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Homo sapiens
81 Downloadable Samples
Affymetrix Human Gene 1.0 ST Array (hugene10st), Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482), Illumina HiSeq 2000
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Epigenetic remodeling in B-cell acute lymphoblastic leukemia occurs in two tracks and employs embryonic stem cell-like signatures.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Mus musculus
- 307 Downloadable Samples
Affymetrix Mouse Gene 1.1 ST Array (mogene11st)
Description
Gene expression levels in normal tissues can differ substantially between individuals, due to inherited polymorphisms acting in cis or trans. Analysis of this variation across a population of genetically distinct individuals allows us to visualize a network of co-expressed genes under normal homeostatic conditions, and the consequences of perturbation by tissue damage or disease development. Here, we explore gene expression networks in normal adult skin from 470 genetically unique mice, and demonstrate the dependence of the architecture of signaling pathways on skin tissue location (dorsal or tail skin) and perturbation by induction of inflammation or tumorigenesis. Gene networks related to specific cell types, as well as signaling pathways including Sonic Hedgehog (Shh), Wnt, Lgr family stem cell markers, and keratins differed at these tissue sites, suggesting mechanisms for the differential susceptibility of dorsal and tail skin to development of skin diseases and tumorigenesis. The Pten tumor suppressor gene network is extensively rewired in premalignant tumors compared to normal tissue, but this response to perturbation is lost during malignant progression. We present a software package for eQTL network analysis and demonstrate how network analysis of whole tissues provides insights into interactions between cell compartments and signaling molecules.
Publication Title
Gene Expression Architecture of Mouse Dorsal and Tail Skin Reveals Functional Differences in Inflammation and Cancer.
Sample Metadata Fields
Sex, Age, Specimen part, Treatment
View Samples- Mus musculus, Mus musculus x mus spretus, Mus spretus
- 132 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Network analysis of skin tumor progression identifies a rewired genetic architecture affecting inflammation and tumor susceptibility.
Sample Metadata Fields
Sex
View Samples
GSE52524- Mus musculus
- 195 Downloadable Samples
- Affymetrix Mouse Gene 1.1 ST Array (mogene11st)
Description
Gene expression levels in normal tissues can differ substantially between individuals, due to inherited polymorphisms acting in cis or trans. Analysis of this variation across a population of genetically distinct individuals allows us to visualize a network of co-expressed genes under normal homeostatic conditions, and the consequences of perturbation by tissue damage or disease development. Here, we explore gene expression networks in normal adult skin from 470 genetically unique mice, and demonstrate the dependence of the architecture of signaling pathways on skin tissue location (dorsal or tail skin) and perturbation by induction of inflammation or tumorigenesis. Gene networks related to specific cell types, as well as signaling pathways including Sonic Hedgehog (Shh), Wnt, Lgr family stem cell markers, and keratins differed at these tissue sites, suggesting mechanisms for the differential susceptibility of dorsal and tail skin to development of skin diseases and tumorigenesis. The Pten tumor suppressor gene network is extensively rewired in premalignant tumors compared to normal tissue, but this response to perturbation is lost during malignant progression. We present a software package for eQTL network analysis and demonstrate how network analysis of whole tissues provides insights into interactions between cell compartments and signaling molecules.
Publication Title
Gene Expression Architecture of Mouse Dorsal and Tail Skin Reveals Functional Differences in Inflammation and Cancer.
Sample Metadata Fields
Sex, Specimen part
View Samples- Homo sapiens
- 164 Downloadable Samples
- Affymetrix Human Genome U133A 2.0 Array (hgu133a2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Analysis of mRNA profiles after MEK1/2 inhibition in human pancreatic cancer cell lines reveals pathways involved in drug sensitivity.
Sample Metadata Fields
Specimen part, Cell line
View Samples GSE52639- Mus musculus
- 153 Downloadable Samples
- Affymetrix Mouse Gene 1.1 ST Array (mogene11st)
Description
Gene expression levels in normal tissues can differ substantially between individuals, due to inherited polymorphisms acting in cis or trans. Analysis of this variation across a population of genetically distinct individuals allows us to visualize a network of co-expressed genes under normal homeostatic conditions, and the consequences of perturbation by tissue damage or disease development. Here, we explore gene expression networks in normal adult skin from 470 genetically unique mice, and demonstrate the dependence of the architecture of signaling pathways on skin tissue location (dorsal or tail skin) and perturbation by induction of inflammation or tumorigenesis. Gene networks related to specific cell types, as well as signaling pathways including Sonic Hedgehog (Shh), Wnt, Lgr family stem cell markers, and keratins differed at these tissue sites, suggesting mechanisms for the differential susceptibility of dorsal and tail skin to development of skin diseases and tumorigenesis. The Pten tumor suppressor gene network is extensively rewired in premalignant tumors compared to normal tissue, but this response to perturbation is lost during malignant progression. We present a software package for eQTL network analysis and demonstrate how network analysis of whole tissues provides insights into interactions between cell compartments and signaling molecules.
Publication Title
Gene Expression Architecture of Mouse Dorsal and Tail Skin Reveals Functional Differences in Inflammation and Cancer.
Sample Metadata Fields
Sex
View Samples- Homo sapiens
- 140 Downloadable Samples
- Affymetrix Human Genome U133A 2.0 Array (hgu133a2)
Description
Analysis of mRNA profiles after MEK1/2 inhibition in human pancreatic cancer cell lines reveals pathways involved in drug sensitivity.
Publication Title
Analysis of mRNA profiles after MEK1/2 inhibition in human pancreatic cancer cell lines reveals pathways involved in drug sensitivity.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Saccharomyces cerevisiae
- 82 Downloadable Samples
- Affymetrix Yeast Genome S98 Array (ygs98)
Description
Using microarrays to genotype the parental origin of progeny resulting from a cross between S96 and YJM789 yeast strains, we mapped the distribution of crossovers that occurred during meiosis. Knowledge of the crossover distribution allowed us to assess changes in crossover control in wild type and mutant strains.
Publication Title
Global analysis of the meiotic crossover landscape.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 130 Downloadable Samples
- Affymetrix Mouse Gene 1.1 ST Array (mogene11st)
Description
Hair follicles are self-renewing organs within the skin which cycle through periods of growth and destruction, with an intervening period of outward quiescence. The hair follicle cycle is driven by Hedgehog and Wnt signaling and affects epithelial thickness, melanin production, immune function, and tumor susceptibility. We have previously shown that somatic alterations to the genome affect the genetic architecture of the skin. This study examines how the hair follicle cycle affects gene the genetic architecture in vivo by genomic and genetic analysis of 343 genetically heterogeneous mice during the hair follicle growth phase (anagen) and quiescent phase (telogen). We use eQTL analysis and differential correlation to identify changes in metabolic and stem cell activity not detected by differential expression. Germline influence in gene expression is profoundly higher during anagen, but this increase is not a simple factor of higher levels of gene expression. The most strongly induced eQTLs were involved in cellular energy metabolism and melanogenesis rather than hair follicle growth or hedgehog signaling. We demonstrate that hair follicle and circadian rhythm pathways are sexually dimorphic, but do not find evidence for an effect of sex on eQTL networks. We also use eQTL gene network analysis to identify candidate causal relationships between expression of genes in the hair follicle and melanin pathways, identifying Mcoln3 as a candidate for the familial melanoma locus on 1p22. To lower the bioinformatic barriers to eQTL network analysis we produced CARMEN, a free open-source stand-alone software package. This study demonstrates how to perform a systems genetic analysis of a heterogeneous tissue studied in vivo under physiologically relevant growth signals.
Publication Title
Gene Expression Architecture of Mouse Dorsal and Tail Skin Reveals Functional Differences in Inflammation and Cancer.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Homo sapiens
- 124 Downloadable Samples
- Affymetrix Human Genome U133B Array (hgu133b)
Description
GBM samples were clusered using gene expression of AKT pathway genes to reveal at least 5 GBM AKT subtypes, having distinct DNA copy number alterations, enrichment in oncogenes and tumor suppressor genes and patterns of expression for PI3K/AKT/mTOR signaling components.
Publication Title
AKT pathway genes define 5 prognostic subgroups in glioblastoma.
Sample Metadata Fields
Sex, Age
View Samples