PSSD Genome Project [Megathread]
Re: PSSD Genome Project [Megathread]
@Mesolimbo
When using the charts remember that:
C = RED
G = GREEN
A = BLUE
T = BLACK
Heterozygotes will be combinations of the above colors.
5HTTPLR allele
- rs25531 (irrelevant on 23+Me apparently - all are called C/C)
- rs25532:
-- 4 SNPs for rs25532 analyzed for frequency --
CC: 0.0
CG: 0.0
GG: 50.0
AA: 0.0
AT: 0.0
TT: 0.0
CT: 0.0
AG: 50.0
AC: 0.0
GT: 0.0
CHART (Click to open):
https://chart.apis.google.com/chart?cht ... ,1,0|1,1,0
- rs2129785:
-- 28 SNPs for rs2129785 analyzed for frequency --
CC: 0.0
CG: 0.0
GG: 0.0
AA: 0.0
AT: 0.0
TT: 85.71428571428571
CT: 14.285714285714285
AG: 0.0
AC: 0.0
GT: 0.0
https://chart.apis.google.com/chart?cht ... ,1,0|1,1,0
- rs11867581:
-- 29 SNPs for rs11867581 analyzed for frequency --
CC: 0.0
CG: 0.0
GG: 13.793103448275861
AA: 37.93103448275862
AT: 0.0
TT: 0.0
CT: 0.0
AG: 48.275862068965516
AC: 0.0
GT: 0.0
https://chart.apis.google.com/chart?cht ... ,1,0|1,1,0
--------------------------------------------------------------------------------------------------------
COMT-Met
- rs4680:
-- 29 SNPs for rs4680 analyzed for frequency --
CC: 0.0
CG: 0.0
GG: 27.586206896551722
AA: 20.689655172413794
AT: 0.0
TT: 0.0
CT: 0.0
AG: 51.724137931034484
AC: 0.0
GT: 0.0
https://chart.apis.google.com/chart?cht ... ,1,0|1,1,0
- rs4633:
-- 28 SNPs for rs4633 analyzed for frequency --
CC: 25.0
CG: 0.0
GG: 0.0
AA: 0.0
AT: 0.0
TT: 21.428571428571427
CT: 53.57142857142857
AG: 0.0
AC: 0.0
GT: 0.0
https://chart.apis.google.com/chart?cht ... ,1,0|1,1,0
- rs165599:
-- 29 SNPs for rs165599 analyzed for frequency --
CC: 0.0
CG: 0.0
GG: 6.896551724137931
AA: 31.03448275862069
AT: 0.0
TT: 0.0
CT: 0.0
AG: 62.06896551724138
AC: 0.0
GT: 0.0
https://chart.apis.google.com/chart?cht ... ,1,0|1,1,0
--------------------------------------------------------------------------------------------------------
FKBP5:
- rs1360780
-- 28 SNPs for rs1360780 analyzed for frequency --
CC: 57.14285714285714
CG: 0.0
GG: 0.0
AA: 0.0
AT: 0.0
TT: 14.285714285714285
CT: 28.57142857142857
AG: 0.0
AC: 0.0
GT: 0.0
https://chart.apis.google.com/chart?cht ... ,1,0|1,1,0
When using the charts remember that:
C = RED
G = GREEN
A = BLUE
T = BLACK
Heterozygotes will be combinations of the above colors.
5HTTPLR allele
- rs25531 (irrelevant on 23+Me apparently - all are called C/C)
- rs25532:
-- 4 SNPs for rs25532 analyzed for frequency --
CC: 0.0
CG: 0.0
GG: 50.0
AA: 0.0
AT: 0.0
TT: 0.0
CT: 0.0
AG: 50.0
AC: 0.0
GT: 0.0
CHART (Click to open):
https://chart.apis.google.com/chart?cht ... ,1,0|1,1,0
- rs2129785:
-- 28 SNPs for rs2129785 analyzed for frequency --
CC: 0.0
CG: 0.0
GG: 0.0
AA: 0.0
AT: 0.0
TT: 85.71428571428571
CT: 14.285714285714285
AG: 0.0
AC: 0.0
GT: 0.0
https://chart.apis.google.com/chart?cht ... ,1,0|1,1,0
- rs11867581:
-- 29 SNPs for rs11867581 analyzed for frequency --
CC: 0.0
CG: 0.0
GG: 13.793103448275861
AA: 37.93103448275862
AT: 0.0
TT: 0.0
CT: 0.0
AG: 48.275862068965516
AC: 0.0
GT: 0.0
https://chart.apis.google.com/chart?cht ... ,1,0|1,1,0
--------------------------------------------------------------------------------------------------------
COMT-Met
- rs4680:
-- 29 SNPs for rs4680 analyzed for frequency --
CC: 0.0
CG: 0.0
GG: 27.586206896551722
AA: 20.689655172413794
AT: 0.0
TT: 0.0
CT: 0.0
AG: 51.724137931034484
AC: 0.0
GT: 0.0
https://chart.apis.google.com/chart?cht ... ,1,0|1,1,0
- rs4633:
-- 28 SNPs for rs4633 analyzed for frequency --
CC: 25.0
CG: 0.0
GG: 0.0
AA: 0.0
AT: 0.0
TT: 21.428571428571427
CT: 53.57142857142857
AG: 0.0
AC: 0.0
GT: 0.0
https://chart.apis.google.com/chart?cht ... ,1,0|1,1,0
- rs165599:
-- 29 SNPs for rs165599 analyzed for frequency --
CC: 0.0
CG: 0.0
GG: 6.896551724137931
AA: 31.03448275862069
AT: 0.0
TT: 0.0
CT: 0.0
AG: 62.06896551724138
AC: 0.0
GT: 0.0
https://chart.apis.google.com/chart?cht ... ,1,0|1,1,0
--------------------------------------------------------------------------------------------------------
FKBP5:
- rs1360780
-- 28 SNPs for rs1360780 analyzed for frequency --
CC: 57.14285714285714
CG: 0.0
GG: 0.0
AA: 0.0
AT: 0.0
TT: 14.285714285714285
CT: 28.57142857142857
AG: 0.0
AC: 0.0
GT: 0.0
https://chart.apis.google.com/chart?cht ... ,1,0|1,1,0
- Medical Student & Friendly poltergeist - Lexapro Sept '14. [Hx] [PSSD Lab] [r/PSSD] [Treatment Plan] - Add "Ghost" in replies so I see it
Re: PSSD Genome Project [Megathread]
I will be starting another iteration of the genome project in the coming weeks.
My computer suddenly crashed this spring and with it I lost a lot of the organization I had with the genome project. I still have copies of all of the genomes, but I either need to find a way to recover some of my scripts and reorganize the data, or do it again - which would take a lot of time.
I'm building a new computer this week and after that will give some updates on how the project is progressing.
Stay tuned.
My computer suddenly crashed this spring and with it I lost a lot of the organization I had with the genome project. I still have copies of all of the genomes, but I either need to find a way to recover some of my scripts and reorganize the data, or do it again - which would take a lot of time.
I'm building a new computer this week and after that will give some updates on how the project is progressing.
Stay tuned.
- Medical Student & Friendly poltergeist - Lexapro Sept '14. [Hx] [PSSD Lab] [r/PSSD] [Treatment Plan] - Add "Ghost" in replies so I see it
Re: PSSD Genome Project [Megathread]
I have the new computer built and it's running a modified version of the old python code to analyze genomes. I'm still re-downloading the genomes that everyone sent me so that I get a big enough database for the next iteration of the analysis.
Expect another update in a few weeks. Things are moving forward again.
Expect another update in a few weeks. Things are moving forward again.
- Medical Student & Friendly poltergeist - Lexapro Sept '14. [Hx] [PSSD Lab] [r/PSSD] [Treatment Plan] - Add "Ghost" in replies so I see it
- AnhedonicApe
- Posts: 289
- Joined: Tue Apr 23, 2019 7:07 am
- Contact:
Re: PSSD Genome Project [Megathread]
Hey, do you have any data on methylation levels?Ghost wrote:I have the new computer built and it's running a modified version of the old python code to analyze genomes. I'm still re-downloading the genomes that everyone sent me so that I get a big enough database for the next iteration of the analysis.
Expect another update in a few weeks. Things are moving forward again.
- AnhedonicApe
- Posts: 289
- Joined: Tue Apr 23, 2019 7:07 am
- Contact:
Re: PSSD Genome Project [Megathread]
I was thinking about it, probably notAnhedonicApe wrote:Hey, do you have any data on methylation levels?Ghost wrote:I have the new computer built and it's running a modified version of the old python code to analyze genomes. I'm still re-downloading the genomes that everyone sent me so that I get a big enough database for the next iteration of the analysis.
Expect another update in a few weeks. Things are moving forward again.
Re: PSSD Genome Project [Megathread]
Only data I have is on genotype, not expression
- Medical Student & Friendly poltergeist - Lexapro Sept '14. [Hx] [PSSD Lab] [r/PSSD] [Treatment Plan] - Add "Ghost" in replies so I see it
Re: PSSD Genome Project [Megathread]
Attention all programmers/coders: I NEED YOUR HELP!!!
Current program is good but it needs to reference a set number of control files to compare with PSSD patients, this is slow and gives a small sample size prone to error
I'd rather compare it to a bigger sample like the ones on SNPedia
I know I'm being vague but I'd help anyone who had ideas...
https://www.snpedia.com/index.php/Bulk - this is the best documentation that I can find.
I want a database of all of the SNPs from SNPedia that have frequency data...
https://www.snpedia.com/index.php/Help_ ... iversity)- Scroll down here and look at the population diversity box. This contains the information I think. But where? How can I use this to turn it into a frequency that I can use for my program?
Someone might also be able to figure this out with hapmap: https://www.genome.gov/10001688/interna ... ap-project
Any help would be GREAT!
Current program is good but it needs to reference a set number of control files to compare with PSSD patients, this is slow and gives a small sample size prone to error
I'd rather compare it to a bigger sample like the ones on SNPedia
I know I'm being vague but I'd help anyone who had ideas...
https://www.snpedia.com/index.php/Bulk - this is the best documentation that I can find.
I want a database of all of the SNPs from SNPedia that have frequency data...
https://www.snpedia.com/index.php/Help_ ... iversity)- Scroll down here and look at the population diversity box. This contains the information I think. But where? How can I use this to turn it into a frequency that I can use for my program?
Someone might also be able to figure this out with hapmap: https://www.genome.gov/10001688/interna ... ap-project
Any help would be GREAT!
- Medical Student & Friendly poltergeist - Lexapro Sept '14. [Hx] [PSSD Lab] [r/PSSD] [Treatment Plan] - Add "Ghost" in replies so I see it
-
- Posts: 286
- Joined: Tue Oct 03, 2017 12:04 pm
- Contact:
Re: PSSD Genome Project [Megathread]
what are you trying to do- compare allele frequencies of PSSD cases with controls?
- TalkingAnt
- Posts: 255
- Joined: Tue Jan 27, 2015 9:04 pm
- Contact:
Re: PSSD Genome Project [Megathread]
Can you start a GitHub repo to make it easier to review and contribute code?
Cured | PSSD 2012-2020 | Log thread
Re: PSSD Genome Project [Megathread]
Genome Project Github: https://github.com/ghostPSSD/GeneFreq
Basically, for each gene we are finding the PSSD group frequency, then the Control group frequency, and then comparing them to each other. This is a really slow process and we could cut the time in half if I found a way to pull all of the SNPedia data from their site and store it in a text file. Then we could reference the PSSD group frequency with the SNPedia frequency (which is also a much bigger sample size than we have so it should be more accurate).
Does that help a bit?
Basically, for each gene we are finding the PSSD group frequency, then the Control group frequency, and then comparing them to each other. This is a really slow process and we could cut the time in half if I found a way to pull all of the SNPedia data from their site and store it in a text file. Then we could reference the PSSD group frequency with the SNPedia frequency (which is also a much bigger sample size than we have so it should be more accurate).
Does that help a bit?
- Medical Student & Friendly poltergeist - Lexapro Sept '14. [Hx] [PSSD Lab] [r/PSSD] [Treatment Plan] - Add "Ghost" in replies so I see it
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