[IGBF-3410] Identify the SL4 and SL5 genes encoding enzymes listed on this slide - JIRA UNCC

Ann Loraine created issue - 15/Aug/23 2:54 PM

Ann Loraine made changes - 15/Aug/23 2:54 PM

Field	Original Value	New Value
Epic Link		IGBF-2993 [ 21429 ]

Ann Loraine made changes - 15/Aug/23 4:31 PM

Description

See attached slide, from group meeting presentation August 15, 2023 from Muhlemann lab (Climate Resilient Crop Production lab, PI Joëlle Muhlemann).

Identify the SL4 and SL5 genes encoding these enzymes.

See attached slide, from group meeting presentation August 15, 2023 from Muhlemann lab (Climate Resilient Crop Production lab, PI Joëlle Muhlemann).

Identify the SL4 and SL5 genes encoding these enzymes.

Products:

* spreadsheet with columns:

# enzyme acronym (e.g., CHS, F3'5'H, FNS, names on the arrows)
# enzymatic product (e.g., naringenin-chalcone)
# gene symbol (e.g., "are" or "NA" if there's no genetic characterization, known mutants, etc)
# SL4 or SL5 gene name
# whether the previous column is from SL4 or SL5

Note:

* Some SL4 genes have no known counterpart in SL5, and vice versa.
* One enzyme may be encoded by zero or many genes in SL4
* One enzyme may be encoded by zero or more genes in SL5

I recommend not using mappings from SL4 onto SL5 as a way to annotate gene names here. Those mappings come from a process we do not know a lot about. It might be wrong. It would be better to apply the same method to SL4 and SL5 protein sets separately from each other. That way, errors in SL4 will not propagate to SL5, and vice versa.

Each step in creating this product should be documented so that we can explain it, sanity-check it, etc.

Ann Loraine made changes - 15/Aug/23 4:35 PM

Description

See attached slide, from group meeting presentation August 15, 2023 from Muhlemann lab (Climate Resilient Crop Production lab, PI Joëlle Muhlemann).

Identify the SL4 and SL5 genes encoding these enzymes.

Products:

* spreadsheet with columns:

# enzyme acronym (e.g., CHS, F3'5'H, FNS, names on the arrows)
# enzymatic product (e.g., naringenin-chalcone)
# gene symbol (e.g., "are" or "NA" if there's no genetic characterization, known mutants, etc)
# SL4 or SL5 gene name
# whether the previous column is from SL4 or SL5

Note:

* Some SL4 genes have no known counterpart in SL5, and vice versa.
* One enzyme may be encoded by zero or many genes in SL4
* One enzyme may be encoded by zero or more genes in SL5

I recommend not using mappings from SL4 onto SL5 as a way to annotate gene names here. Those mappings come from a process we do not know a lot about. It might be wrong. It would be better to apply the same method to SL4 and SL5 protein sets separately from each other. That way, errors in SL4 will not propagate to SL5, and vice versa.

Each step in creating this product should be documented so that we can explain it, sanity-check it, etc.

See attached slide, from group meeting presentation August 15, 2023 from Muhlemann lab (Climate Resilient Crop Production lab, PI Joëlle Muhlemann).

Identify the SL4 and SL5 genes encoding these enzymes.

Desired product:

* 1 xlsx (MS Excel) spreadsheet document with columns:

# enzyme acronym (e.g., CHS, F3'5'H, FNS, names on the arrows)
# enzymatic product (e.g., naringenin-chalcone)
# gene symbol (e.g., "are" or "NA" if there's no genetic characterization, known mutants, etc)
# SL4 or SL5 gene name
# whether the previous column is from SL4 or SL5 ("SL4", "SL5" are the two possible values)

Note:

Don't use mappings from SL4 onto SL5 as a way to annotate gene names here. Those mappings come from a process we do not know a lot about. It might be wrong. It would be better to develop and apply the same method to SL4 and SL5 protein sets separately from each other. That way, errors in SL4 will not propagate to SL5, and vice versa.

Each step in creating this product should be documented so that we can explain it, sanity-check it, etc.

Ann Loraine made changes - 16/Aug/23 5:15 AM

Description

See attached slide, from group meeting presentation August 15, 2023 from Muhlemann lab (Climate Resilient Crop Production lab, PI Joëlle Muhlemann).

Identify the SL4 and SL5 genes encoding these enzymes.

Desired product:

* 1 xlsx (MS Excel) spreadsheet document with columns:

# enzyme acronym (e.g., CHS, F3'5'H, FNS, names on the arrows)
# enzymatic product (e.g., naringenin-chalcone)
# gene symbol (e.g., "are" or "NA" if there's no genetic characterization, known mutants, etc)
# SL4 or SL5 gene name
# whether the previous column is from SL4 or SL5 ("SL4", "SL5" are the two possible values)

Note:

Don't use mappings from SL4 onto SL5 as a way to annotate gene names here. Those mappings come from a process we do not know a lot about. It might be wrong. It would be better to develop and apply the same method to SL4 and SL5 protein sets separately from each other. That way, errors in SL4 will not propagate to SL5, and vice versa.

Each step in creating this product should be documented so that we can explain it, sanity-check it, etc.

See attached slide, from group meeting presentation August 15, 2023 from Muhlemann lab (Climate Resilient Crop Production lab, PI Joëlle Muhlemann).

Identify the SL4 and SL5 genes encoding these enzymes.

Desired product:

* 1 xlsx (MS Excel) spreadsheet document with columns:

# enzyme acronym (e.g., CHS, F3'5'H, FNS, names on the arrows from the slide)
# enzymatic product (e.g., naringenin-chalcone)
# gene symbol (e.g., "are" or "NA" if there's no genetic characterization, known mutants, etc)
# SL4 or SL5 gene name
# whether the previous column is from SL4 or SL5 ("SL4", "SL5" are the two possible values)

Note:

Don't use mappings from SL4 onto SL5 as a way to annotate gene names here. Those mappings come from the people who made the SL5 assembly. They might be wrong. It would be better to develop and apply an enzyme assignment method and use it on SL4 and SL5 protein annotations separately from each other. That way, errors in SL4 will not propagate to SL5, and vice versa.

Each step in creating this product should be documented so that we can explain it, sanity-check it, etc.

Molly Davis made changes - 29/Aug/23 11:46 AM

Sprint

Summer 8 2023 Aug 21 [ 177 ]

Testing 2 : 4 Nov - 15 Nov [ 82 ]

Ann Loraine made changes - 12/Sep/23 10:11 AM

Description

See attached slide, from group meeting presentation August 15, 2023 from Muhlemann lab (Climate Resilient Crop Production lab, PI Joëlle Muhlemann).

Identify the SL4 and SL5 genes encoding these enzymes.

Desired product:

* 1 xlsx (MS Excel) spreadsheet document with columns:

# enzyme acronym (e.g., CHS, F3'5'H, FNS, names on the arrows from the slide)
# enzymatic product (e.g., naringenin-chalcone)
# gene symbol (e.g., "are" or "NA" if there's no genetic characterization, known mutants, etc)
# SL4 or SL5 gene name
# whether the previous column is from SL4 or SL5 ("SL4", "SL5" are the two possible values)

Note:

Don't use mappings from SL4 onto SL5 as a way to annotate gene names here. Those mappings come from the people who made the SL5 assembly. They might be wrong. It would be better to develop and apply an enzyme assignment method and use it on SL4 and SL5 protein annotations separately from each other. That way, errors in SL4 will not propagate to SL5, and vice versa.

Each step in creating this product should be documented so that we can explain it, sanity-check it, etc.

See attached slide, from group meeting presentation August 15, 2023 from Muhlemann lab (Climate Resilient Crop Production lab, PI Joëlle Muhlemann).

Identify the SL4 and SL5 genes encoding these enzymes.

Desired product: xlsx (MS Excel) spreadsheet document with columns:

# enzyme acronym (e.g., CHS, F3'5'H, FNS, names on the arrows from the slide)
# enzymatic product (e.g., naringenin-chalcone)
# gene symbol (e.g., "are" or "NA" if there's no genetic characterization, known mutants, etc)
# SL4 or SL5 gene name
# whether the previous column is from SL4 or SL5 ("SL4", "SL5" are the two possible values)

Note:

Don't use mappings from SL4 onto SL5 as a way to annotate gene names here. Those mappings come from the people who made the SL5 assembly. They might be wrong. It would be better to develop and apply an enzyme assignment method and use it on SL4 and SL5 protein annotations separately from each other. That way, errors in SL4 will not propagate to SL5, and vice versa.

Each step in creating this product should be documented so that we can explain it, sanity-check it, etc.

Ann Loraine made changes - 18/Sep/23 11:10 AM

Epic Link

IGBF-2993 [ 21429 ]

IGBF-3446 [ 22548 ]

Ann Loraine made changes - 18/Sep/23 11:10 AM

Story Points

5

2

Ann Loraine made changes - 18/Sep/23 11:10 AM

Description

See attached slide, from group meeting presentation August 15, 2023 from Muhlemann lab (Climate Resilient Crop Production lab, PI Joëlle Muhlemann).

Identify the SL4 and SL5 genes encoding these enzymes.

Desired product: xlsx (MS Excel) spreadsheet document with columns:

# enzyme acronym (e.g., CHS, F3'5'H, FNS, names on the arrows from the slide)
# enzymatic product (e.g., naringenin-chalcone)
# gene symbol (e.g., "are" or "NA" if there's no genetic characterization, known mutants, etc)
# SL4 or SL5 gene name
# whether the previous column is from SL4 or SL5 ("SL4", "SL5" are the two possible values)

Note:

Don't use mappings from SL4 onto SL5 as a way to annotate gene names here. Those mappings come from the people who made the SL5 assembly. They might be wrong. It would be better to develop and apply an enzyme assignment method and use it on SL4 and SL5 protein annotations separately from each other. That way, errors in SL4 will not propagate to SL5, and vice versa.

Each step in creating this product should be documented so that we can explain it, sanity-check it, etc.

See attached slide, from group meeting presentation August 15, 2023 from Muhlemann lab (Climate Resilient Crop Production lab, PI Joëlle Muhlemann).

Identify the SL4 and SL5 genes encoding these enzymes.

Desired product: xlsx (MS Excel) spreadsheet document with columns:

# enzyme acronym (e.g., CHS, F3'5'H, FNS, names on the arrows from the slide)
# enzymatic product (e.g., naringenin-chalcone)
# gene symbol (e.g., "are" or "NA" if there's no genetic characterization, known mutants, etc)
# SL4 or SL5 gene name
# whether the previous column is from SL4 or SL5 ("SL4", "SL5" are the two possible values)

Ann Loraine made changes - 18/Sep/23 11:11 AM

Sprint

Fall 1 - Sep 5 [ 82 ]

Ann Loraine made changes - 26/Sep/23 4:06 PM

Description

See attached slide, from group meeting presentation August 15, 2023 from Muhlemann lab (Climate Resilient Crop Production lab, PI Joëlle Muhlemann).

Identify the SL4 and SL5 genes encoding these enzymes.

Desired product: xlsx (MS Excel) spreadsheet document with columns:

# enzyme acronym (e.g., CHS, F3'5'H, FNS, names on the arrows from the slide)
# enzymatic product (e.g., naringenin-chalcone)
# gene symbol (e.g., "are" or "NA" if there's no genetic characterization, known mutants, etc)
# SL4 or SL5 gene name
# whether the previous column is from SL4 or SL5 ("SL4", "SL5" are the two possible values)

See attached slide, from group meeting presentation August 15, 2023 from Muhlemann lab (Climate Resilient Crop Production lab, PI Joëlle Muhlemann).

It would be nice to investigate how or if enzymes involved flavonoid biosynthesis are differentially expressed in response to the heat stress treatment. To do that, it would help if we knew the SL4 and SL5 genes that might encode these enzymes. If we knew that, we could very easily test for over- or under-enrichment of these genes in the DE gene set or the expressed gene set in our target tissue.

Desired product: xlsx (MS Excel) spreadsheet document with columns:

# enzyme acronym (e.g., CHS, F3'5'H, FNS, names on the arrows from the slide)
# enzymatic product (e.g., naringenin-chalcone)
# gene symbol (e.g., "are" or "NA" if there's no genetic characterization, known mutants, etc)
# SL4 or SL5 gene name
# whether the previous column is from SL4 or SL5 ("SL4", "SL5" are the two possible values)

Ann Loraine made changes - 26/Sep/23 4:06 PM

Description

See attached slide, from group meeting presentation August 15, 2023 from Muhlemann lab (Climate Resilient Crop Production lab, PI Joëlle Muhlemann).

It would be nice to investigate how or if enzymes involved flavonoid biosynthesis are differentially expressed in response to the heat stress treatment. To do that, it would help if we knew the SL4 and SL5 genes that might encode these enzymes. If we knew that, we could very easily test for over- or under-enrichment of these genes in the DE gene set or the expressed gene set in our target tissue.

Desired product: xlsx (MS Excel) spreadsheet document with columns:

# enzyme acronym (e.g., CHS, F3'5'H, FNS, names on the arrows from the slide)
# enzymatic product (e.g., naringenin-chalcone)
# gene symbol (e.g., "are" or "NA" if there's no genetic characterization, known mutants, etc)
# SL4 or SL5 gene name
# whether the previous column is from SL4 or SL5 ("SL4", "SL5" are the two possible values)

See attached slide, from group meeting presentation August 15, 2023 from Muhlemann lab (Climate Resilient Crop Production lab, PI Joëlle Muhlemann).

It would be nice to investigate how or if enzymes involved flavonoid biosynthesis are differentially expressed in response to the heat stress treatment. To do that, it would help if we knew the SL4 and SL5 genes that might encode these enzymes. If we knew that, we could very easily test for over- or under-enrichment of these genes in the DE gene set or the expressed gene set in our target tissue.

Desired product: xlsx (MS Excel) spreadsheet document with columns:

# enzyme acronym (e.g., CHS, F3'5'H, FNS)
# longer name of the enzyme / enzymatic activity
# enzymatic product (e.g., naringenin-chalcone)
# gene symbol (e.g., "are" or "NA" if there's no genetic characterization, known mutants, etc)
# SL4 or SL5 gene name
# whether the previous column is from SL4 or SL5 ("SL4", "SL5" are the two possible values)