Data Outputs

Relaxin, a small peptide hormone of the insulin/relaxin family, demonstrated antifibrotic, organ protective, vasodilatory, and proangiogenic properties in clinical trials and several animal models of human diseases.

Data Outputs

Postby efrain.gonzalez0 » Thu Dec 14, 2017 5:26 pm

This will contain all data
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Coding for Samples

Postby efrain.gonzalez0 » Thu Dec 14, 2017 5:30 pm

Good afternoon,

I have attached the coding for the samples here. Please use it as a reference when looking at any of the other data files under this topic.

Respectfully,

Efrain Gonzalez
Attachments
LX-2 RNAseq sample codes.docx
Coding for Samples
(11.91 KiB) Downloaded 184 times
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HTSEQ Text Files

Postby efrain.gonzalez0 » Thu Dec 14, 2017 6:13 pm

Good evening,

I have attached the outputs of HTSEQ below.

Respectfully,

Efrain Gonzalez
Attachments
HTSEQ_Counts.tar.gz
This contains all of the counts for HTSEQ outputs
(2.25 MiB) Downloaded 169 times
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Re: Data Outputs

Postby hoong » Wed Jan 03, 2018 10:15 pm

Hi Efrain,

Could you please provide us with some updates on the project? Bryan has uploaded the output generated from Partek, so please let us know if you need more information.

Thanks,
Hooi
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Gene Check

Postby efrain.gonzalez0 » Mon Jan 08, 2018 1:49 pm

Good afternoon,

Here I have attached the results of checking the HTSEQ outputs for the genes that Brian provided. In summary all of the genes provided in the abbreviated list were present for each one of the HTSEQ outputs.

Respectfully,

Efrain Gonzalez
Attachments
Abbrev_Gene_Check.ods
(15.88 KiB) Downloaded 176 times
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Re: Data Outputs

Postby hoong » Tue Jan 09, 2018 7:03 pm

Thank you. We would like to have a more detailed analysis of our data as discussed in our meeting last year.
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Differentially Expressed genes

Postby efrain.gonzalez0 » Tue Jan 16, 2018 1:06 pm

Good afternoon,

I will be beginning my analysis of the HTSEQ-Counts results this week. I will be using a software called DeSeq2 in order to answer the question "do different sample groups express genes differentially?" As I have not used this software before it make take me some time to run all the files.

Respectfully,

Efrain Gonzalez
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Posts: 138
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Results from DESeq2 Analysis

Postby efrain.gonzalez0 » Thu Jan 25, 2018 3:00 pm

Good afternoon,

The results of the DESeq2 analysis on the data provided. I have also included the R commands that were used. Technical replicates were combined meaning that we were left only with the three different treatments. The fact that there were no biological replicates for each one of the treatments led to a problem with the analysis. The problem is best summarized by the creators of DESeq2 in their documentation:
Experiments without biological replicates do not allow for estimation of the dispersion of counts around the expected value for each group, which is critical for differential expression analysis. If an experimental design is supplied which does not contain the necessary degrees of freedom for differential analysis, DESeq will provide a warning to the user and follow the strategy outlined in Anders and Huber (2010) under the section 'Working without replicates', wherein all the samples are considered as replicates of a single group for the estimation of dispersion. As noted in the reference above: "Some overestimation of the variance may be expected, which will make that approach conservative." Furthermore, "while one may not want to draw strong conclusions from such an analysis, it may still be useful for exploration and hypothesis generation." We provide this approach for data exploration only, but for accurately identifying differential expression, biological replicates are required.


Respectfully,

Efrain Gonzalez
Attachments
RCommandsforDESeq2.txt
R commands
(1.79 KiB) Downloaded 175 times
R1_R4_results.txt
R1 vs R4
(4.06 MiB) Downloaded 175 times
R4_R5_results.txt
R4 vs R5
(4.04 MiB) Downloaded 171 times
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DESeq2 Analysis for Biological Replicates

Postby efrain.gonzalez0 » Thu Feb 01, 2018 5:44 pm

Good afternoon,

I have attached the results of the DESeq2 analysis on the data provided. In this case the replicates for each treatment were considered biological replicates. The definition that I have been using to differentiate between biological replicates and technical replicates is the following:
A technical replicate is when you test the same sample multiple times - it's used to test the variability in the testing protocol itself. A biological replicate is where you perform the same test on multiple samples of the same material / type of cells / tissue.

You will find that the column names are shifted over to the left by one column. This should be an easy fix if you intend to look at this data in Excel. I have included the names of the genes in these files.
Respectfully,

Efrain Gonzalez
Attachments
R1_R4_results.txt
Treatment R1 vs Treatment R4
(4.37 MiB) Downloaded 160 times
R4_R5_results.txt
Treatment R4 vs Treatment R5
(4.44 MiB) Downloaded 160 times
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Re: Data Outputs

Postby efrain.gonzalez0 » Tue Feb 13, 2018 2:53 pm

Good afternoon,

I believe that the video link that I have attached here provides the necessary information for continued analysis of this data. If ones interest is just in the gene ontology and pathway analysis then one should skip to minute 42:38.
Link: https://www.youtube.com/watch?v=xh_wpWj0AzM&t=2361s

Respectfully,

Efrain Gonzalez
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