Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:3
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Sprint:Fall 2 2023 Sep 17, Fall 3 2023 Oct 2
Description
We want to group genes into clusters based on their expression over time, focusing on just the genes that were found to be responsive to the heat stress.
For this task, investigate how we can generate clusters.
For example, there might be some genes that increase expression in response to heat stress in every time point, with bigger increases in later time points.
Or, there might be some genes that don't increase at all until one of the middle points. There are many possible patterns.
Here, we want to identify and cluster genes based on their basic expression patterns or their fold-change patterns.
Cosult with Johnson Lab (Rasha and Sorel) to replicate what they did for their very similar time course data set.
Ann suggests looking at "mufz" https://www.bioconductor.org/packages/release/bioc/html/Mfuzz.html
An RShiny tool for mfuz: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8825645/
Attachments
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-2993 [ 21429 ] |
| Summary | Compare across timepoints in R | Investigate: Compare across timepoints in R |
| Description |
Similar to 3442, we want to compare across time points to find DEGs.
An end goal here would be to take all of the DEGs identified in this and in 3442 and make a large clustered heatmap similar to what the Johnson lab created. |
Similar to 3442, we want to compare across time points to find DEGs, similar to what Rasha and Sorel did for the Johnson Lab time course dataset.
An end goal here would be to take all of the DEGs identified in this and in 3442 and make a large clustered heatmap similar to what the Johnson lab created. |
| Description |
Similar to 3442, we want to compare across time points to find DEGs, similar to what Rasha and Sorel did for the Johnson Lab time course dataset.
An end goal here would be to take all of the DEGs identified in this and in 3442 and make a large clustered heatmap similar to what the Johnson lab created. |
We want to group genes into clusters based on their expression over time, focusing on just the genes that were found to be responsive to the heat stress.
For this task, investigate how we can generate clusters. For example, there might be some genes that increase expression in response to heat stress in every time point, with bigger increases in later time points. Or, there might be some genes that don't increase at all until one of the middle points. There are many possible patterns. Here, we want to identify and cluster genes based on their basic expression patterns or their fold-change patterns. Cosult with Johnson Lab (Rasha and Sorel) to replicate what they did for their very similar time course data set. |
| Summary | Investigate: Compare across timepoints in R | Investigate: Cluster genes over time |
| Assignee | Ann Loraine [ aloraine ] |
| Description |
We want to group genes into clusters based on their expression over time, focusing on just the genes that were found to be responsive to the heat stress.
For this task, investigate how we can generate clusters. For example, there might be some genes that increase expression in response to heat stress in every time point, with bigger increases in later time points. Or, there might be some genes that don't increase at all until one of the middle points. There are many possible patterns. Here, we want to identify and cluster genes based on their basic expression patterns or their fold-change patterns. Cosult with Johnson Lab (Rasha and Sorel) to replicate what they did for their very similar time course data set. |
We want to group genes into clusters based on their expression over time, focusing on just the genes that were found to be responsive to the heat stress.
For this task, investigate how we can generate clusters. For example, there might be some genes that increase expression in response to heat stress in every time point, with bigger increases in later time points. Or, there might be some genes that don't increase at all until one of the middle points. There are many possible patterns. Here, we want to identify and cluster genes based on their basic expression patterns or their fold-change patterns. Cosult with Johnson Lab (Rasha and Sorel) to replicate what they did for their very similar time course data set. One such program to use is "mfold" that generates clusters. |
| Description |
We want to group genes into clusters based on their expression over time, focusing on just the genes that were found to be responsive to the heat stress.
For this task, investigate how we can generate clusters. For example, there might be some genes that increase expression in response to heat stress in every time point, with bigger increases in later time points. Or, there might be some genes that don't increase at all until one of the middle points. There are many possible patterns. Here, we want to identify and cluster genes based on their basic expression patterns or their fold-change patterns. Cosult with Johnson Lab (Rasha and Sorel) to replicate what they did for their very similar time course data set. One such program to use is "mfold" that generates clusters. |
We want to group genes into clusters based on their expression over time, focusing on just the genes that were found to be responsive to the heat stress.
For this task, investigate how we can generate clusters. For example, there might be some genes that increase expression in response to heat stress in every time point, with bigger increases in later time points. Or, there might be some genes that don't increase at all until one of the middle points. There are many possible patterns. Here, we want to identify and cluster genes based on their basic expression patterns or their fold-change patterns. Cosult with Johnson Lab (Rasha and Sorel) to replicate what they did for their very similar time course data set. One such program to use is "mfold" that generates clusters. Ann suggests looking at "mufz" https://www.bioconductor.org/packages/release/bioc/html/Mfuzz.html |
| Description |
We want to group genes into clusters based on their expression over time, focusing on just the genes that were found to be responsive to the heat stress.
For this task, investigate how we can generate clusters. For example, there might be some genes that increase expression in response to heat stress in every time point, with bigger increases in later time points. Or, there might be some genes that don't increase at all until one of the middle points. There are many possible patterns. Here, we want to identify and cluster genes based on their basic expression patterns or their fold-change patterns. Cosult with Johnson Lab (Rasha and Sorel) to replicate what they did for their very similar time course data set. One such program to use is "mfold" that generates clusters. Ann suggests looking at "mufz" https://www.bioconductor.org/packages/release/bioc/html/Mfuzz.html |
We want to group genes into clusters based on their expression over time, focusing on just the genes that were found to be responsive to the heat stress.
For this task, investigate how we can generate clusters. For example, there might be some genes that increase expression in response to heat stress in every time point, with bigger increases in later time points. Or, there might be some genes that don't increase at all until one of the middle points. There are many possible patterns. Here, we want to identify and cluster genes based on their basic expression patterns or their fold-change patterns. Cosult with Johnson Lab (Rasha and Sorel) to replicate what they did for their very similar time course data set. Ann suggests looking at "mufz" https://www.bioconductor.org/packages/release/bioc/html/Mfuzz.html |
| Description |
We want to group genes into clusters based on their expression over time, focusing on just the genes that were found to be responsive to the heat stress.
For this task, investigate how we can generate clusters. For example, there might be some genes that increase expression in response to heat stress in every time point, with bigger increases in later time points. Or, there might be some genes that don't increase at all until one of the middle points. There are many possible patterns. Here, we want to identify and cluster genes based on their basic expression patterns or their fold-change patterns. Cosult with Johnson Lab (Rasha and Sorel) to replicate what they did for their very similar time course data set. Ann suggests looking at "mufz" https://www.bioconductor.org/packages/release/bioc/html/Mfuzz.html |
We want to group genes into clusters based on their expression over time, focusing on just the genes that were found to be responsive to the heat stress.
For this task, investigate how we can generate clusters. For example, there might be some genes that increase expression in response to heat stress in every time point, with bigger increases in later time points. Or, there might be some genes that don't increase at all until one of the middle points. There are many possible patterns. Here, we want to identify and cluster genes based on their basic expression patterns or their fold-change patterns. Cosult with Johnson Lab (Rasha and Sorel) to replicate what they did for their very similar time course data set. Ann suggests looking at "mufz" https://www.bioconductor.org/packages/release/bioc/html/Mfuzz.html An RShiny tool for mfuz: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8825645/ |
| Sprint | Fall 2 2023 Sep 17 [ 178 ] | Fall 2 2023 Sep 17, Fall 3 2023 Oct 2 [ 178, 179 ] |
| Rank | Ranked higher |
This is now been consumed by IGBF-I 3454 and has been made redundant.
| Status | To-Do [ 10305 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
Related to this, is IBGF-3454.
It will test out EB-Seq and see how well it clusters.
It might solve much of this task!