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Physiology, pathology and relatedness of human tissues from gene expression meta-analysis.

Greco D, Somervuo P, Di Lieto A, Raitila T, Nitsch L, Castrén E, Auvinen P - PLoS ONE (2008)

Bottom Line: Using co-citation driven gene network technique and promoter analysis, we predicted a transcriptional module where the co-operation of the transcription factors E2F and NF-kappaB can possibly regulate a number of genes involved in the neurogenesis that takes place in the adult hippocampus.Here we propose that integration of gene expression data from Affymetrix GeneChip experiments is possible through re-annotation and commonly used pre-processing methods.We suggest that some functional aspects of the tissues can be explained by the co-operation of multiple transcription factors that regulate the expression of selected groups of genes.

View Article: PubMed Central - PubMed

Affiliation: Institute of Biotechnology, University of Helsinki, Helsinki, Finland. dario.greco@helsinki.fi

ABSTRACT

Background: Development and maintenance of the identity of tissues is of central importance for multicellular organisms. Based on gene expression profiles, it is possible to divide genes in housekeeping genes and those whose expression is preferential in one or a few tissues and which provide specialized functions that have a strong effect on the physiology of the whole organism.

Results: We have surveyed the gene expression in 78 normal human tissues integrating publicly available microarray gene expression data. A total amount of 1601 genes were identified as selectively expressed in one or more tissues. The tissue-selective genes covered a wide range of cellular and molecular functions, and could be linked to 361 human diseases with Mendelian inheritance. Based on the gene expression profiles, we were able to form a network of tissues reflecting their functional relatedness and, to certain extent, their development. Using co-citation driven gene network technique and promoter analysis, we predicted a transcriptional module where the co-operation of the transcription factors E2F and NF-kappaB can possibly regulate a number of genes involved in the neurogenesis that takes place in the adult hippocampus.

Conclusions: Here we propose that integration of gene expression data from Affymetrix GeneChip experiments is possible through re-annotation and commonly used pre-processing methods. We suggest that some functional aspects of the tissues can be explained by the co-operation of multiple transcription factors that regulate the expression of selected groups of genes.

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Related in: MedlinePlus

Tissue Connectome.Color code: Central Nervous System RED; Peripheral Nervous System ORANGE; Testis YELLOW; Muscles GREEN; immune cells LIGHT BLUE; Immune Organs DARK BLUE; Respiratory System PINK; Pancreas and Islets DARK PINK; Adrenal Gland and Adrenal Cortex LIGHT PINK; Thyroid and Fetal Thyroid SEPIA; Others WHITE. The edges have been drawn between tissue nodes sharing: a) 30 or more genes; b) 20 or more genes; c) 5 or more genes. d) the number of edges as a function of tissue-selective genes shared by two or more tissues. The tissue indexes are reported in Table 1.
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pone-0001880-g001: Tissue Connectome.Color code: Central Nervous System RED; Peripheral Nervous System ORANGE; Testis YELLOW; Muscles GREEN; immune cells LIGHT BLUE; Immune Organs DARK BLUE; Respiratory System PINK; Pancreas and Islets DARK PINK; Adrenal Gland and Adrenal Cortex LIGHT PINK; Thyroid and Fetal Thyroid SEPIA; Others WHITE. The edges have been drawn between tissue nodes sharing: a) 30 or more genes; b) 20 or more genes; c) 5 or more genes. d) the number of edges as a function of tissue-selective genes shared by two or more tissues. The tissue indexes are reported in Table 1.

Mentions: The number of edges in the network was computed as a function of the number of shared genes between the tissues and three cutoff values (30 or more genes, 20 or more genes, and 5 or more genes) were chosen as representative of different degrees of connectivity (Figure 1d).


Physiology, pathology and relatedness of human tissues from gene expression meta-analysis.

Greco D, Somervuo P, Di Lieto A, Raitila T, Nitsch L, Castrén E, Auvinen P - PLoS ONE (2008)

Tissue Connectome.Color code: Central Nervous System RED; Peripheral Nervous System ORANGE; Testis YELLOW; Muscles GREEN; immune cells LIGHT BLUE; Immune Organs DARK BLUE; Respiratory System PINK; Pancreas and Islets DARK PINK; Adrenal Gland and Adrenal Cortex LIGHT PINK; Thyroid and Fetal Thyroid SEPIA; Others WHITE. The edges have been drawn between tissue nodes sharing: a) 30 or more genes; b) 20 or more genes; c) 5 or more genes. d) the number of edges as a function of tissue-selective genes shared by two or more tissues. The tissue indexes are reported in Table 1.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC2268968&req=5

pone-0001880-g001: Tissue Connectome.Color code: Central Nervous System RED; Peripheral Nervous System ORANGE; Testis YELLOW; Muscles GREEN; immune cells LIGHT BLUE; Immune Organs DARK BLUE; Respiratory System PINK; Pancreas and Islets DARK PINK; Adrenal Gland and Adrenal Cortex LIGHT PINK; Thyroid and Fetal Thyroid SEPIA; Others WHITE. The edges have been drawn between tissue nodes sharing: a) 30 or more genes; b) 20 or more genes; c) 5 or more genes. d) the number of edges as a function of tissue-selective genes shared by two or more tissues. The tissue indexes are reported in Table 1.
Mentions: The number of edges in the network was computed as a function of the number of shared genes between the tissues and three cutoff values (30 or more genes, 20 or more genes, and 5 or more genes) were chosen as representative of different degrees of connectivity (Figure 1d).

Bottom Line: Using co-citation driven gene network technique and promoter analysis, we predicted a transcriptional module where the co-operation of the transcription factors E2F and NF-kappaB can possibly regulate a number of genes involved in the neurogenesis that takes place in the adult hippocampus.Here we propose that integration of gene expression data from Affymetrix GeneChip experiments is possible through re-annotation and commonly used pre-processing methods.We suggest that some functional aspects of the tissues can be explained by the co-operation of multiple transcription factors that regulate the expression of selected groups of genes.

View Article: PubMed Central - PubMed

Affiliation: Institute of Biotechnology, University of Helsinki, Helsinki, Finland. dario.greco@helsinki.fi

ABSTRACT

Background: Development and maintenance of the identity of tissues is of central importance for multicellular organisms. Based on gene expression profiles, it is possible to divide genes in housekeeping genes and those whose expression is preferential in one or a few tissues and which provide specialized functions that have a strong effect on the physiology of the whole organism.

Results: We have surveyed the gene expression in 78 normal human tissues integrating publicly available microarray gene expression data. A total amount of 1601 genes were identified as selectively expressed in one or more tissues. The tissue-selective genes covered a wide range of cellular and molecular functions, and could be linked to 361 human diseases with Mendelian inheritance. Based on the gene expression profiles, we were able to form a network of tissues reflecting their functional relatedness and, to certain extent, their development. Using co-citation driven gene network technique and promoter analysis, we predicted a transcriptional module where the co-operation of the transcription factors E2F and NF-kappaB can possibly regulate a number of genes involved in the neurogenesis that takes place in the adult hippocampus.

Conclusions: Here we propose that integration of gene expression data from Affymetrix GeneChip experiments is possible through re-annotation and commonly used pre-processing methods. We suggest that some functional aspects of the tissues can be explained by the co-operation of multiple transcription factors that regulate the expression of selected groups of genes.

Show MeSH
Related in: MedlinePlus