Interpretome

[Olavsson]

I discovered this when I looked into Polako's blog today.

They basically let you upload your genetic data, so that you can analyse it using many cool functions.

Click this link for more informations:

http://esquilax.stanford.edu/



EDIT: I just saw that this was already posted. Feel free to delete this thread! :p

[Barreldriver]

In the latest Eurogenes entry there was a link to a tool called Interpretome: http://esquilax.stanford.edu/#painting

This is the painting generated for my 23andMe raw data at Davidski/Polako's recommended settings of 40 SNPs/120 Kb with 50 samples and everything else default for the Hapmap 2 source -

http://i326.photobucket.com/albums/k438/ragnarok1227/InterpretomepaintingforSethReeder.jpg

[Barreldriver]

This tool also has a function to look up Neanderthal, I got 3 Neanderthal alleles.

[Barreldriver]

PCA Plots, not too great since the HGDP doesn't have proper sampling from across the British Isle's, so with the absence of English and Irish I'm again in between the Orcadians and French, more close to French than Orcadian:

http://i326.photobucket.com/albums/k438/ragnarok1227/PCAplot1v2SethReeder.jpg
http://i326.photobucket.com/albums/k438/ragnarok1227/PCAplot1v4SethReeder.jpg

[Barreldriver]

POPRES European plot, more accurate than the HGDP:

http://i326.photobucket.com/albums/k438/ragnarok1227/PCAplot1v4SethReederPOPRESV3.jpg

[Beorn]

I'll wait till the amount of French is overwhelmed by actual Northern Europeans.

[Barreldriver]

I'll wait till the amount of French is overwhelmed by actual Northern Europeans.

The HGDP was odd in their sampling and such methinks, the POPRES is a bit better in this regard, the POPRES run was quite accurate for me while the HGDP one was not so much.

[Beorn]

11288

11289

11290

11291

11292

[Amapola]

43,000 SNPs option, plotting PC1 vs. PC4 (as recommended by Polako for the most accurate results)

http://img269.imageshack.us/img269/7470/imagen2bfe.jpg

:shy:

[Barreldriver]

^I bumped it up to the high res from the low res (43,000) and got very slightly more accurate results for my known genealogy, it was nothing major in difference. :p

[Amapola]

^I bumped it up to the high res from the low res (43,000) and got very slightly more accurate results for my known genealogy, it was nothing major in difference. :p

To be honest, with the high res, I get some "funny" results

http://img600.imageshack.us/img600/5963/funnythingv.jpg

Which I can't REALLY explain. So I suppose the above posted is more accurate. :cool:

[Frederick]

Hmm.
Isnt it so, that the "high resolution" is the new V3 chip? (1,5 Million SNP or so?)
While the "Low resolution" is for the old 23 chip? (1 Million SNP)

I think, since I have not updated to the V3 chip, I need to use the V2 setting?

Using the V3 setting is pushing my result northwards btw. Wich seems the case with everyone?

[Mortimer]

http://esquilax.stanford.edu/

http://s7.postimage.org/oey17r0wb/HGDPWorl.jpg (http://postimage.org/)

http://s7.postimage.org/tevhfp6iz/Hap_Map_World.jpg (http://postimage.org/)

http://s7.postimage.org/8969yul3f/Popres_European.jpg (http://postimage.org/)


upload images (http://postimage.org/)

[Mark]

Interpretome http://esquilax.stanford.edu/#pca

Regional - Using 1,000 - 100,000 SNP's

27797

27798

27799

Detailed Regional - Using 1,000 - 100,000 SNP's

27800

27801

27802

[Sikeliot]

It'd be easier to judge the accuracy of these results if there were more East Mediterranean groups used for comparison.

[Mark]

It'd be easier to judge the accuracy of these results if there were more East Mediterranean groups used for comparison.
I think you're right.

[Mark]

Here's another one using X Axis: PC1 and Y Axis: PC10 - detailed regional with 100,00 SNP's.

27811

[Insuperable]

www.interpretome.com


http://imageshack.us/a/img835/2926/pc1vspc2hgdpworld.png
http://imageshack.us/a/img203/3051/hgdpeuropean.png

[Graham]

Where is the link to that? Forgot.

Edit: I see the link on your image. :)

[Graham]

http://imageshack.us/a/img842/7551/36130057.png
http://imageshack.us/a/img10/3104/60749317.png

[Insuperable]

@Graham

I find your results slightly strange, but did you upload your file unzipped or zipped? I ask because you have to upload it unzipped.


edit: once you get your results do not forget to zoom out a little (shift+numpad minus)

[Graham]

Yes I did, will try again & edit my post.

[Mark]

Europe

http://i.imgur.com/q2TRi6T.jpg

World

http://i.imgur.com/x9DUNV8.jpg

[Loki]

http://i49.tinypic.com/314s2uf.jpg

[Patches]

Mine:
http://i1154.photobucket.com/albums/p535/PureEvil91/Interpret2_zpsc0b4fc15.png (http://s1154.photobucket.com/user/PureEvil91/media/Interpret2_zpsc0b4fc15.png.html)

http://i1154.photobucket.com/albums/p535/PureEvil91/Interpret1_zps47335ea2.png (http://s1154.photobucket.com/user/PureEvil91/media/Interpret1_zps47335ea2.png.html)

[Atlantic Islander]

http://i1302.photobucket.com/albums/ag131/FocalReady/0G/clusterregionaldetail_zps75f573d6.png
http://i1302.photobucket.com/albums/ag131/FocalReady/0G/clusterregional_zpseb9277a5.png
http://i1302.photobucket.com/albums/ag131/FocalReady/0G/clusterworld_zps944587fe.png
http://i1302.photobucket.com/albums/ag131/FocalReady/0G/cluster1_zps182b08e5.png
http://i1302.photobucket.com/albums/ag131/FocalReady/0G/cluster2_zps03eae51f.png

[Mark]

Here's a detailed regional shot. I'm not really anywhere conclusive. Sikeliot made a point that they may not use East Med populations. If they did, I would be pulled more S. East.

http://i.imgur.com/dPKFlHZ.jpg

[Patches]

http://i1154.photobucket.com/albums/p535/PureEvil91/Interpret4_zps247cb4f4.png (http://s1154.photobucket.com/user/PureEvil91/media/Interpret4_zps247cb4f4.png.html)

http://i1154.photobucket.com/albums/p535/PureEvil91/Interpret5_zps9ed2ddc0.png (http://s1154.photobucket.com/user/PureEvil91/media/Interpret5_zps9ed2ddc0.png.html)

One more(without British, Eastern, and Southern components):
http://i1154.photobucket.com/albums/p535/PureEvil91/Interpret6_zpsfa4d723e.png (http://s1154.photobucket.com/user/PureEvil91/media/Interpret6_zpsfa4d723e.png.html)

[Sikeliot]

Here's a detailed regional shot. I'm not really anywhere conclusive. Sikeliot made a point that they may not use East Med populations. If they did, I would be pulled more S. East.

http://i.imgur.com/dPKFlHZ.jpg

If there were southern Italians you would cluster between them and Cypriots.

[Kazimiera]

World

http://i1162.photobucket.com/albums/q526/katzentatzen79/Interpretome/WorldHGDPPC1vsPC2_zps58aea302.jpg


European

http://i1162.photobucket.com/albums/q526/katzentatzen79/Interpretome/EuropeanHGDPPC1vsPC2_zps650366db.jpg

http://i1162.photobucket.com/albums/q526/katzentatzen79/Interpretome/EuropeanHGDPdetailedPC1vsPC2_zps50cfdf43.jpg

[Patches]

Some other clusters in the POPRES tool...
More Southern Components:
http://i1154.photobucket.com/albums/p535/PureEvil91/InterpretSouth_zpsd6a16d1e.png (http://s1154.photobucket.com/user/PureEvil91/media/InterpretSouth_zpsd6a16d1e.png.html)

More Eastern Components:
http://i1154.photobucket.com/albums/p535/PureEvil91/Interpreteast_zps934b01a1.png (http://s1154.photobucket.com/user/PureEvil91/media/Interpreteast_zps934b01a1.png.html)

Main cluster:
http://i1154.photobucket.com/albums/p535/PureEvil91/Maincluster_zpsd18540d4.png (http://s1154.photobucket.com/user/PureEvil91/media/Maincluster_zpsd18540d4.png.html)
(Belgians and Brits)

[Atlantic Islander]

I had no idea we could remove populations lol.

[MfA_]

HDGP: World
http://abload.de/img/1nvqh6.png

HDGP: European (Detailed Region)
http://abload.de/img/2agu7i.png



Hapmap: World
http://abload.de/img/3dfopj.png

Hapmap: World (Local Clusters)
http://abload.de/img/4ogi30.png



POPRES: European (PCA1-4)
http://abload.de/img/5i2uk0.png



Mid-East/Jewish
http://abload.de/img/8ylude.png

Mid-East/Jewish (Local Clusters)
http://abload.de/img/9quupr.png



Referance Populations
PCA1-2
http://abload.de/img/7zvohl.png

PCA1-4
http://abload.de/img/6mdqc0.png

[safinator]

EUROPEAN

http://i.imgur.com/35A5NJm.png

WORLD

http://i.imgur.com/sFLWyVv.png

POPRES EUROPEAN

http://i.imgur.com/wjca903.png

REFERENCE POPULATIONS

http://i.imgur.com/wno2KEm.png

[Mark]

These were done more recently, mostly using the default view settings. It places me at the cusp of the Near East and Europe. Makes sense.

Europe 1

http://i.imgur.com/VVeCbFQ.png

Europe 2

http://i.imgur.com/dPKFlHZ.jpg

Europe 3

http://i.imgur.com/ocGiDPv.png

World 1

http://i.imgur.com/vK0vgjW.png

World 2

http://i.imgur.com/MDt8xaB.png

World 3

http://i.imgur.com/yBlcShT.png

Asia

http://i.imgur.com/dwlJ4TP.png

Middle-East

http://i.imgur.com/qD0bgmy.png

Africa

http://i.imgur.com/qJphkXO.png

[Equilibrium]

HGDP: WORLD
http://imageshack.us/a/img542/7021/kho8.png


HGDP: WORLD ZOOM-IN
http://imageshack.us/a/img24/5716/9rzl.png




HGDP: EUROPE
http://imageshack.us/a/img163/3671/gwwq.png




POPRES
http://imageshack.us/a/img546/6267/6a3v.png


POPRES ZOOM-IN
http://imageshack.us/a/img826/5458/8xjr.png




HGDP: MID-EAST/JEWISH
http://imageshack.us/a/img46/8499/1c4q.png


HGDP: MID-EAST/JEWISH ZOOM-IN
http://imageshack.us/a/img845/6307/v3ag.png

[Mark]

Did this one again recently using different parameters, not sure how accurate it is:

http://i.imgur.com/ZC2wpBo.jpg

[JQP4545]

Lol my mum is off the maps:

50356

[JQP4545]

Isn't that strange

[JQP4545]

http://oi62.tinypic.com/2aeoi8.jpg

http://oi59.tinypic.com/28kk9xy.jpg