZNF160 is a known transcriptional repressor of TLR4, which contributes to amyloid peptide-induced microglial toxicity (27), suggesting a possible known molecular link between M9h and AD.…”

Section: Differences In Mouse and Human Modules Provide Insight Into Admentioning

confidence: 76%

“…Many genes are expressed in more than one tissue (43,44); therefore, such filtering emphasizes transcriptional correlations based on brain-specific gene functions. Second, we include data from multiple studies across array platforms, resulting in more functionally relevant coexpression relationships (26,45). Our unbiased preprocessing steps lead to much higher comparability than previous studies, as measured by correlation of ranked expression between species (Fig.…”

Section: Discussionmentioning

confidence: 99%

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Divergence of human and mouse brain transcriptome highlights Alzheimer disease pathways

Miller

Horvath²,

Geschwind³

2010

Proc. Natl. Acad. Sci. U.S.A.

431

442

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Because mouse models play a crucial role in biomedical research related to the human nervous system, understanding the similarities and differences between mouse and human brain is of fundamental importance. Studies comparing transcription in human and mouse have come to varied conclusions, in part because of their relatively small sample sizes or underpowered methodologies. To better characterize gene expression differences between mouse and human, we took a systems-biology approach by using weighted gene coexpression network analysis on more than 1,000 microarrays from brain. We find that global network properties of the brain transcriptome are highly preserved between species. Furthermore, all modules of highly coexpressed genes identified in mouse were identified in human, with those related to conserved cellular functions showing the strongest between-species preservation. Modules corresponding to glial and neuronal cells were sufficiently preserved between mouse and human to permit identification of cross species cell-class marker genes. We also identify several robust human-specific modules, including one strongly correlated with measures of Alzheimer disease progression across multiple data sets, whose hubs are poorly-characterized genes likely involved in Alzheimer disease. We present multiple lines of evidence suggesting links between neurodegenerative disease and glial cell types in human, including human-specific correlation of presenilin-1 with oligodendrocyte markers, and significant enrichment for known neurodegenerative disease genes in microglial modules. Together, this work identifies convergent and divergent pathways in mouse and human, and provides a systematic framework that will be useful for understanding the applicability of mouse models for human brain disorders.neurodegenerative disease | systems biology | evolution | metaanalysis | gene expression

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Section: Differences In Mouse and Human Modules Provide Insight Into Admentioning

confidence: 76%

Section: Discussionmentioning

confidence: 99%

Divergence of human and mouse brain transcriptome highlights Alzheimer disease pathways

Miller

Horvath²,

Geschwind³

2010

Proc. Natl. Acad. Sci. U.S.A.

431

442

View full text Add to dashboard Cite

show abstract

“…Unlike Iowa eyes, donors from the second cohort were reserved for validation purposes (Oregon eyes, n = 30, RPE-choroid only). As a measure of quality control, we evaluated samples from both cohorts for postmortem RNA degradation, inter-array concordance, and agreement with previously published transcriptome experiments [36,38,[115][116][117], and found our data to be of high quality and suitable for genomics analysis (see Additional file 4 for a detailed discussion of sample and array quality control measures).…”

Section: Amd Transcriptome Profilingmentioning

confidence: 99%

Systems-level analysis of age-related macular degeneration reveals global biomarkers and phenotype-specific functional networks

Newman

Gallo²,

Hancox

et al. 2012

Genome Medicine

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Background: Age-related macular degeneration (AMD) is a leading cause of blindness that affects the central region of the retinal pigmented epithelium (RPE), choroid, and neural retina. Initially characterized by an accumulation of sub-RPE deposits, AMD leads to progressive retinal degeneration, and in advanced cases, irreversible vision loss. Although genetic analysis, animal models, and cell culture systems have yielded important insights into AMD, the molecular pathways underlying AMD's onset and progression remain poorly delineated. We sought to better understand the molecular underpinnings of this devastating disease by performing the first comparative transcriptome analysis of AMD and normal human donor eyes.

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“…Methods for the processing of samples are previously described. 22 Briefly, using default parameters, RMA from the Bioconductor R library was used to quantify and normalize the samples relative to other microarrays of the same Affymetrix platform with a comparison group of 50 samples randomly selected from the database.…”

mentioning

confidence: 99%

Bevacizumab and chemotherapy for recurrent glioblastoma

Nghiemphu¹,

Liu²,

Lee³

et al. 2009

Neurology

227

148

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Objective: Bevacizumab has been shown to be effective in the treatment of recurrent glioblastoma in combination with chemotherapy compared with historic controls but not in randomized trials. Methods:We conducted a retrospective analysis of patients treated for recurrent glioblastoma with bevacizumab vs a control group of patients, comparing progression-free survival (PFS) and overall survival (OS) between the two groups, and performed subgroup analysis based on age and performance status. Expression of vascular endothelial growth factor (VEGF) based on age was examined using DNA microarray analysis. We also evaluated the impact of bevacizumab on quality of life.

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Celsius: a community resource for Affymetrix microarray data

Cited by 60 publications

References 37 publications

Divergence of human and mouse brain transcriptome highlights Alzheimer disease pathways

Divergence of human and mouse brain transcriptome highlights Alzheimer disease pathways

Systems-level analysis of age-related macular degeneration reveals global biomarkers and phenotype-specific functional networks

Bevacizumab and chemotherapy for recurrent glioblastoma

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