Local Prettybase Input File:

EGP Finished Gene Prettybase Input File: --NONE, use local file-- ABCB1 ABCB4 ABCC1 ABL1 ABL2 ABP1 ACTB ADAM33 ADH1A ADH1B ADH1C ADH4 ADH5 ADH6 ADM ADPRT ADPRTL2 AHR AKT2 ALAD ALDH1A1 ALDH1A2 ANAPC10 ANGPTL7 AOC2 AOC3 APEX APEX2 API5 APP APRT AREG ARNT ARSA ASNA1 ATF3 ATM ATOX1 ATRX ATXN3 BACE1 BAK1 BAX BCL2 BID BIK BIRC2 BIRC3 BIRC4 BIRC5 BLM BLVRA BLVRB BNIP1 BNIP2 BNIP3 BRCA1 BRCA2 BTG1 BZRP CALCA CAPN1 CAPN2 CAPN3 CAPN6 CAPN9 CAPNS1 CASP10 CASP2 CASP3 CASP4 CASP5 CASP6 CASP8 CASP9 CCK CCL5 CCNA2 CCNB1 CCNB2 CCND1 CCND2 CCND3 CCNE1 CCNE2 CCNG1 CCNG2 CCNH CCNI CCNK CCNT2 CCRK CD3Z CD4 CDC14A CDC14B CDC16 CDC2 CDC20 CDC23 CDC25A CDC25B CDC25C CDC27 CDC2L5 CDC34 CDC37 CDC42 CDC42BPB CDC42EP2 CDC45L CDC5L CDC6 CDC7 CDH1 CDK2 CDK3 CDK4 CDK5R1 CDK5R2 CDK6 CDK7 CDK9 CDKL1 CDKN1A CDKN1B CDKN2A CDKN2B CDKN2C CDKN2D CDKN3 CES2 CETN2 CHC1L CHEK1 CHEK2 CHRNA4 CHST1 CIZ1 CKB CKN1 CKS2 CLU COMT CSK CTNNA1 CTNNAL1 CTNNB1 CTNND1 CTNND2 CX3CR1 CXCR6 CYC1 CYP17A1 CYP19A1 CYP1A1 CYP1A2 CYP1B1 CYP27B1 CYP2A6 CYP2B6 CYP2C19 CYP2C8 CYP2C9 CYP2E1 CYP2J2 CYP3A4 CYP3A5 CYP4B1 CYP4V2 CYR61 DAD1 DAP DAPK1 DCLRE1A DCLRE1B DCLRE1C DDB1 DDB2 DDC DDIT3 DEPC1 DIA1 DMC1 DNAJC3 DNCH1 DTR DUSP1 DUT E2F1 E2F2 E2F3 E2F4 E2F5 ECE1 EDN1 EDN2 EDN3 EDNRA EDNRB EEF1A1 EGF EGFR ELA1 ELA2 ENO1 EPHX1 EPX ERBB2 ERCC1 ERCC2 ERCC3 ERCC4 ERCC5 ERCC6 ESR1 ESRRA ESRRG EXO1 FAAH FADD FANCA FANCC FANCD2 FANCE FANCF FANCG FAU FBP1 FDXR FEN1 FGF1 FGF10 FGF11 FGF13 FGF17 FGF2 FGF20 FGF21 FGF22 FGF23 FGF5 FGF6 FGF8 FGF9 FGFR1 FGFR2 FGFR3 FGFR4 FIBP FLJ35220 FMO1 FMO2 FMO3 FMO4 FMO5 FOS FOSB FOXM1 G22P1 GAB1 GAD1 GAD2 GADD45A GADD45B GADD45G GAP43 GAPD GCKR GCLC GCLM GCSH GLP1R GLRX GLRX2 GPI GPX1 GPX2 GPX3 GPX4 GPX5 GPX6 GPX7 GRM8 GSR GSS GSTA3 GSTA4 GSTM2 GSTM3 GSTP1 GSTZ1 GTF2H1 GTF2H3 GTF2H4 H2AFX HCNP HFE HGF HK2 HMOX2 HPRT1 HRAS HSD17B2 HSD17B3 HSF2 HSPA1A HSPA1B HSPA1L HSPA2 HSPA5 HSPA6 HSPA9B HSPB1 HSPB2 HSU24186 HTATIP HUS1 IFNA1 IGF1 IGF1R IGF2R IGFBP1 IGFBP2 IGFBP3 IGFBP4 IGFBP5 IGFBP6 IGFBP7 ITGAL ITM2B JUN JUNB JUND LCMT2 LIG1 LIG3 LIG4 LIPF LPO LTA LTB MAD2L2 MAP2K4 MAPK1 MAPK11 MAPK9 MARCKS MB MBD4 MCL1 MCM2 MCM3 MCM3AP MCM4 MCM5 MCM6 MDM2 MDM4 MGST1 MGST2 MGST3 MIF MLH1 MLH3 MLL MLP MMP1 MMP10 MMP11 MMP12 MMP13 MMP14 MMP15 MMP16 MMP19 MMP2 MMP20 MMP21 MMP7 MMP8 MMP9 MMS19L MN1 MNAT1 MPG MPO MRE11A MRPL37 MSH2 MSH3 MSH4 MSH5 MSH6 MSR1 MT2A MT3 MTHFR MUC1 MUC2 MUC5AC MUTYH MYBPC3 MYC NAT1 NAT2 NBS1 NCOA3 NEIL1 NEIL2 NEIL3 NELL1 NF1 NFKB1 NFKB2 NGB NOS1 NOS2A NQO1 NQO2 NR3C1 NRAS NTHL1 NUDT1 OAZ1 ODC1 OGG1 OPRM1 ORC2L ORC3L ORC4L OSR1 OXR1 OXSR1 PAWR PAX1 PAX3 PCK1 PCNA PDLIM1 PGR PKLR PKM2 PKMYT1 PLA2G1B PLA2G2A PLA2G2D PLA2G4A PLA2G4C PLA2G5 PLA2G6 PLCG1 PLK3 PMS1 PNKP POLA POLB POLD1 POLD2 POLD4 POLE POLE2 POLE3 POLG POLH POLI POLK POLL POLM POLN POLS POR PPARD PPIA PPIB PPIC PPID PRDX1 PRDX2 PRDX3 PRDX5 PRDX6 PRKCB1 PRKD1 PRKDC PRKR PTCH PTCH2 PTEN PTGS2 RAC1 RAD1 RAD17 RAD18 RAD21 RAD23A RAD23B RAD51 RAD51C RAD51L1 RAD51L3 RAD52 RAD54L RAD9A RAF1 RAG1 RB1 RECQL4 REQ RETN REV1L REV3L RFC1 RFC2 RFC3 RFC4 RFC5 RPA1 RPA2 RPA3 RPS3 RRM2B RXRA SCARA3 SEI1 SEPP1 SHH SIRT1 SLC22A7 SLC4A2 SLC6A3 SLC6A4 SMARCB1 SMUG1 SNCA SNN SOD1 SOD2 SOD3 SPHAR SPO11 SPRR1A SPRR1B SPRR3 SRD5A1 SRD5A2 STAT1 STAT2 STE STK25 SULT1C2 SULT2A1 TAF1 TAF10 TAF11 TAF12 TAF15 TAF1C TAF4 TAF6 TAF6 TAF9 TBX1 TBXA2R TCF15 TDG TDP1 TERF1 TERT TFDP1 TFDP2 TGFB1I1 TGFB2 TGFB3 TGFBI TGFBR1 TGFBR2 TGFBR3 TGM1 TGM2 TGM3 TIPIN TJP1 TNF TNFRSF11B TNFRSF14 TNFRSF17 TNFRSF1B TNFRSF25 TNFRSF4 TNFRSF5 TNFRSF6 TNFRSF7 TNFRSF8 TNFRSF9 TP53 TP53BP1 TP53I3 TPO TRAF4 TREX1 TREX2 TRIM5 TRPM2 TUBA1 TUBA2 TXN TXNRD1 UBA52 UBE2A UBE2B UBE2V2 UCP2 UGT1A1 UGT2B4 UHRF1 UMPS UNG VDR VNN1 VNN2 VNN3 WRN WT1 XDH XPA XPC XRCC1 XRCC2 XRCC3 XRCC4 XRCC5 ZFP36

Rare Allele Percentage (integer, 0 to 50): Cluster and/or Draw Trees For: NOTHING SITESITE WITH TREESAMPLESAMPLE WITH TREESITE AND SAMPLESITE AND SAMPLE WITH SITE TREESITE AND SAMPLE WITH SAMPLE TREESITE AND SAMPLE WITH SITE AND SAMPLE TREES

Linkage Disequilibrium Plot: NO THANKSr^2D'   LD Shader Mode: Black & WhiteGreyscaleRainbow

LD Min.:    LD Max.:

Displaying Genotype Data: Visual Genotypes

The display and interpretation of large genotype data sets can be simplified by using a graphical display. We have found it useful to present complete raw datasets of individuals' genotype data using a display format called a visual genotype (VG) (see Nickerson et al., Nature Genetics, 19:233-240, 1998, and Rieder et al., Nature Genetics, 22:59-60, 1999). This format presents all data in an array of samples (rows) x polymorphic sites (columns) and encodes each diallelic polymorphism according to a general color scheme where:

blue - homozygous genotype for the common allele

red - heterozygous genotype (both common and rare allele)

yellow - homozygous genotype for the rare allele

gray - missing data (N)

This array format allows one to visually inspect the data across both individual's diplotypes and polymorphic sites to make comparisons.

We have established a specific format for the uploading of genotype data. See below for complete formatting guidelines.

Displaying Your Own Data

Using this page you are able to upload a file (using the browse button to find a file on your own computer) and have a visual genotype produced. This image will appear in a separate browser window.

Displaying EGP Finished Data

You are also able to directly view data from our Finished Genes list and interactively display these visual genotypes. Use the drop-down list titled "EGP Finished Gene Prettybase Input File" to select a gene.

Display Options

The format of the visual genotype can be adjusted by filtering out polymorphisms below a minimum allele frequency. This is simply done by entering your minimum cutoff in the Rare Allele Percentage box.

In order to cluster sites, we calculate r² for all pairs of sites in a file, and then cluster sites such that sites with similar patterns of genotype (high r²) are shown near one another. We use an unweighted average linkage algorithm (UPGMA) to generate a hierarchical tree of cluster relationships (see more on VG2 site clustering).

How to Save A Visual Genotype Image

1. Move the mouse pointer over the image you wish to save.
2. Press right mouse button.
3. Move the pointer over "Save Image As..." (Netscape) or "Save Picture As..." (Internet Explorer)
4. Choose target directory to save to and type in desired filename.
5. Click "Ok" button.

Formatting Guidelines

Genotype Data Format:

This file must be a tab-delimited file with four fields on each line, in the format:

<Site Position><tab><Sample ID><tab><Allele 1><tab><Allele 2>

e.g.

200 IND1 A A

This line would represent a polymorphism at position 200, from a sample named IND1, with a homozygous genotype of allele A (both Allele 1 and Allele 2 are A). This format must be repeated on each line of your input file for *all* samples listed in your input file. If you have not genotyped a sample at a specific site, it would be entered with a genotype of "N N").

Multiple Site Example:

200 IND1 A A
200 IND2 A G
200 IND3 G G
300 IND1 N N
300 IND2 C C
300 IND3 C T
(etc. for more sites)

If you have questions about the data format please see our Finished Genes page, and select a gene and view the Individual Genotypes file.