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Generating and evaluating a ranked candidate gene list for potential vertebrate heart field regulators.

Musso G, Mosimann C, Panáková D, Burger A, Zhou Y, Zon LI, MacRae CA - Genom Data (2015)

Bottom Line: We found that key transcription factors that regulate septation and chamber formation in higher vertebrates, including Tbx5 and Pitx2, influence relative FHF and SHF contributions to the zebrafish heart tube.To identify molecular modulators of heart field migration, we used microarray-based expression profiling following inhibition of tbx5a and pitx2ab in embryonic zebrafish (Mosimann & Panakova, et al, 2015; GSE70750).Here, we describe in more detail the procedure used to process, prioritize, and analyze the expression data for functional enrichment.

View Article: PubMed Central - PubMed

Affiliation: Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.

ABSTRACT
The vertebrate heart develops from two distinct lineages of cardiomyocytes that arise from the first and second heart fields (FHF and SHF, respectively). The FHF forms the primitive heart tube, while adding cells from the SHF allows elongation at both poles of the tube. Initially seen as an exclusive characteristic of higher vertebrates, recent work has demonstrated the presence of a distinct FHF and SHF in lower vertebrates, including zebrafish. We found that key transcription factors that regulate septation and chamber formation in higher vertebrates, including Tbx5 and Pitx2, influence relative FHF and SHF contributions to the zebrafish heart tube. To identify molecular modulators of heart field migration, we used microarray-based expression profiling following inhibition of tbx5a and pitx2ab in embryonic zebrafish (Mosimann & Panakova, et al, 2015; GSE70750). Here, we describe in more detail the procedure used to process, prioritize, and analyze the expression data for functional enrichment.

No MeSH data available.


Related in: MedlinePlus

Normalization and GSEA enrichment analysis results. Boxplots (A & B) show the expression intensity values for each CEL file both before (A) and after (B) RMA normalization. Plots outputted by GSEA (C & D) show enrichment for genes annotated as being involved in homophilic cell adhesion following pitx2 (C) and tbx5 (D) knockdown.
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f0005: Normalization and GSEA enrichment analysis results. Boxplots (A & B) show the expression intensity values for each CEL file both before (A) and after (B) RMA normalization. Plots outputted by GSEA (C & D) show enrichment for genes annotated as being involved in homophilic cell adhesion following pitx2 (C) and tbx5 (D) knockdown.

Mentions: Raw CEL files were processed using the Oligo package [4] as part of the Bioconductor suite (www.bioconductor.org) in the R statistical framework (www.r-project.org), using a customized script (Supplementary Script 1). Specifically, background subtraction and normalization were performed using the Robust Multiarray Average (RMA) method implemented in the Oligo package. Boxplots of intensity values were compared for all chips before and after normalization to visualize the corresponding effects on mean and quartile values (Fig. 1A–B). Following normalization, probeset IDs were matched to corresponding transcript IDs. Specifically, the zebrafish 1.0 ST array NetAffx annotation file was downloaded in CSV format from the Affymetrix website (www.affymetrix.com), and transcript/gene IDs corresponding to given probe IDs were extracted (Supplementary Table 1). In the interest of representing the data using a single gene annotation framework, all transcript and gene IDs were mapped to corresponding Ensemble gene IDs. For Ensemble transcript IDs, corresponding Ensemble gene IDs were obtained using the BioMart community portal [5]. The Synergizer web application [6] was used to convert gene IDs from other annotation frameworks to Ensemble gene IDs. The resulting table (Supplementary Table 2) was then merged with the table of probeset expression data. In instances where a gene ID matched multiple probesets, probeset values were averaged (see Supplementary Script 1).


Generating and evaluating a ranked candidate gene list for potential vertebrate heart field regulators.

Musso G, Mosimann C, Panáková D, Burger A, Zhou Y, Zon LI, MacRae CA - Genom Data (2015)

Normalization and GSEA enrichment analysis results. Boxplots (A & B) show the expression intensity values for each CEL file both before (A) and after (B) RMA normalization. Plots outputted by GSEA (C & D) show enrichment for genes annotated as being involved in homophilic cell adhesion following pitx2 (C) and tbx5 (D) knockdown.
© Copyright Policy - CC BY-NC-ND
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4664750&req=5

f0005: Normalization and GSEA enrichment analysis results. Boxplots (A & B) show the expression intensity values for each CEL file both before (A) and after (B) RMA normalization. Plots outputted by GSEA (C & D) show enrichment for genes annotated as being involved in homophilic cell adhesion following pitx2 (C) and tbx5 (D) knockdown.
Mentions: Raw CEL files were processed using the Oligo package [4] as part of the Bioconductor suite (www.bioconductor.org) in the R statistical framework (www.r-project.org), using a customized script (Supplementary Script 1). Specifically, background subtraction and normalization were performed using the Robust Multiarray Average (RMA) method implemented in the Oligo package. Boxplots of intensity values were compared for all chips before and after normalization to visualize the corresponding effects on mean and quartile values (Fig. 1A–B). Following normalization, probeset IDs were matched to corresponding transcript IDs. Specifically, the zebrafish 1.0 ST array NetAffx annotation file was downloaded in CSV format from the Affymetrix website (www.affymetrix.com), and transcript/gene IDs corresponding to given probe IDs were extracted (Supplementary Table 1). In the interest of representing the data using a single gene annotation framework, all transcript and gene IDs were mapped to corresponding Ensemble gene IDs. For Ensemble transcript IDs, corresponding Ensemble gene IDs were obtained using the BioMart community portal [5]. The Synergizer web application [6] was used to convert gene IDs from other annotation frameworks to Ensemble gene IDs. The resulting table (Supplementary Table 2) was then merged with the table of probeset expression data. In instances where a gene ID matched multiple probesets, probeset values were averaged (see Supplementary Script 1).

Bottom Line: We found that key transcription factors that regulate septation and chamber formation in higher vertebrates, including Tbx5 and Pitx2, influence relative FHF and SHF contributions to the zebrafish heart tube.To identify molecular modulators of heart field migration, we used microarray-based expression profiling following inhibition of tbx5a and pitx2ab in embryonic zebrafish (Mosimann & Panakova, et al, 2015; GSE70750).Here, we describe in more detail the procedure used to process, prioritize, and analyze the expression data for functional enrichment.

View Article: PubMed Central - PubMed

Affiliation: Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.

ABSTRACT
The vertebrate heart develops from two distinct lineages of cardiomyocytes that arise from the first and second heart fields (FHF and SHF, respectively). The FHF forms the primitive heart tube, while adding cells from the SHF allows elongation at both poles of the tube. Initially seen as an exclusive characteristic of higher vertebrates, recent work has demonstrated the presence of a distinct FHF and SHF in lower vertebrates, including zebrafish. We found that key transcription factors that regulate septation and chamber formation in higher vertebrates, including Tbx5 and Pitx2, influence relative FHF and SHF contributions to the zebrafish heart tube. To identify molecular modulators of heart field migration, we used microarray-based expression profiling following inhibition of tbx5a and pitx2ab in embryonic zebrafish (Mosimann & Panakova, et al, 2015; GSE70750). Here, we describe in more detail the procedure used to process, prioritize, and analyze the expression data for functional enrichment.

No MeSH data available.


Related in: MedlinePlus