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accession-icon GSE62037
Integrated ordination of miRNA and mRNA expression profiles
  • organism-icon Homo sapiens
  • sample-icon 59 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Integrated ordination of miRNA and mRNA expression profiles.

Alternate Accession IDs

E-GEOD-62037

Sample Metadata Fields

Specimen part

View Samples
accession-icon GSE62029
Integrated ordination of miRNA and mRNA expression profiles [mRNA]
  • organism-icon Homo sapiens
  • sample-icon 29 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Several studies have shown that negative and positive miRNA-mRNA correlations are symmetrically distributed. While negative correlations are consistent with a faster degradation of miRNA targets, the presence of positive correlations suggests bidirectional interactions between the two classes of molecules. However, a comprehensive study of miRNA and mRNA correlations is lacking. A homogeneous map of miRNA and mRNA relationships was obtained by multidimensional scaling (MDS) applied to a single matrix including both heterologous (miRNA-mRNA) and homologous (miRNA-miRNA and mRNA-mRNA) correlations.

Publication Title

Integrated ordination of miRNA and mRNA expression profiles.

Alternate Accession IDs

E-GEOD-62029

Sample Metadata Fields

Specimen part

View Samples
accession-icon GSE38941
Liver Regeneration Gene Signature in Hepatitis B virus (HBV)-Associated Acute Liver Failure Identified by Gene Expression Profiling
  • organism-icon Homo sapiens
  • sample-icon 27 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

The liver has inherent regenerative capacity via mitotic division of mature hepatocytes. However, if the hepatic loss is massive or mature hepatocyte proliferation is impaired by chronic liver injury, HSPC are activated to support liver regeneration. Access to liver tissue from 4 patients who underwent liver transplantation for hepatitis B virus (HBV)- associated acute liver failure (ALF) provided us with the opportunity to investigate the molecular mechanisms of liver regeneration in humans by means of gene expression profiling and immunohistochemistry (IHC). Gene expression profiling of 17 liver specimens from the 4 ALF cases and individual liver specimens from 10 liver donors documented a distinct gene signature for ALF. However, unsupervised multidimensional scaling and hierarchical clustering identified two-well defined clusters that segregated according to the histopathological severity, i.e. massive hepatic necrosis (MHN; 2 patients) and submassive hepatic necrosis (SHN; 2 patients). We found that ALF is characterized by a strong hepatic stem/progenitor cell (HSPC) gene signature, as also confirmed by IHC, along with ductular reaction, both of which are more prominent in MHN. Interestingly, no evidence of further lineage differentiation was seen in MHN, whereas in SHN we detected cells with hepatocyte-like morphology. Strikingly, ALF was associated with a strong tumorigenesis gene signature. MHN had the greatest upregulation of cancer stem cell genes (EpCAM, CK19 and CK7), whereas the most upregulated genes in SHN were related to cellular growth and proliferation (AKR1B10, NQO1, RRM2, SFN, TOP2A, CCNB1, CDC20, ANLN and KI67). The extent of liver necrosis correlated with an overriding fibrogenesis gene signature, reflecting the wound healing process. Conclusion: Our data provide evidence of marked HSPC cell activation and fibrogenesis in HBV-associated ALF, which positively correlate with the extent of liver necrosis. Moreover, we detected a strong tumorigenesis gene signature in ALF, which underlines the relationship between liver regeneration and liver cancer.

Publication Title

Liver regeneration signature in hepatitis B virus (HBV)-associated acute liver failure identified by gene expression profiling.

Alternate Accession IDs

E-GEOD-38941

Sample Metadata Fields

Specimen part, Disease, Disease stage, Subject

View Samples
accession-icon SRP043431
A Dach2-Hdac9-Myog-Gdf5 signaling system regulates regeneration of neuromuscular synapses
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

Muscle denervation due to injury, disease or aging results in impaired motor function. Restoring neuromuscular communication requires axonal regrowth and regeneration of neuromuscular synapses. Muscle activity inhibits neuromuscular synapse regeneration. The mechanism by which muscle activity regulates regeneration of synapses is poorly understood. Dach2 and Hdac9 are activity-regulated transcriptional co-repressors that are highly expressed in innervated muscle and suppressed following muscle denervation. Here, we report that Dach2 and Hdac9 inhibit regeneration of neuromuscular synapses. Importantly, we identified Myog and Gdf5 as muscle-specific Dach2/Hdac9-regulated genes that stimulate neuromuscular regeneration in denervated muscle. Interestingly, Gdf5 also stimulates presynaptic differentiation and inhibits branching of regenerating neurons. Finally, we found that Dach2 and Hdac9 suppress miR206 expression, a microRNA involved in enhancing neuromuscular regeneration. Overall design: RNAseq on innervated and 3 day denervated adult soleus muscle from wildtype mice is compared with that from 3 day denervated soleus muscle from Dach2/Hdac9 deleted mice to identify Dach2/Hdac9-regulated genes.

Publication Title

Dach2-Hdac9 signaling regulates reinnervation of muscle endplates.

Alternate Accession IDs

GSE58669

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE14668
B-Cell Gene Signature with Massive Intrahepatic Production of Antibodies to Hepatitis B Core Antigen in HBV-Associated Acute Liver Failure
  • organism-icon Homo sapiens
  • sample-icon 27 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Hepatitis B virus (HBV)-associated acute liver failure (ALF) is a dramatic clinical syndrome due to a sudden loss of hepatic cells leading to multiorgan failure. The mechanisms whereby HBV induces ALF are unknown. We used gene expression profiling to establish a molecular definition of hepatitis B virus (HBV)-associated ALF. Two patients who underwent liver transplantation for HBV-associated ALF were studied. Gene expression profiling was performed on 8 liver specimens obtained from the two patients with ALF (4 samples per liver) and individual liver specimens from 8 liver donors and normal livers from 11 patients who underwent resection for angioma. Statistical analyses were used to identify the signature genes of HBV-associated ALF. Multivariate permutation analysis identified 1,368 transcripts that were differentially expressed in ALF; 709 were up-regulated and 659 down-regulated. The most represented up-regulated transcripts were those involved in the immune response, whereas the most abundant down-regulated transcripts were those involved in metabolism and hepatic synthesis. ALF was characterized by overriding B-cell signature comprising genes related to mature B cells and plasma cells with abundant polyclonal expression of immunoglobulin genes. By contrast, there was a limited T-cell signature and up-regulation of several inhibitors of T-cell activation. Immunohistochemical analysis confirmed the prominent B-cell signature showing diffuse liver infiltration by plasma blasts and plasma cells with strong cytoplasmic staining for IgM and IgG, associated with a significant deposition of complement factors. Using phage display technology, we demonstrated that the molecular target of the massive intrahepatic antibody response is the hepatitis B core antigen (HBcAg). These data suggest that the humoral immunity may exert a primary role in the pathogenesis of HBV-associated ALF.

Publication Title

B cell gene signature with massive intrahepatic production of antibodies to hepatitis B core antigen in hepatitis B virus-associated acute liver failure.

Alternate Accession IDs

E-GEOD-14668

Sample Metadata Fields

Specimen part

View Samples
accession-icon GSE107170
Molecular Signature of Hepatitis D Virus-Associated Hepatocellular Carcinoma
  • organism-icon Homo sapiens
  • sample-icon 298 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

To investigate the role of viral and host factors in HDV-associated HCC we carried out an integrated clinicopathological and gene expression study of tissue specimens and laser microdissected hepatocytes obtained at the time of liver transplantation from livers with HDV-HCC, HDV-cirrhosis without HCC, HCV-HCC and HBV-HCC. References to GSM series of HDV and HBV livers, already deposited in GEO, are included in this series. Part of data of HCV livers are a re-analysis of GSE series GSE69715 and GSE78737, the re-analyzed GSM is indicated in the 'description' column and with a link at the bottom of the page.

Publication Title

Molecular Signature and Mechanisms of Hepatitis D Virus-Associated Hepatocellular Carcinoma.

Alternate Accession IDs

E-GEOD-107170

Sample Metadata Fields

Sex, Specimen part, Disease, Disease stage, Subject

View Samples
accession-icon GSE78737
Infection with Hepatitis C Virus Depends on TACSTD2, a Regulator of Claudin-1 and Occludin Highly Downregulated in Hepatocellular Carcinoma
  • organism-icon Homo sapiens
  • sample-icon 102 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Infection with hepatitis C virus depends on TACSTD2, a regulator of claudin-1 and occludin highly downregulated in hepatocellular carcinoma.

Alternate Accession IDs

E-GEOD-78737

Sample Metadata Fields

Sex, Age, Specimen part, Cell line

View Samples
accession-icon GSE69715
Infection with Hepatitis C Virus Depends on TACSTD2, a Regulator of Claudin-1 and Occludin Highly Downregulated in Hepatocellular Carcinoma [patient]
  • organism-icon Homo sapiens
  • sample-icon 98 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Our study identifies TACSTD2 as a novel regulator of two major HCV entry factors, CLDN1 and OCLN, which is strongly downregulated in malignant hepatocytes. These results provide new insights into the complex process of HCV entry into hepatocytes and may assist in the development of more efficient cellular systems for HCV propagation in vitro.

Publication Title

Infection with hepatitis C virus depends on TACSTD2, a regulator of claudin-1 and occludin highly downregulated in hepatocellular carcinoma.

Alternate Accession IDs

E-GEOD-69715

Sample Metadata Fields

Sex, Age, Specimen part

View Samples
accession-icon GSE98383
Molecular Signature of Hepatitis D Virus-Associated Hepatocellular Carcinoma
  • organism-icon Homo sapiens
  • sample-icon 72 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

To investigate the role of viral and host factors in HDV-related HCC we analyzed the serum, tissue specimens and laser microdissected hepatocytes obtained at the time of liver transplantation from five patients with HDV-HCC. Livers of seven patients with HDV-cirrhosis without HCC were also analyzed. We carried out an integrated clinicopathological analysis and gene expression profiling,

Publication Title

Molecular Signature and Mechanisms of Hepatitis D Virus-Associated Hepatocellular Carcinoma.

Alternate Accession IDs

E-GEOD-98383

Sample Metadata Fields

Specimen part, Disease, Disease stage

View Samples
accession-icon GSE78736
Infection with Hepatitis C Virus Depends on TACSTD2, a Regulator of Claudin-1 and Occludin Highly Downregulated in Hepatocellular Carcinoma [cell line]
  • organism-icon Homo sapiens
  • sample-icon 4 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Our study identifies TACSTD2 as a novel regulator of two major HCV entry factors, CLDN1 and OCLN, which is strongly downregulated in malignant hepatocytes. These results provide new insights into the complex process of HCV entry into hepatocytes and may assist in the development of more efficient cellular systems for HCV propagation in vitro.

Publication Title

Infection with hepatitis C virus depends on TACSTD2, a regulator of claudin-1 and occludin highly downregulated in hepatocellular carcinoma.

Alternate Accession IDs

E-GEOD-78736

Sample Metadata Fields

Cell line

View Samples
...

refine.bio is a repository of uniformly processed and normalized, ready-to-use transcriptome data from publicly available sources. refine.bio is a project of the Childhood Cancer Data Lab (CCDL)

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Cite refine.bio

Casey S. Greene, Dongbo Hu, Richard W. W. Jones, Stephanie Liu, David S. Mejia, Rob Patro, Stephen R. Piccolo, Ariel Rodriguez Romero, Hirak Sarkar, Candace L. Savonen, Jaclyn N. Taroni, William E. Vauclain, Deepashree Venkatesh Prasad, Kurt G. Wheeler. refine.bio: a resource of uniformly processed publicly available gene expression datasets.
URL: https://www.refine.bio

Note that the contributor list is in alphabetical order as we prepare a manuscript for submission.

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