PDA

View Full Version : Interpretome POPRES: European



MitchellSince1893
03-08-2014, 06:45 PM
I was looking through the various PCA tools on this site http://www.interpretome.com and was trying different combinations on the POPRES: European tool and found a combination that seemed quite useful/intuitive.

1. After you load up your genome results (click "Begin Exploring" in the upper right corner to upload them)
2. Choose PCA
3. Select POPRES: European
4. Select 74,000 (v3)
5. Set X axis to PC 5: PC 5 "Reveals a north-to-south cline within Europeans"
6. Set the Y axis to PC 1: PC 1 "Distinguishes Africans from non-Africans"
6. Click visualize
7. Reverse the y axis so that the Northern Europeans are at the top and the Southern Europeans are at the bottom of the graph.
8. Click on the all the country initials at the bottom to turn them off and then turn on only the ones you want to see. This helps to unclutter the graph and to see what populations you fall within.

This particular PC combination seemed to do the best job in clustering the country results and placing them in relation to each other.

I loaded my parents and my 23andme genome results into the graph and here are some of the results for countries that we fit into (British, German, Irish, Dutch, Belgian). Besides these 5 we also were are the Northern edge of France, the Western edge of Poland, and the Northwestern edge of Austria. I'm the upper right square, my mom is in between, and dad is lower left.

15721573157415751576

MitchellSince1893
03-08-2014, 07:01 PM
Here are the French, Polish, and Austrian graphs157715781579

DMXX
03-08-2014, 08:56 PM
Although not your target audience, I attempted your steps to see what the result was. My result landed me somewhere between the North and Central European areas. This does actually agree with my ADMIXTURE scores on certain project runs (e.g. more North_European than Atlantic_Med on Dodecad K12b). Great share!

vettor
03-08-2014, 09:28 PM
I was looking through the various PCA tools on this site http://www.interpretome.com and was trying different combinations on the POPRES: European tool and found a combination that seemed quite useful/intuitive.

1. After you load up your genome results (click "Begin Exploring" in the upper right corner to upload them)
2. Choose PCA
3. Select POPRES: European
4. Select 74,000 (v3)
5. Set X axis to PC 5: PC 5 "Reveals a north-to-south cline within Europeans"
6. Set the Y axis to PC 1: PC 1 "Distinguishes Africans from non-Africans"
6. Click visualize
7. Reverse the y axis so that the Northern Europeans are at the top and the Southern Europeans are at the bottom of the graph.
8. Click on the all the country initials at the bottom to turn them off and then turn on only the ones you want to see. This helps to unclutter the graph and to see what populations you fall within.

This particular PC combination seemed to do the best job in clustering the country results and placing them in relation to each other.

I loaded my parents and my 23andme genome results into the graph and here are some of the results for countries that we fit into (British, German, Irish, Dutch, Belgian). Besides these 5 we also were are the Northern edge of France, the Western edge of Poland, and the Northwestern edge of Austria. I'm the upper right square, my mom is in between, and dad is lower left.

15721573157415751576

thanks

for your step 8 , why don't you just use mouse to highlight your block which then brings up the zoomed version.

as for my results.........they are the same , circled by french, italian and swiss flags with a single portuguese flag also......

it states to use PCA1 and PCA4 to match info below
http://www.ncbi.nlm.nih.gov/pubmed/18760391

If I use PCA4 instead of your recommended PCA5 , the portuguese flag drops off...the rest remain

AJL
03-08-2014, 09:34 PM
(14.0, –53.65)

Pretty much in the Alps, overlapping Austria, France, Switzerland. Italy is slightly too far south, Germany too far north, and Spain too far west, but all barely miss.

My mother ends up at (14.0, –61.175) in a fairly solid UK cluster, or put another way, within that mythical spot where Ireland and Belgium meet.

MitchellSince1893
03-08-2014, 10:56 PM
...why don't you just use mouse to highlight your block which then brings up the zoomed version.

http://www.ncbi.nlm.nih.gov/pubmed/18760391

If I use PCA4 instead of your recommended PCA5 , the portuguese flag drops off...the rest remain

I find that by not zooming in and only showing one or 2 countries (at least turn off the UK with covers up many other results); it's easier to see where one fit into the bigger picture for a group.

Yes I saw that PC 4 comment, but when I read that the PC 5 showed a North/South European cline, I found that this PC along with PC 1, and reversing the Y axis, put the nationalities in a configuration similar to European geography. Ireland to the Northwest, Scandinavian countries at the top, Iberian countries to the southwest, Poland and Baltic countries to the Northeast etc.

vettor
03-08-2014, 11:22 PM
I find that by not zooming in and only showing one or 2 countries (at least turn off the UK with covers up many other results); it's easier to see where one fit into the bigger picture for a group.

Yes I saw that PC 4 comment, but when I read that the PC 5 showed a North/South European cline, I found that this PC along with PC 1, and reversing the Y axis, put the nationalities in a configuration similar to European geography. Ireland to the Northwest, Scandinavian countries at the top, Iberian countries to the southwest, Poland and Baltic countries to the Northeast etc.

ok , mine is below......I still had to zoom because it was congested between FRA, ITA and CH ( swiss)

http://imageshack.com/scaled/medium/547/5ktn.jpg (http://imageshack.com/photo/my-images/547/5ktn.jpg/) Uploaded with ImageShack.us (http://imageshack.com)

Tolan
03-09-2014, 06:01 AM
I'm closer to German than French!
1587

Below: France, UK, Germany, Ireland, Italy, Spain:
1588

Humanist
03-09-2014, 07:01 AM
Although not your target audience, I attempted your steps to see what the result was. My result landed me somewhere between the North and Central European areas. This does actually agree with my ADMIXTURE scores on certain project runs (e.g. more North_European than Atlantic_Med on Dodecad K12b). Great share!

Would you mind posting your location? :) Interestingly, out of the populations from the region (excluding the Italians), my spot would probably be most near to the average for the Greeks (and even the Albanians, and perhaps Bulgarians), rather than the Turks or Cypriots.

http://i1096.photobucket.com/albums/g326/dok101/Faces/popres_europe_hum.png

DMXX
03-22-2014, 04:24 PM
Would you mind posting your location? :)

Most certainly. Please see the attached. I'm basically in the centre of the Swiss cluster and the southern part of the British one.

1647

vettor
03-22-2014, 05:42 PM
Most certainly. Please see the attached. I'm basically in the centre of the Swiss cluster and the southern part of the British one.

1647

Swiss like me.........he he
Maybe I am ancient armenian ( like your flag)............someone did state to me a long time ago, your ancestors are from Colchis ( Armenia on the black sea)

DMXX
03-22-2014, 05:48 PM
Swiss like me.........he he
Maybe I am ancient armenian ( like your flag)............someone did state to me a long time ago, your ancestors are from Colchis ( Armenia on the black sea)

Or alternatively, the POPRES European map just indicates my combination of components specific to Europe are very Swiss-like. :)

Wulf Warrior
07-30-2014, 08:24 AM
I uploaded my genome files, but a message popped up saying that only 37 SNPS were loaded and results may be unreliable, I'm not sure why?

2147

Anyhow.. I seem to be north to Swedesh people. Though taken with a grain of salt due to that message....

vettor
07-30-2014, 10:11 AM
I uploaded my genome files, but a message popped up saying that only 37 SNPS were loaded and results may be unreliable, I'm not sure why?

2147

Anyhow.. I seem to be north to Swedesh people. Though taken with a grain of salt due to that message....

you loaded it wrong

unzip file first in your folder then load that .txt file in interpretome

The message you got was that you loaded a file which was unzipped

Wulf Warrior
07-30-2014, 10:26 AM
you loaded it wrong

unzip file first in your folder then load that .txt file in interpretome

The message you got was that you loaded a file which was unzipped

Thanks Vettor, I'll do it correctly now :)

There we go...

2148

Alpine Hominin
07-30-2014, 06:14 PM
Here are my charts. Seems I fall in the North Sea area. I'll have to include the last 2 charts in a follow up post

2149 2150 2151 2152 2153

Alpine Hominin
07-30-2014, 06:16 PM
My last 2 charts.

2154 2155

vettor
07-30-2014, 07:18 PM
Thanks Vettor, I'll do it correctly now :)

There we go...

2148

np

what was you neaderthal .........mine was 0.7
23andme has me 3.1
natgeno has me 2.4 denis and 0.7 neand .............so it matches NAtgeno2

test the beta chromosome .........its also interesting

vettor
07-30-2014, 07:19 PM
Thanks Vettor, I'll do it correctly now :)

There we go...

2148

np

you are Pure English ............you can zoom in

what was you neaderthal .........mine was 0.7
23andme has me 3.1
natgeno has me 2.4 denis and 0.7 neand .............so it matches NAtgeno2

test the beta chromosome .........its also interesting

vettor
07-30-2014, 07:21 PM
My last 2 charts.

2154 2155

I think it states to select european ( on the top right side ) and use PCA 1 and 4 if you are european

Isidro
07-30-2014, 07:30 PM
Mine seem further north from other plots I have seen where I land in north Iberian dots.

Using these settings:

3. Select POPRES: European
4. Select 74,000 (v3)
5. Set X axis to PC 5: PC 5 "Reveals a north-to-south cline within Europeans"
6. Set the Y axis to PC 1: PC 1 "Distinguishes Africans from non-Africans"

21562157

vettor
07-30-2014, 07:31 PM
Mine seem further north from other plots I have seen where I land in north Iberian dots.

Using these settings:

3. Select POPRES: European
4. Select 74,000 (v3)
5. Set X axis to PC 5: PC 5 "Reveals a north-to-south cline within Europeans"
6. Set the Y axis to PC 1: PC 1 "Distinguishes Africans from non-Africans"

21562157

what does zooming into the second show...........portuguese?

Isidro
07-30-2014, 07:37 PM
Well is not clear, usually there is a gap cluster with French. I will try to make a closer look.

Alpine Hominin
07-30-2014, 07:42 PM
I didn't see the part about selecting European, thanks Vettor. I ran my data again at 1v5 with European selected, but only noticed a difference in the Poland and UK maps, where I was pulled very slightly Westward in both. I'll upload my 1v4 too later today for comparison.

Isidro
07-30-2014, 07:51 PM
Here is a closer look, file names show testing company. 23andme seem more accurate but both show higher than other plots I have seen where I land within Iberians. 21582159

CelticGerman
09-15-2014, 06:24 PM
I like Interpretome. Picture reflects well the real origins:
-me, North German, left side (to be seen as North)
-followed by my uncle, German, but more south due to the origins of his father
-than our four children
-and at the right (southern) side my French wife and her father

2594

CelticGerman
09-15-2014, 06:31 PM
my position in comparision with some selected nationalities2595

Stephen1986
09-15-2014, 07:44 PM
Here's my charts, I included every country, except the UK as that one is obvious, which I fell within the group. These countries are Austria, Belgium, Switzerland, Germany, France, Ireland and the Netherlands.

Stephen1986
09-15-2014, 07:46 PM
Here's my Dutch and Irish charts. I'll get results for my brother as well.

Stephen1986
09-15-2014, 08:11 PM
Here are the charts for my brother. Again excluding the UK due to that being a huge group around him anyway, he is within the Austrian, Belgian, German, French, Irish, Dutch and Polish groups.

Stephen1986
09-15-2014, 08:12 PM
Here are his two remaining charts.

CelticGerman
04-23-2015, 10:09 PM
Zoom 4419

firemonkey
08-28-2015, 11:19 AM
http://i4.photobucket.com/albums/y126/labile/genealogy/pop%20res2.png

http://i4.photobucket.com/albums/y126/labile/genealogy/pop%20res3.png

Showing Ireland/United Kingdom connection.

firemonkey
08-28-2015, 03:46 PM
Ireland, Scotland and UK. I wonder whether this indicates that a lot of my Scottish ancestry is in fact Irish.

5697


5698

5699

firemonkey
08-28-2015, 03:51 PM
Denmark,Norway and Sweden. More Swedish?

5700

5701

5702

firemonkey
08-28-2015, 03:57 PM
France, Germany and Netherlands. More German?



5703

5704

5705

evon
08-28-2015, 04:43 PM
Mine..

Nordic:
http://i412.photobucket.com/albums/pp207/vulcanphoto/chart1.png
Think the Norwegian samples are from Eastern Norway, that could explain my plot.


Same with my maternal grandmother (We cluster together) and paternal aunt included:
http://i412.photobucket.com/albums/pp207/vulcanphoto/chart.png

AmieLynn
09-02-2015, 04:08 AM
5756 5757

Can someone please tell me where I fit? I have trouble interpreting.

Thanks

anglesqueville
10-31-2015, 11:08 AM
Unbelievable: I did'nt know Interpretome... Thanks to the op for his explanations. I got a simplified pca for me, my mother and my wife:
6491 (btw, very more northern-oriented than the global similarity map of 23andMe)

NewAlbion
02-28-2017, 10:23 AM
http://rsmg.pbsrc.com/albums/v336/naudiz/Screenshot_20170228-050955_zpsejzymy3h.png?w=480&h=480&fit=clip

NewAlbion
02-28-2017, 10:30 AM
http://rsmg.pbsrc.com/albums/v336/naudiz/Screenshot_20170228-050955_zpsejzymy3h.png?w=480&h=480&fit=clip

I dunno not finding that incredibly useful. Closest flag is the British then Irish then German, Scandinavian, and the Dutch.Not clustering that close with the Scots but that could just mean they only like did lowland Scotland. I mean if you look at Europe only like the Benelux and Britain are celto-germanic. So if you ask me that makes me most like the Scots just not the ones sampled there.