CLASS_IDX_START = 10
DIFF_THRESHOLD = 3The Sei framework is a practical solution for unraveling the intricate relationship between genetic sequences and regulatory functions, shedding light on how genome variations contribute to traits and diseases. Here's a simple breakdown of how Sei works, what it requires as input, and what you can expect as output:
How Sei Works:
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Prediction and Profiling: Sei employs deep learning to predict and profile regulatory activities. It learns from extensive data, enabling it to understand the connection between genetic sequences and regulatory behaviors.
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Global Mapping: Sei creates a global map of sequence regulatory activities. This map covers various types of regulatory actions, such as enhancer and promoter activities, across the entire genome.
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Sequence Classes: Sei introduces the concept of "sequence classes," which serve as a vocabulary for describing different regulatory activities. These classes are derived from predictions made by the deep learning model.
Input Requirements:
- Genetic Sequences: Provide the genetic sequence or variant you're interested in analyzing. This could be a DNA segment associated with a specific trait or disease.
Outputs Generated:
-
Sequence Class Assignment: Sei assigns a sequence class to the input genetic sequence. This class encapsulates regulatory information, such as enhancer or promoter activity, providing a deeper understanding of its role.
-
Quantitative Regulatory Impact: Sei quantifies the impact of the input sequence on regulatory activities. You'll get insights into whether the mutation increases, decreases, or has no effect on specific regulatory behaviors.
Practical Applications:
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Trait-Disease Linkage: Sei helps you understand how genetic variations relate to traits and diseases. It provides insights into regulatory mechanisms underlying complex health conditions.
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Mutation Analysis: Sei aids in the interpretation of disease-related mutations. By quantifying regulatory impact, it distinguishes between gain-of-function and loss-of-function mutations.
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Research Tool: Sei is a valuable resource for researchers studying genetics. It allows systematic classification and scoring of sequences, enhancing our understanding of genetic regulation.
To start using Sei, you need the genetic sequence you want to explore. Run the framework using the code available on GitHub: https://github.com/FunctionLab/sei-framework. Alternatively, access a user-friendly web server for ease of use: hb.flatironinstitute.org/sei. For a deeper dive into the technical aspects, you can explore the original research article published in Nature. Sei gives practical insights into the regulatory basis of complex traits and diseases, advancing our understanding of genetic influences.
This notebook presents an analysis of Sei outputs concerning a curated list of quality variants (n=12,976). The script responsible for generating the data described in this notebook is accessible here. For access to both the input and output raw data, please follow this link.
The Sei framework assigns each genetic sequence a specific label from a predefined set of sequence class categories. These labels correspond to different regulatory activities associated with the sequences. The following table outlines the sequence class labels, their corresponding names, ranks by size, and group assignments:
| Sequence Class Label | Sequence Class Name | # | Group |
|---|---|---|---|
| PC1 | Polycomb / Heterochromatin | 0 | PC |
| L1 | Low signal | 1 | L |
| TN1 | Transcription | 2 | TN |
| TN2 | Transcription | 3 | TN |
| L2 | Low signal | 4 | L |
| E1 | Stem cell | 5 | E |
| E2 | Multi-tissue | 6 | E |
| E3 | Brain / Melanocyte | 7 | E |
| L3 | Low signal | 8 | L |
| E4 | Multi-tissue | 9 | E |
| TF1 | NANOG / FOXA1 | 10 | TF |
| HET1 | Heterochromatin | 11 | HET |
| E5 | B-cell-like | 12 | E |
| E6 | Weak epithelial | 13 | E |
| TF2 | CEBPB | 14 | TF |
| PC2 | Weak Polycomb | 15 | PC |
| E7 | Monocyte / Macrophage | 16 | E |
| E8 | Weak multi-tissue | 17 | E |
| L4 | Low signal | 18 | L |
| TF3 | FOXA1 / AR / ESR1 | 19 | TF |
| PC3 | Polycomb | 20 | PC |
| TN3 | Transcription | 21 | TN |
| L5 | Low signal | 22 | L |
| HET2 | Heterochromatin | 23 | HET |
| L6 | Low signal | 24 | L |
| P | Promoter | 25 | P |
| E9 | Liver / Intestine | 26 | E |
| CTCF | CTCF-Cohesin | 27 | CTCF |
| TN4 | Transcription | 28 | TN |
| HET3 | Heterochromatin | 29 | HET |
| E10 | Brain | 30 | E |
| TF4 | OTX2 | 31 | TF |
| HET4 | Heterochromatin | 32 | HET |
| L7 | Low signal | 33 | L |
| PC4 | Polycomb / Bivalent stem cell Enh | 34 | PC |
| HET5 | Centromere | 35 | HET |
| E11 | T-cell | 36 | E |
| TF5 | AR | 37 | TF |
| E12 | Erythroblast-like | 38 | E |
| HET6 | Centromere | 39 | HET |
The Sei mutation analysis script outputs the difference between predictions.
We proceed with the hypothesis that a variant resulting in a substantial alteration in classification signifies a noteworthy impact.
Please note that the provided information covers the primary insights from the analysis. If any additional details are required, feel free to ask.
The following are the first rows of the output
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| seqclass_max_absdiff | index | chrom | pos | name | ref | alt | strand | ref_match | contains_unk | ... | E10 Brain | TF4 OTX2 | HET4 Heterochromatin | L7 Low signal | PC4 Polycomb / Bivalent stem cell Enh | HET5 Centromere | E11 T-cell | TF5 AR | E12 Erythroblast-like | HET6 Centromere | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | 28.598381 | 2541 | chr10 | 71696897 | . | C | T | + | True | False | ... | -4.335888 | -2.783544 | -1.008678 | -0.506140 | -2.323609 | -1.797118 | -5.420297 | -2.725370 | -8.208790 | -0.950999 |
| 1 | 23.510495 | 6939 | chr17 | 72557120 | . | C | T | + | True | False | ... | -5.114744 | -3.753617 | -0.780645 | -0.728461 | -1.664326 | -2.443387 | -6.780809 | -3.353350 | -9.804309 | -1.495238 |
| 2 | 22.635229 | 9874 | chr3 | 50273087 | . | C | T | + | True | False | ... | -5.018271 | -3.174477 | -0.664671 | -0.640114 | 1.289407 | -2.616225 | -5.714324 | -3.128774 | -11.653957 | -1.827755 |
| 3 | 22.292243 | 1022 | chr1 | 202693135 | . | G | A | + | True | False | ... | -4.274951 | -3.420390 | -0.753183 | -0.425143 | -1.472327 | -1.613177 | -4.872271 | -2.677505 | -7.735443 | -0.929981 |
| 4 | 22.148657 | 2641 | chr10 | 117176134 | . | G | A | + | True | False | ... | -4.883025 | -3.470859 | -1.069819 | -0.548899 | -1.193743 | -2.060631 | -6.247415 | -3.265896 | -8.063337 | -1.170694 |
5 rows × 50 columns
Columns legend:
-
seqclass_max_absdiff: This column represents the maximal score difference for a particular variant's sequence class prediction. It indicates the largest absolute difference in scores among the predicted sequence classes for the given variant. -
index: The index refers to the unique identifier assigned to each variant in the dataset. It helps in keeping track of individual variants and their associated information. -
chrom: This column specifies the chromosome on which the variant is located. Chromosome information helps in identifying the genomic context of the variant. -
pos: The 'pos' column denotes the position of the variant on the chromosome. It provides the exact genomic location of the variant within the chromosome. -
name: The 'name' column typically holds the name or identifier of the variant. It can include additional information about the variant's characteristics. -
ref: The 'ref' column displays the reference allele of the variant. This is the allele that is present in the reference genome at the given genomic position. -
alt: The 'alt' column represents the alternate allele of the variant. This allele is the alternative to the reference allele and signifies the variation at that particular genomic position. -
strand: This column indicates the DNA strand on which the variant is located. The strand information helps in understanding the orientation of the variant within the DNA sequence. -
ref_match: The 'ref_match' column assesses whether the variant's reference allele matches the reference genome. It's a binary indicator (True/False) that is useful for quality control checks. -
contains_unk: This column informs whether the variant contains unknown or ambiguous bases. These bases are usually represented by 'N' and indicate uncertainty in the sequence data.
the remaining columns, which include specific sequence class labels (such as 'PC1', 'L1', 'TN1', and so forth), demonstrate the score difference between the prediction for the given sequence class in the reference sequence versus the alternate sequence.
class_score[['ref_match','contains_unk']].describe().T
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| count | unique | top | freq | |
|---|---|---|---|---|
| ref_match | 12976 | 1 | True | 12976 |
| contains_unk | 12976 | 1 | False | 12976 |
The table indicates that all variants align perfectly with the hg38 reference genome, evidenced by the term "Reference Matches." Importantly, neighboring positions of these variants do not contain any unknown characters, underscoring the alignment's accuracy and integrity.
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n(t);f=m-,h=g-w,p=v-T,d=1/Math.sqrt(ff+hh+pp),a=x(p*=d)-b*(h*=d),o=b*(f*=d)-yp,s=yh-xf,(d=Math.sqrt(aa+oo+ss))?(a*=d=1/d,o*=d,s*=d):(a=0,o=0,s=0);l=hs-po,c=pa-fs,u=fo-ha,(d=Math.sqrt(ll+cc+uu))?(l=d=1/d,c*=d,u*=d):(l=0,c=0,u=0);return t[0]=a,t[1]=l,t[2]=f,t[3]=0,t[4]=o,t[5]=c,t[6]=h,t[7]=0,t[8]=s,t[9]=u,t[10]=p,t[11]=0,t[12]=-(am+og+sv),t[13]=-(lm+cg+uv),t[14]=-(fm+hg+p*v),t[15]=1,t}},{"./identity":209}],213:[function(t,e,r){e.exports=function(t,e,r){var n=e[0],i=e[1],a=e[2],o=e[3],s=e[4],l=e[5],c=e[6],u=e[7],f=e[8],h=e[9],p=e[10],d=e[11],m=e[12],g=e[13],v=e[14],y=e[15],x=r[0],b=r[1],=r[2],w=r[3];return t[0]=xn+bs+f+wm,t[1]=xi+bl+h+wg,t[2]=xa+bc+p+wv,t[3]=xo+bu+d+wy,x=r[4],b=r[5],=r[6],w=r[7],t[4]=xn+bs+f+wm,t[5]=xi+bl+h+wg,t[6]=xa+bc+p+wv,t[7]=xo+bu+d+wy,x=r[8],b=r[9],=r[10],w=r[11],t[8]=xn+bs+f+wm,t[9]=xi+bl+h+wg,t[10]=xa+bc+p+wv,t[11]=xo+bu+d+wy,x=r[12],b=r[13],=r[14],w=r[15],t[12]=xn+bs+f+wm,t[13]=xi+bl+h+wg,t[14]=xa+bc+p+wv,t[15]=xo+bu+d+wy,t}},{}],214:[function(t,e,r){e.exports=function(t,e,r,n,i,a,o){var s=1/(e-r),l=1/(n-i),c=1/(a-o);return t[0]=-2s,t[1]=0,t[2]=0,t[3]=0,t[4]=0,t[5]=-2l,t[6]=0,t[7]=0,t[8]=0,t[9]=0,t[10]=2c,t[11]=0,t[12]=(e+r)s,t[13]=(i+n)l,t[14]=(o+a)c,t[15]=1,t}},{}],215:[function(t,e,r){e.exports=function(t,e,r,n,i){var a=1/Math.tan(e/2),o=1/(n-i);return t[0]=a/r,t[1]=0,t[2]=0,t[3]=0,t[4]=0,t[5]=a,t[6]=0,t[7]=0,t[8]=0,t[9]=0,t[10]=(i+n)o,t[11]=-1,t[12]=0,t[13]=0,t[14]=2ino,t[15]=0,t}},{}],216:[function(t,e,r){e.exports=function(t,e,r,n){var i=Math.tan(e.upDegreesMath.PI/180),a=Math.tan(e.downDegreesMath.PI/180),o=Math.tan(e.leftDegreesMath.PI/180),s=Math.tan(e.rightDegreesMath.PI/180),l=2/(o+s),c=2/(i+a);return t[0]=l,t[1]=0,t[2]=0,t[3]=0,t[4]=0,t[5]=c,t[6]=0,t[7]=0,t[8]=-(o-s)l.5,t[9]=(i-a)c.5,t[10]=n/(r-n),t[11]=-1,t[12]=0,t[13]=0,t[14]=n*r/(r-n),t[15]=0,t}},{}],217:[function(t,e,r){e.exports=function(t,e,r,n){var i,a,o,s,l,c,u,f,h,p,d,m,g,v,y,x,b,,w,T,k,A,M,S,E=n[0],L=n[1],C=n[2],P=Math.sqrt(EE+LL+CC);if(Math.abs(P)<1e-6)return null;E=P=1/P,L*=P,C*=P,i=Math.sin(r),a=Math.cos(r),o=1-a,s=e[0],l=e[1],c=e[2],u=e[3],f=e[4],h=e[5],p=e[6],d=e[7],m=e[8],g=e[9],v=e[10],y=e[11],x=EEo+a,b=LEo+Ci,_=CEo-Li,w=ELo-Ci,T=LLo+a,k=CLo+Ei,A=ECo+Li,M=LCo-Ei,S=CCo+a,t[0]=sx+fb+m*,t[1]=lx+hb+g*,t[2]=cx+pb+v*,t[3]=ux+db+y*,t[4]=sw+fT+mk,t[5]=lw+hT+gk,t[6]=cw+pT+vk,t[7]=uw+dT+yk,t[8]=sA+fM+mS,t[9]=lA+hM+gS,t[10]=cA+pM+vS,t[11]=uA+dM+yS,e!==t&&(t[12]=e[12],t[13]=e[13],t[14]=e[14],t[15]=e[15]);return 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t[0]=ai+cn,t[1]=oi+un,t[2]=si+fn,t[3]=li+hn,t[4]=ci-an,t[5]=ui-on,t[6]=fi-sn,t[7]=hi-ln,t}},{}],221:[function(t,e,r){e.exports=function(t,e,r){var n=r[0],i=r[1],a=r[2];return t[0]=e[0]*n,t[1]=e[1]*n,t[2]=e[2]*n,t[3]=e[3]*n,t[4]=e[4]*i,t[5]=e[5]*i,t[6]=e[6]*i,t[7]=e[7]*i,t[8]=e[8]*a,t[9]=e[9]*a,t[10]=e[10]a,t[11]=e[11]a,t[12]=e[12],t[13]=e[13],t[14]=e[14],t[15]=e[15],t}},{}],222:[function(t,e,r){e.exports=function(t){return"mat4("+t[0]+", "+t[1]+", "+t[2]+", "+t[3]+", "+t[4]+", "+t[5]+", "+t[6]+", "+t[7]+", "+t[8]+", "+t[9]+", "+t[10]+", "+t[11]+", "+t[12]+", "+t[13]+", "+t[14]+", "+t[15]+")"}},{}],223:[function(t,e,r){e.exports=function(t,e,r){var 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n=t("css-font"),i=t("pick-by-alias"),a=t("regl"),o=t("gl-util/context"),s=t("es6-weak-map"),l=t("color-normalize"),c=t("font-atlas"),u=t("typedarray-pool"),f=t("parse-rect"),h=t("is-plain-obj"),p=t("parse-unit"),d=t("to-px"),m=t("detect-kerning"),g=t("object-assign"),v=t("font-measure"),y=t("flatten-vertex-data"),x=t("bit-twiddle").nextPow2,b=new s,=!1;if(document.body){var w=document.body.appendChild(document.createElement("div"));w.style.font="italic small-caps bold condensed 16px/2 cursive",getComputedStyle(w).fontStretch&&(=!0),document.body.removeChild(w)}var T=function(t){!function(t){return"function"==typeof t&&t.gl&&t.prop&&t.texture&&t.buffer}(t)?this.gl=o(t):(t={regl:t},this.gl=t.regl.gl),this.shader=b.get(this.gl),this.shader?this.regl=this.shader.regl:this.regl=t.regl||a({gl:this.gl}),this.charBuffer=this.regl.buffer({type:"uint8",usage:"stream"}),this.sizeBuffer=this.regl.buffer({type:"float",usage:"stream"}),this.shader||(this.shader=this.createShader(),b.set(this.gl,this.shader)),this.batch=[],this.fontSize=[],this.font=[],this.fontAtlas=[],this.draw=this.shader.draw.bind(this),this.render=function(){this.regl.refresh(),this.draw(this.batch)},this.canvas=this.gl.canvas,this.update(h(t)?t:{})};T.prototype.createShader=function(){var t=this.regl,e=t({blend:{enable:!0,color:[0,0,0,1],func:{srcRGB:"src alpha",dstRGB:"one minus src alpha",srcAlpha:"one minus dst 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t.offset&&(t.offset=[t.offset,0]),this.positionOffset=y(t.offset)),t.direction&&(this.direction=t.direction),t.range&&(this.range=t.range,this.scale=[1/(t.range[2]-t.range[0]),1/(t.range[3]-t.range[1])],this.translate=[-t.range[0],-t.range[1]]),t.scale&&(this.scale=t.scale),t.translate&&(this.translate=t.translate),this.scale||(this.scale=[1/this.viewport.width,1/this.viewport.height]),this.translate||(this.translate=[0,0]),this.font.length||t.font||(t.font=T.baseFontSize+"px sans-serif");var r,a=!1,o=!1;if(t.font&&(Array.isArray(t.font)?t.font:[t.font]).forEach((function(t,r){if("string"==typeof t)try{t=n.parse(t)}catch(e){t=n.parse(T.baseFontSize+"px "+t)}else t=n.parse(n.stringify(t));var i=n.stringify({size:T.baseFontSize,family:t.family,stretch:?t.stretch:void 0,variant:t.variant,weight:t.weight,style:t.style}),s=p(t.size),l=Math.round(s[0]*d(s[1]));if(l!==e.fontSize[r]&&(o=!0,e.fontSize[r]=l),!(e.font[r]&&i==e.font[r].baseString||(a=!0,e.font[r]=T.fonts[i],e.font[r]))){var c=t.family.join(", "),u=[t.style];t.style!=t.variant&&u.push(t.variant),t.variant!=t.weight&&u.push(t.weight),&&t.weight!=t.stretch&&u.push(t.stretch),e.font[r]={baseString:i,family:c,weight:t.weight,stretch:t.stretch,style:t.style,variant:t.variant,width:{},kerning:{},metrics:v(c,{origin:"top",fontSize:T.baseFontSize,fontStyle:u.join(" ")})},T.fonts[i]=e.font[r]}})),(a||o)&&this.font.forEach((function(r,i){var a=n.stringify({size:e.fontSize[i],family:r.family,stretch:?r.stretch:void 0,variant:r.variant,weight:r.weight,style:r.style});if(e.fontAtlas[i]=e.shader.atlas[a],!e.fontAtlas[i]){var o=r.metrics;e.shader.atlas[a]=e.fontAtlas[i]={fontString:a,step:2Math.ceil(e.fontSize[i]o.bottom.5),em:e.fontSize[i],cols:0,rows:0,height:0,width:0,chars:[],ids:{},texture:e.regl.texture()}}null==t.text&&(t.text=e.text)})),"string"==typeof t.text&&t.position&&t.position.length>2){for(var s=Array(.5t.position.length),h=0;h<s.length;h++)s[h]=t.text;t.text=s}if(null!=t.text||a){if(this.textOffsets=[0],Array.isArray(t.text)){this.count=t.text[0].length,this.counts=[this.count];for(var b=1;b<t.text.length;b++)this.textOffsets[b]=this.textOffsets[b-1]+t.text[b-1].length,this.count+=t.text[b].length,this.counts.push(t.text[b].length);this.text=t.text.join("")}else this.text=t.text,