Understanding MiRNA Profile Analysis: Exploring Bar Diagrams from GSE94799

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In summary, the conversation discusses two types of bar diagrams and includes questions about their interpretation. The first digram shows bars hanging below 0, and the second has bars shooting from -6 and being below 0. The questions also touch on the use of F and logFC values in gene expression analysis and suggest consulting tutorials or an advisor for further clarification. The conversation also mentions the lack of labeling on the graphs and the relevance of the F statistic in statistical tests.
  • #1
TytoAlba95
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Hi there. I'm a PhD student learning how to interpret raw microarray data. I have selected a miRNA expression profile of mice liver tissue, of three groups: Control, High-fat diet(HFD) and HFD+drug.
microarry.png

Picture source:GSE94799

Following are the two different types of bar-digram that were observed. My questions are:
1. What do bars hanging below 0 mean in the first dig. ?
2. What do bars shooting from -6 mean, also why are they below 0?
3. Like a normal gene (non-ncRNA gene) expression profile where the expression level is measured by the logFC value, is F the parameter that is analogous to logFC here? Could you shed some light as how F works?
 
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  • #2
This is outside my field, so I googled for 'microarray data analysis' and found some tutorials. I would suggest starting there.

When I hit problems, in Grad school, that I did not understand my first stop was to check in with my advisor, have you done that?
 
  • #3
The y-axis of your graphs aren't labeled, so I don't think anyone can figure out what the values are supposed to mean. You'll probably need to consult the documentation from the program you used to obtain those graphs.

For logFC, this is short for the logarithm (usually base two) of the fold change of RNA abundance. For example, if the TPM of a gene A is 100 before treatment, and 200 after treatment, the fold change FC = 2 and log2(FC) = 1. Similarly for a gene that goes from 100 before treatment to 25 after treatment, FC = 0.25 and log2(FC) = -2.

In this context, I would assume that the F represented here refers to the F statistic for a statistical test such as ANOVA. The F is not directly related to log(FC), but is used to calculate the p-value.
 
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  • #4
Hi
I had googled but with narrower keywords, which displayed nothing relevant. I was attending a lousy workshop on (protein coding gene) microarray data analysis. So miRNA microarray analysis naturally came to my mind. The resource person could not answer my questions so I decided to post here.

No, I haven't checked it with my advisor yet.
Thanks
 

1. What is miRNA profile analysis?

MiRNA profile analysis is a method used to study the expression levels of microRNAs (miRNAs) in a biological sample. MiRNAs are small non-coding RNA molecules that play important roles in gene regulation and have been linked to various diseases. By analyzing the miRNA profile, researchers can gain insights into the regulatory mechanisms and potential biomarkers for diseases.

2. What is GSE94799?

GSE94799 is a unique identifier assigned to a dataset in the Gene Expression Omnibus (GEO) database. This dataset contains miRNA expression data from a study on the effects of prenatal alcohol exposure on the developing brain. It can be accessed and analyzed by researchers to further understand the role of miRNAs in fetal alcohol spectrum disorders.

3. What are bar diagrams in miRNA profile analysis?

Bar diagrams are visual representations of miRNA expression levels in a sample. Each bar represents the expression level of a specific miRNA, and the height of the bar indicates the expression level. Bar diagrams are commonly used to compare the expression levels of different miRNAs between samples or experimental conditions.

4. How can bar diagrams from GSE94799 be interpreted?

Bar diagrams from GSE94799 can be interpreted by comparing the expression levels of miRNAs between different experimental groups. For example, if the bar for a specific miRNA is higher in the alcohol-exposed group compared to the control group, it suggests that this miRNA may be upregulated by prenatal alcohol exposure. Additionally, the overall pattern of expression levels in the bar diagrams can provide insights into the regulatory mechanisms and potential functions of the miRNAs.

5. How can understanding miRNA profile analysis benefit scientific research?

Understanding miRNA profile analysis can benefit scientific research in several ways. It can provide insights into the regulatory mechanisms and potential functions of miRNAs, which can lead to the discovery of new biomarkers and therapeutic targets for diseases. Additionally, miRNA profile analysis can also help to elucidate the complex interactions between miRNAs and their target genes, contributing to a better understanding of gene regulation and disease mechanisms.

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