Identification of novel reference genes based on MeSH categories.
Transcriptome experiments are performed to assess protein abundance through mRNA expression analysis. Expression levels of genes vary depending on the experimental conditions and the cell response. Transcriptome data must be diverse and yet comparable in reference to stably expressed genes, even if...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2014-01-01
|
| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC3969360?pdf=render |
| _version_ | 1819274206963040256 |
|---|---|
| author | Tulin Ersahin Levent Carkacioglu Tolga Can Ozlen Konu Volkan Atalay Rengul Cetin-Atalay |
| author_facet | Tulin Ersahin Levent Carkacioglu Tolga Can Ozlen Konu Volkan Atalay Rengul Cetin-Atalay |
| author_sort | Tulin Ersahin |
| collection | DOAJ |
| description | Transcriptome experiments are performed to assess protein abundance through mRNA expression analysis. Expression levels of genes vary depending on the experimental conditions and the cell response. Transcriptome data must be diverse and yet comparable in reference to stably expressed genes, even if they are generated from different experiments on the same biological context from various laboratories. In this study, expression patterns of 9090 microarray samples grouped into 381 NCBI-GEO datasets were investigated to identify novel candidate reference genes using randomizations and Receiver Operating Characteristic (ROC) curves. The analysis demonstrated that cell type specific reference gene sets display less variability than a united set for all tissues. Therefore, constitutively and stably expressed, origin specific novel reference gene sets were identified based on their coefficient of variation and percentage of occurrence in all GEO datasets, which were classified using Medical Subject Headings (MeSH). A large number of MeSH grouped reference gene lists are presented as novel tissue specific reference gene lists. The most commonly observed 17 genes in these sets were compared for their expression in 8 hepatocellular, 5 breast and 3 colon carcinoma cells by RT-qPCR to verify tissue specificity. Indeed, commonly used housekeeping genes GAPDH, Actin and EEF2 had tissue specific variations, whereas several ribosomal genes were among the most stably expressed genes in vitro. Our results confirm that two or more reference genes should be used in combination for differential expression analysis of large-scale data obtained from microarray or next generation sequencing studies. Therefore context dependent reference gene sets, as presented in this study, are required for normalization of expression data from diverse technological backgrounds. |
| first_indexed | 2024-12-23T23:04:45Z |
| format | Article |
| id | doaj.art-400b651814f04370a98ea2a5f93d0b6c |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-23T23:04:45Z |
| publishDate | 2014-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-400b651814f04370a98ea2a5f93d0b6c2022-12-21T17:26:49ZengPublic Library of Science (PLoS)PLoS ONE1932-62032014-01-0193e9334110.1371/journal.pone.0093341Identification of novel reference genes based on MeSH categories.Tulin ErsahinLevent CarkaciogluTolga CanOzlen KonuVolkan AtalayRengul Cetin-AtalayTranscriptome experiments are performed to assess protein abundance through mRNA expression analysis. Expression levels of genes vary depending on the experimental conditions and the cell response. Transcriptome data must be diverse and yet comparable in reference to stably expressed genes, even if they are generated from different experiments on the same biological context from various laboratories. In this study, expression patterns of 9090 microarray samples grouped into 381 NCBI-GEO datasets were investigated to identify novel candidate reference genes using randomizations and Receiver Operating Characteristic (ROC) curves. The analysis demonstrated that cell type specific reference gene sets display less variability than a united set for all tissues. Therefore, constitutively and stably expressed, origin specific novel reference gene sets were identified based on their coefficient of variation and percentage of occurrence in all GEO datasets, which were classified using Medical Subject Headings (MeSH). A large number of MeSH grouped reference gene lists are presented as novel tissue specific reference gene lists. The most commonly observed 17 genes in these sets were compared for their expression in 8 hepatocellular, 5 breast and 3 colon carcinoma cells by RT-qPCR to verify tissue specificity. Indeed, commonly used housekeeping genes GAPDH, Actin and EEF2 had tissue specific variations, whereas several ribosomal genes were among the most stably expressed genes in vitro. Our results confirm that two or more reference genes should be used in combination for differential expression analysis of large-scale data obtained from microarray or next generation sequencing studies. Therefore context dependent reference gene sets, as presented in this study, are required for normalization of expression data from diverse technological backgrounds.http://europepmc.org/articles/PMC3969360?pdf=render |
| spellingShingle | Tulin Ersahin Levent Carkacioglu Tolga Can Ozlen Konu Volkan Atalay Rengul Cetin-Atalay Identification of novel reference genes based on MeSH categories. PLoS ONE |
| title | Identification of novel reference genes based on MeSH categories. |
| title_full | Identification of novel reference genes based on MeSH categories. |
| title_fullStr | Identification of novel reference genes based on MeSH categories. |
| title_full_unstemmed | Identification of novel reference genes based on MeSH categories. |
| title_short | Identification of novel reference genes based on MeSH categories. |
| title_sort | identification of novel reference genes based on mesh categories |
| url | http://europepmc.org/articles/PMC3969360?pdf=render |
| work_keys_str_mv | AT tulinersahin identificationofnovelreferencegenesbasedonmeshcategories AT leventcarkacioglu identificationofnovelreferencegenesbasedonmeshcategories AT tolgacan identificationofnovelreferencegenesbasedonmeshcategories AT ozlenkonu identificationofnovelreferencegenesbasedonmeshcategories AT volkanatalay identificationofnovelreferencegenesbasedonmeshcategories AT rengulcetinatalay identificationofnovelreferencegenesbasedonmeshcategories |