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Mapping the global mRNA transcriptome during development of the murine first molar.

Landin MA, Nygård S, Shabestari MG, Babaie E, Reseland JE, Osmundsen H - Front Genet (2015)

Bottom Line: Differentially expressed genes (p < 0.05) were subjected to bioinformatic analysis to identify cellular activities significantly associated with these genes.The remaining 2441 genes were subjected to further statistical analysis using a supervised procedure.Differentially expressed genes (DE) not described earlier during murine tooth development; Inositol 1, 4, 5-triphosphate receptor 3 (Itpr3), metallothionein 1(Mt1), cyclin-dependent kinase 4 (Cdk4), cathepsin D (Ctsd), keratin complex 2, basic, gene 6a (Krt2-6a), cofilin 1, non-muscle (Cfl1), cyclin 2 (Ccnd2), were verified by real-time RT-PCR.

View Article: PubMed Central - PubMed

Affiliation: Department of Oral Biology, Faculty of Dentistry, University of Oslo Oslo, Norway.

ABSTRACT
The main objective of this study was to map global gene expression in order to provide information about the populations of mRNA species participating in murine tooth development at 24 h intervals, starting at the 11th embryonic day (E11.5) up to the 7th post-natal day (P7). The levels of RNA species expressed during murine tooth development were mesured using a total of 58 deoxyoligonucleotide microarrays. Microarray data was validated using real-time RT-PCR. Differentially expressed genes (p < 0.05) were subjected to bioinformatic analysis to identify cellular activities significantly associated with these genes. Using ANOVA the microarray data yielded 4362 genes as being differentially expressed from the 11th embryonic day (E11.5) up to 7 days post-natal (P7), 1921 of these being genes without known functions. The remaining 2441 genes were subjected to further statistical analysis using a supervised procedure. Bioinformatic analysis results for each time-point studied suggests that the main molecular functions associated with genes expressed at the early pre-natal stages (E12.5-E18.5) were cell cycle progression, cell morphology, lipid metabolism, cellular growth, proliferation, senescence and apoptosis, whereas most genes expressed at post-natal and secretory stages (P0-P7) were significantly associated with regulation of cell migration, biosynthesis, differentiation, oxidative stress, polarization and cell death. Differentially expressed genes (DE) not described earlier during murine tooth development; Inositol 1, 4, 5-triphosphate receptor 3 (Itpr3), metallothionein 1(Mt1), cyclin-dependent kinase 4 (Cdk4), cathepsin D (Ctsd), keratin complex 2, basic, gene 6a (Krt2-6a), cofilin 1, non-muscle (Cfl1), cyclin 2 (Ccnd2), were verified by real-time RT-PCR.

No MeSH data available.


Related in: MedlinePlus

Transcription factor analysis (IPA). Bioinformatics transcription factor analysis performed using Ingenuity Pathway Analysis (IPA) for the 4362 genes throughout the time-course (A–O) exhibiting a p-value of overlap <0.01 associating significantly ~1000 genes with 63 transcription factors. Pre-natal stages: Bud stages [A (E12.5), B (E13.5)]. Enamel knot stage [C (E14.5)]. Bell stages [D (E15.5), E (E16.5), F (E17.5), and G (E18.5)]. Day of birth (P0). Post-natal stages: Differentiation of odontoblasts (I–K), start of mineralization: dentin deposition (N–L), enamel deposition (O).
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Figure 3: Transcription factor analysis (IPA). Bioinformatics transcription factor analysis performed using Ingenuity Pathway Analysis (IPA) for the 4362 genes throughout the time-course (A–O) exhibiting a p-value of overlap <0.01 associating significantly ~1000 genes with 63 transcription factors. Pre-natal stages: Bud stages [A (E12.5), B (E13.5)]. Enamel knot stage [C (E14.5)]. Bell stages [D (E15.5), E (E16.5), F (E17.5), and G (E18.5)]. Day of birth (P0). Post-natal stages: Differentiation of odontoblasts (I–K), start of mineralization: dentin deposition (N–L), enamel deposition (O).

Mentions: Transcription factor analysis suggested that 19 transcription factors are involved in the transcription of 23 genes during the invagination of the epithelium into the mesenchyme at E12.5 (Table 2). The transcription factor (TF) Huntingtin (Htt) in the tooth germ regulated other transcription factors e.g., Hif1a, Purb, and C/ebp (Figure 3A).


Mapping the global mRNA transcriptome during development of the murine first molar.

Landin MA, Nygård S, Shabestari MG, Babaie E, Reseland JE, Osmundsen H - Front Genet (2015)

Transcription factor analysis (IPA). Bioinformatics transcription factor analysis performed using Ingenuity Pathway Analysis (IPA) for the 4362 genes throughout the time-course (A–O) exhibiting a p-value of overlap <0.01 associating significantly ~1000 genes with 63 transcription factors. Pre-natal stages: Bud stages [A (E12.5), B (E13.5)]. Enamel knot stage [C (E14.5)]. Bell stages [D (E15.5), E (E16.5), F (E17.5), and G (E18.5)]. Day of birth (P0). Post-natal stages: Differentiation of odontoblasts (I–K), start of mineralization: dentin deposition (N–L), enamel deposition (O).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4362327&req=5

Figure 3: Transcription factor analysis (IPA). Bioinformatics transcription factor analysis performed using Ingenuity Pathway Analysis (IPA) for the 4362 genes throughout the time-course (A–O) exhibiting a p-value of overlap <0.01 associating significantly ~1000 genes with 63 transcription factors. Pre-natal stages: Bud stages [A (E12.5), B (E13.5)]. Enamel knot stage [C (E14.5)]. Bell stages [D (E15.5), E (E16.5), F (E17.5), and G (E18.5)]. Day of birth (P0). Post-natal stages: Differentiation of odontoblasts (I–K), start of mineralization: dentin deposition (N–L), enamel deposition (O).
Mentions: Transcription factor analysis suggested that 19 transcription factors are involved in the transcription of 23 genes during the invagination of the epithelium into the mesenchyme at E12.5 (Table 2). The transcription factor (TF) Huntingtin (Htt) in the tooth germ regulated other transcription factors e.g., Hif1a, Purb, and C/ebp (Figure 3A).

Bottom Line: Differentially expressed genes (p < 0.05) were subjected to bioinformatic analysis to identify cellular activities significantly associated with these genes.The remaining 2441 genes were subjected to further statistical analysis using a supervised procedure.Differentially expressed genes (DE) not described earlier during murine tooth development; Inositol 1, 4, 5-triphosphate receptor 3 (Itpr3), metallothionein 1(Mt1), cyclin-dependent kinase 4 (Cdk4), cathepsin D (Ctsd), keratin complex 2, basic, gene 6a (Krt2-6a), cofilin 1, non-muscle (Cfl1), cyclin 2 (Ccnd2), were verified by real-time RT-PCR.

View Article: PubMed Central - PubMed

Affiliation: Department of Oral Biology, Faculty of Dentistry, University of Oslo Oslo, Norway.

ABSTRACT
The main objective of this study was to map global gene expression in order to provide information about the populations of mRNA species participating in murine tooth development at 24 h intervals, starting at the 11th embryonic day (E11.5) up to the 7th post-natal day (P7). The levels of RNA species expressed during murine tooth development were mesured using a total of 58 deoxyoligonucleotide microarrays. Microarray data was validated using real-time RT-PCR. Differentially expressed genes (p < 0.05) were subjected to bioinformatic analysis to identify cellular activities significantly associated with these genes. Using ANOVA the microarray data yielded 4362 genes as being differentially expressed from the 11th embryonic day (E11.5) up to 7 days post-natal (P7), 1921 of these being genes without known functions. The remaining 2441 genes were subjected to further statistical analysis using a supervised procedure. Bioinformatic analysis results for each time-point studied suggests that the main molecular functions associated with genes expressed at the early pre-natal stages (E12.5-E18.5) were cell cycle progression, cell morphology, lipid metabolism, cellular growth, proliferation, senescence and apoptosis, whereas most genes expressed at post-natal and secretory stages (P0-P7) were significantly associated with regulation of cell migration, biosynthesis, differentiation, oxidative stress, polarization and cell death. Differentially expressed genes (DE) not described earlier during murine tooth development; Inositol 1, 4, 5-triphosphate receptor 3 (Itpr3), metallothionein 1(Mt1), cyclin-dependent kinase 4 (Cdk4), cathepsin D (Ctsd), keratin complex 2, basic, gene 6a (Krt2-6a), cofilin 1, non-muscle (Cfl1), cyclin 2 (Ccnd2), were verified by real-time RT-PCR.

No MeSH data available.


Related in: MedlinePlus