PSSD Genome Project [Megathread]

[Ghost]

I've done some more digging around in the dataset. Here is a list of the top 25 rsids I've found that are different between the groups. What now?

rs4871622
rs1467809
rs11994900
rs6887352
rs7113273
rs9294483
rs231023
rs231024
rs2894113
rs4552410
rs7173365
rs10884674
rs2253372
rs2939402
rs588765
rs6555885
rs680244
rs12138053
rs1264704
rs1927393
rs4728731
rs6419647
rs6677662
i6058149
rs10449236

Here is the output using the Build 2.0 numbers (n=16, n=30). Soon I'll update those databases so i can use more PSSD genomes if wanted.
Difference == 0

GREAT work on these though... I'll have to add them to my site soon.

### rs4871622 ###
PSSD AA: %0.0 -- CONTROL AA: %0.0
PSSD AC: %0.0 -- CONTROL AC: %0.0
PSSD AG: %0.0 -- CONTROL AG: %0.0
PSSD AT: %0.0 -- CONTROL AT: %0.0
PSSD CA: %0.0 -- CONTROL CA: %0.0
PSSD CC: %0.0 -- CONTROL CC: %21.05
PSSD CG: %0.0 -- CONTROL CG: %0.0
PSSD CT: %20.0 -- CONTROL CT: %78.95
PSSD GA: %0.0 -- CONTROL GA: %0.0
PSSD GC: %0.0 -- CONTROL GC: %0.0
PSSD GG: %0.0 -- CONTROL GG: %0.0
PSSD GT: %0.0 -- CONTROL GT: %0.0
PSSD TA: %0.0 -- CONTROL TA: %0.0
PSSD TC: %0.0 -- CONTROL TC: %0.0
PSSD TG: %0.0 -- CONTROL TG: %0.0
PSSD TT: %80.0 -- CONTROL TT: %0.0


### rs1467809 ###
PSSD AA: %93.33 -- CONTROL AA: %15.79
PSSD AC: %0.0 -- CONTROL AC: %0.0
PSSD AG: %6.67 -- CONTROL AG: %63.16
PSSD AT: %0.0 -- CONTROL AT: %0.0
PSSD CA: %0.0 -- CONTROL CA: %0.0
PSSD CC: %0.0 -- CONTROL CC: %0.0
PSSD CG: %0.0 -- CONTROL CG: %0.0
PSSD CT: %0.0 -- CONTROL CT: %0.0
PSSD GA: %0.0 -- CONTROL GA: %0.0
PSSD GC: %0.0 -- CONTROL GC: %0.0
PSSD GG: %0.0 -- CONTROL GG: %21.05
PSSD GT: %0.0 -- CONTROL GT: %0.0
PSSD TA: %0.0 -- CONTROL TA: %0.0
PSSD TC: %0.0 -- CONTROL TC: %0.0
PSSD TG: %0.0 -- CONTROL TG: %0.0
PSSD TT: %0.0 -- CONTROL TT: %0.0


### rs11994900 ###
PSSD AA: %0.0 -- CONTROL AA: %5.26
PSSD AC: %0.0 -- CONTROL AC: %0.0
PSSD AG: %80.0 -- CONTROL AG: %10.53
PSSD AT: %0.0 -- CONTROL AT: %0.0
PSSD CA: %0.0 -- CONTROL CA: %0.0
PSSD CC: %0.0 -- CONTROL CC: %0.0
PSSD CG: %0.0 -- CONTROL CG: %0.0
PSSD CT: %0.0 -- CONTROL CT: %0.0
PSSD GA: %0.0 -- CONTROL GA: %0.0
PSSD GC: %0.0 -- CONTROL GC: %0.0
PSSD GG: %20.0 -- CONTROL GG: %84.21
PSSD GT: %0.0 -- CONTROL GT: %0.0
PSSD TA: %0.0 -- CONTROL TA: %0.0
PSSD TC: %0.0 -- CONTROL TC: %0.0
PSSD TG: %0.0 -- CONTROL TG: %0.0
PSSD TT: %0.0 -- CONTROL TT: %0.0


### rs6887352 ###
PSSD AA: %6.67 -- CONTROL AA: %57.89
PSSD AC: %0.0 -- CONTROL AC: %0.0
PSSD AG: %93.33 -- CONTROL AG: %21.05
PSSD AT: %0.0 -- CONTROL AT: %0.0
PSSD CA: %0.0 -- CONTROL CA: %0.0
PSSD CC: %0.0 -- CONTROL CC: %0.0
PSSD CG: %0.0 -- CONTROL CG: %0.0
PSSD CT: %0.0 -- CONTROL CT: %0.0
PSSD GA: %0.0 -- CONTROL GA: %0.0
PSSD GC: %0.0 -- CONTROL GC: %0.0
PSSD GG: %0.0 -- CONTROL GG: %21.05
PSSD GT: %0.0 -- CONTROL GT: %0.0
PSSD TA: %0.0 -- CONTROL TA: %0.0
PSSD TC: %0.0 -- CONTROL TC: %0.0
PSSD TG: %0.0 -- CONTROL TG: %0.0
PSSD TT: %0.0 -- CONTROL TT: %0.0


### rs7113273 ###
PSSD AA: %0.0 -- CONTROL AA: %0.0
PSSD AC: %0.0 -- CONTROL AC: %0.0
PSSD AG: %0.0 -- CONTROL AG: %0.0
PSSD AT: %0.0 -- CONTROL AT: %0.0
PSSD CA: %0.0 -- CONTROL CA: %0.0
PSSD CC: %0.0 -- CONTROL CC: %13.33
PSSD CG: %0.0 -- CONTROL CG: %0.0
PSSD CT: %100.0 -- CONTROL CT: %33.33
PSSD GA: %0.0 -- CONTROL GA: %0.0
PSSD GC: %0.0 -- CONTROL GC: %0.0
PSSD GG: %0.0 -- CONTROL GG: %0.0
PSSD GT: %0.0 -- CONTROL GT: %0.0
PSSD TA: %0.0 -- CONTROL TA: %0.0
PSSD TC: %0.0 -- CONTROL TC: %0.0
PSSD TG: %0.0 -- CONTROL TG: %0.0
PSSD TT: %0.0 -- CONTROL TT: %53.33


### rs9294483 ###
PSSD AA: %20.0 -- CONTROL AA: %5.26
PSSD AC: %0.0 -- CONTROL AC: %0.0
PSSD AG: %26.67 -- CONTROL AG: %94.74
PSSD AT: %0.0 -- CONTROL AT: %0.0
PSSD CA: %0.0 -- CONTROL CA: %0.0
PSSD CC: %0.0 -- CONTROL CC: %0.0
PSSD CG: %0.0 -- CONTROL CG: %0.0
PSSD CT: %0.0 -- CONTROL CT: %0.0
PSSD GA: %0.0 -- CONTROL GA: %0.0
PSSD GC: %0.0 -- CONTROL GC: %0.0
PSSD GG: %53.33 -- CONTROL GG: %0.0
PSSD GT: %0.0 -- CONTROL GT: %0.0
PSSD TA: %0.0 -- CONTROL TA: %0.0
PSSD TC: %0.0 -- CONTROL TC: %0.0
PSSD TG: %0.0 -- CONTROL TG: %0.0
PSSD TT: %0.0 -- CONTROL TT: %0.0

[Ghost]

@ Cipro

These are the ones with n >= 10, which was the case for the ones I just posted above too:


### rs2606345 ###
PSSD AA: %56.25 -- CONTROL AA: %53.33
PSSD AC: %43.75 -- CONTROL AC: %43.33
PSSD AG: %0.0 -- CONTROL AG: %0.0
PSSD AT: %0.0 -- CONTROL AT: %0.0
PSSD CA: %0.0 -- CONTROL CA: %0.0
PSSD CC: %0.0 -- CONTROL CC: %3.33
PSSD CG: %0.0 -- CONTROL CG: %0.0
PSSD CT: %0.0 -- CONTROL CT: %0.0
PSSD GA: %0.0 -- CONTROL GA: %0.0
PSSD GC: %0.0 -- CONTROL GC: %0.0
PSSD GG: %0.0 -- CONTROL GG: %0.0
PSSD GT: %0.0 -- CONTROL GT: %0.0
PSSD TA: %0.0 -- CONTROL TA: %0.0
PSSD TC: %0.0 -- CONTROL TC: %0.0
PSSD TG: %0.0 -- CONTROL TG: %0.0
PSSD TT: %0.0 -- CONTROL TT: %0.0


### rs2228099 ###
PSSD AA: %0.0 -- CONTROL AA: %0.0
PSSD AC: %0.0 -- CONTROL AC: %0.0
PSSD AG: %0.0 -- CONTROL AG: %0.0
PSSD AT: %0.0 -- CONTROL AT: %0.0
PSSD CA: %0.0 -- CONTROL CA: %0.0
PSSD CC: %53.33 -- CONTROL CC: %33.33
PSSD CG: %40.0 -- CONTROL CG: %50.0
PSSD CT: %0.0 -- CONTROL CT: %0.0
PSSD GA: %0.0 -- CONTROL GA: %0.0
PSSD GC: %0.0 -- CONTROL GC: %0.0
PSSD GG: %6.67 -- CONTROL GG: %16.67
PSSD GT: %0.0 -- CONTROL GT: %0.0
PSSD TA: %0.0 -- CONTROL TA: %0.0
PSSD TC: %0.0 -- CONTROL TC: %0.0
PSSD TG: %0.0 -- CONTROL TG: %0.0
PSSD TT: %0.0 -- CONTROL TT: %0.0


### rs1051740 ###
PSSD AA: %0.0 -- CONTROL AA: %0.0
PSSD AC: %0.0 -- CONTROL AC: %0.0
PSSD AG: %0.0 -- CONTROL AG: %0.0
PSSD AT: %0.0 -- CONTROL AT: %0.0
PSSD CA: %0.0 -- CONTROL CA: %0.0
PSSD CC: %6.25 -- CONTROL CC: %10.0
PSSD CG: %0.0 -- CONTROL CG: %0.0
PSSD CT: %31.25 -- CONTROL CT: %53.33
PSSD GA: %0.0 -- CONTROL GA: %0.0
PSSD GC: %0.0 -- CONTROL GC: %0.0
PSSD GG: %0.0 -- CONTROL GG: %0.0
PSSD GT: %0.0 -- CONTROL GT: %0.0
PSSD TA: %0.0 -- CONTROL TA: %0.0
PSSD TC: %0.0 -- CONTROL TC: %0.0
PSSD TG: %0.0 -- CONTROL TG: %0.0
PSSD TT: %62.5 -- CONTROL TT: %36.67


### rs1056836 ###
PSSD AA: %0.0 -- CONTROL AA: %0.0
PSSD AC: %0.0 -- CONTROL AC: %0.0
PSSD AG: %0.0 -- CONTROL AG: %0.0
PSSD AT: %0.0 -- CONTROL AT: %0.0
PSSD CA: %0.0 -- CONTROL CA: %0.0
PSSD CC: %12.5 -- CONTROL CC: %30.0
PSSD CG: %56.25 -- CONTROL CG: %53.33
PSSD CT: %0.0 -- CONTROL CT: %0.0
PSSD GA: %0.0 -- CONTROL GA: %0.0
PSSD GC: %0.0 -- CONTROL GC: %0.0
PSSD GG: %31.25 -- CONTROL GG: %16.67
PSSD GT: %0.0 -- CONTROL GT: %0.0
PSSD TA: %0.0 -- CONTROL TA: %0.0
PSSD TC: %0.0 -- CONTROL TC: %0.0
PSSD TG: %0.0 -- CONTROL TG: %0.0
PSSD TT: %0.0 -- CONTROL TT: %0.0


### rs1799814 ###
PSSD AA: %0.0 -- CONTROL AA: %0.0
PSSD AC: %0.0 -- CONTROL AC: %0.0
PSSD AG: %0.0 -- CONTROL AG: %0.0
PSSD AT: %0.0 -- CONTROL AT: %0.0
PSSD CA: %0.0 -- CONTROL CA: %0.0
PSSD CC: %0.0 -- CONTROL CC: %0.0
PSSD CG: %0.0 -- CONTROL CG: %0.0
PSSD CT: %0.0 -- CONTROL CT: %0.0
PSSD GA: %0.0 -- CONTROL GA: %0.0
PSSD GC: %0.0 -- CONTROL GC: %0.0
PSSD GG: %87.5 -- CONTROL GG: %100.0
PSSD GT: %12.5 -- CONTROL GT: %0.0
PSSD TA: %0.0 -- CONTROL TA: %0.0
PSSD TC: %0.0 -- CONTROL TC: %0.0
PSSD TG: %0.0 -- CONTROL TG: %0.0
PSSD TT: %0.0 -- CONTROL TT: %0.0


### rs2234922 ###
PSSD AA: %56.25 -- CONTROL AA: %73.33
PSSD AC: %0.0 -- CONTROL AC: %0.0
PSSD AG: %43.75 -- CONTROL AG: %23.33
PSSD AT: %0.0 -- CONTROL AT: %0.0
PSSD CA: %0.0 -- CONTROL CA: %0.0
PSSD CC: %0.0 -- CONTROL CC: %0.0
PSSD CG: %0.0 -- CONTROL CG: %0.0
PSSD CT: %0.0 -- CONTROL CT: %0.0
PSSD GA: %0.0 -- CONTROL GA: %0.0
PSSD GC: %0.0 -- CONTROL GC: %0.0
PSSD GG: %0.0 -- CONTROL GG: %3.33
PSSD GT: %0.0 -- CONTROL GT: %0.0
PSSD TA: %0.0 -- CONTROL TA: %0.0
PSSD TC: %0.0 -- CONTROL TC: %0.0
PSSD TG: %0.0 -- CONTROL TG: %0.0
PSSD TT: %0.0 -- CONTROL TT: %0.0


### rs2260863 ###
PSSD AA: %0.0 -- CONTROL AA: %0.0
PSSD AC: %0.0 -- CONTROL AC: %0.0
PSSD AG: %0.0 -- CONTROL AG: %0.0
PSSD AT: %0.0 -- CONTROL AT: %0.0
PSSD CA: %0.0 -- CONTROL CA: %0.0
PSSD CC: %37.5 -- CONTROL CC: %63.33
PSSD CG: %43.75 -- CONTROL CG: %33.33
PSSD CT: %0.0 -- CONTROL CT: %0.0
PSSD GA: %0.0 -- CONTROL GA: %0.0
PSSD GC: %0.0 -- CONTROL GC: %0.0
PSSD GG: %18.75 -- CONTROL GG: %3.33
PSSD GT: %0.0 -- CONTROL GT: %0.0
PSSD TA: %0.0 -- CONTROL TA: %0.0
PSSD TC: %0.0 -- CONTROL TC: %0.0
PSSD TG: %0.0 -- CONTROL TG: %0.0
PSSD TT: %0.0 -- CONTROL TT: %0.0

[Ghost]

General update: I put a lot of time into the SNP list today. A lot more SNPs have some substance now.

[DrugsAreBad]

Ghost: Have you looked at plink? Looks like it might be useful. Links below.

Also, could you publish a list of all the snp files?

https://www.cog-genomics.org/plink/1.9/
http://zzz.bwh.harvard.edu/plink/dist/p ... c-1.07.pdf

[Ghost]

Yes I've looked at plink. It's probably what I'll be doing in the future. It's just a lot of setup that I don't understand yet. it's what the PFS guys and I are going to do.

As for the SNP list. it's on my site:

https://pssdlab.wordpress.com/snps/

[fema4psyciatrists]

You may have found a common altered gene in us? It was altered or activated or when we were born with it? It is a problem with taking in sunshine? Has that got anything to do with Serotonin's relationship with melatonin?

Do you need more people to put their interest in getting a 23andme spit test here? Maybe we can help them pay for it with donations if they do not have the money but are interested?

[DrugsAreBad]

I meant the files containing snp:s, not just the list of specific snp:s.

[Ciprofloxacin]

@Ghost
Please check these:

Code: Select all

https://drive.google.com/open?id=10cNlGrph93tboQZ69KTdNA8gKTcCzTBI

Code: Select all

https://drive.google.com/open?id=1gqOeyLavAmLyFh8T_w6OIR4HJ_oYy26k

Also, I just saw this. Looks like the tool we need.

https://blast.ncbi.nlm.nih.gov/Blast.cg ... =blasthome

There is a video about that.

https://www.youtube.com/watch?v=gKRDe7-l42M

What a coincidence, on the video, I saw these :d

https://drive.google.com/open?id=14WpNp ... Z_ReyNb6hS

Anyway. Maybe it saves time.

[Ghost]

@Cipro, will run those tonight and look at those links today.

Note to everyone: There are a lot of new results posted on my site: https://pssdlab.wordpress.com/logging/

[Ghost]

This may be of interest for a sample set:

NESDA sample
NESDA is a longitudinal, naturalistic cohort study examining the course and consequences of depressive and anxiety disorders. The collection and genotyping of the NESDA sample has been described elsewhere.17 In brief, 2981 participants were recruited through mental health care organizations (n=807), the community setting (n=564) and primary care (n=1610). They were assessed using the Composite Interview Diagnostic Instrument to diagnose depressive and anxiety disorders according to the Diagnostic and Statistical Manual of Mental Disorders—Fourth Edition. The interview also provided information on age of onset, number of major depressive disorder episodes and specific symptoms of depression. At baseline, detailed assessment was made of psychopathology using different inventories and scales. Many other data were collected including sociodemographic data and health indicators.

https://www.nature.com/articles/tpj201216
(Read about the significance of this gene in my loggings)