Gene Comparison
Explore differential RNA and protein expression results for 20k+
- genes. Build custom result sets by sorting, filtering, and
+ human genes. Build custom result sets by sorting, filtering, and
searching for genes of particular interest.
@@ -266,7 +267,7 @@ Gene Comparison
Gene Search
- Find one of 20K+ genes in the Agora database and get detailed
+ Search for genes in the Agora database to get detailed
information about Experimental Evidence, Nominations, and
Association with Alzheimer's Disease.
@@ -279,7 +280,7 @@
Gene Search
Nominated Targets
Browse genes that research teams have nominated as potential new
- targets for Alzheimer's Disease treatment or prevention.
+ therapeutic targets for Alzheimer's Disease treatment or prevention.
diff --git a/src/app/features/genes/components/gene-evidence-proteomics/gene-evidence-proteomics.component.spec.ts b/src/app/features/genes/components/gene-evidence-proteomics/gene-evidence-proteomics.component.spec.ts
index 6391565b2..29d8f2526 100644
--- a/src/app/features/genes/components/gene-evidence-proteomics/gene-evidence-proteomics.component.spec.ts
+++ b/src/app/features/genes/components/gene-evidence-proteomics/gene-evidence-proteomics.component.spec.ts
@@ -36,4 +36,24 @@ describe('Component: Gene Proteomics', () => {
it('should create', () => {
expect(component).toBeTruthy();
});
+
+ it('should create the right tooltip text', () => {
+ const item =
+ {
+ '_id': '65a5f61467fa5462e23fe5eb',
+ 'uniqid': 'PLEC|Q15149',
+ 'hgnc_symbol': 'PLEC',
+ 'uniprotid': 'Q15149',
+ 'ensembl_gene_id': 'ENSG00000178209',
+ 'tissue': 'DLPFC',
+ 'log2_fc': 0.111785229513828,
+ 'ci_upr': 0.147173483154117,
+ 'ci_lwr': 0.0763969758735386,
+ 'pval': 4.54382282575789e-9,
+ 'cor_pval': 0.00000174186460237858
+ };
+ const tooltipText = component.getTooltipText(item);
+ const expected = 'PLEC is significantly differentially expressed in DLPFC with a log fold change value of 0.112 and an adjusted p-value of 0.00000174.';
+ expect(tooltipText).toBe(expected);
+ });
});
diff --git a/src/app/features/genes/components/gene-evidence-proteomics/gene-evidence-proteomics.component.ts b/src/app/features/genes/components/gene-evidence-proteomics/gene-evidence-proteomics.component.ts
index 72a619af8..b4e08f3bd 100644
--- a/src/app/features/genes/components/gene-evidence-proteomics/gene-evidence-proteomics.component.ts
+++ b/src/app/features/genes/components/gene-evidence-proteomics/gene-evidence-proteomics.component.ts
@@ -84,6 +84,32 @@ export class GeneEvidenceProteomicsComponent {
this.initTMT();
}
+ processDifferentialExpressionData(item: any, data: any, dataYAxisMin: number | undefined, dataYAxisMax: number | undefined, proteomicData: any) {
+ const yAxisMin = item.log2_fc < data.min ? item.log2_fc : data.min;
+ const yAxisMax = item.log2_fc > data.max ? item.log2_fc : data.max;
+
+ if (dataYAxisMin === undefined || yAxisMin < dataYAxisMin) {
+ dataYAxisMin = yAxisMin;
+ }
+
+ if (dataYAxisMax == undefined || yAxisMax > dataYAxisMax) {
+ dataYAxisMax = yAxisMax;
+ }
+
+ proteomicData.push({
+ key: data.tissue,
+ value: [data.min, data.median, data.max],
+ circle: {
+ value: item.log2_fc,
+ tooltip: this.getTooltipText(item)
+ },
+ quartiles:
+ data.first_quartile > data.third_quartile
+ ? [data.third_quartile, data.median, data.first_quartile]
+ : [data.first_quartile, data.median, data.third_quartile],
+ });
+ }
+
initSRM() {
this.geneService.getDistribution().subscribe((data: any) => {
const distribution = data.proteomics_SRM;
@@ -93,7 +119,7 @@ export class GeneEvidenceProteomicsComponent {
return item.uniprotid === this.selectedUniProtId;
}) || [];
- const SRMData: any = [];
+ const proteomicData: any = [];
differentialExpression.forEach((item: any) => {
const data: any = distribution.find((d: any) => {
@@ -101,39 +127,7 @@ export class GeneEvidenceProteomicsComponent {
});
if (data) {
- const yAxisMin = item.log2_fc < data.min ? item.log2_fc : data.min;
- const yAxisMax = item.log2_fc > data.max ? item.log2_fc : data.max;
-
- if (this.SRMYAxisMin == undefined || yAxisMin < this.SRMYAxisMin) {
- this.SRMYAxisMin = yAxisMin;
- }
-
- if (this.SRMYAxisMax == undefined || yAxisMax > this.SRMYAxisMax) {
- this.SRMYAxisMax = yAxisMax;
- }
-
- SRMData.push({
- key: data.tissue,
- value: [data.min, data.median, data.max],
- circle: {
- value: item.log2_fc,
- tooltip:
- (item.hgnc_symbol || item.ensembl_gene_id) +
- ' is ' +
- (item.cor_pval <= 0.05 ? ' ' : 'not ') +
- 'significantly differentially expressed in ' +
- item.tissue +
- ' with a log fold change value of ' +
- this.helperService.getSignificantFigures(item.log2_fc, 3) +
- ' and an adjusted p-value of ' +
- this.helperService.getSignificantFigures(item.cor_pval, 3) +
- '.',
- },
- quartiles:
- data.first_quartile > data.third_quartile
- ? [data.third_quartile, data.median, data.first_quartile]
- : [data.first_quartile, data.median, data.third_quartile],
- });
+ this.processDifferentialExpressionData(item, data, this.SRMYAxisMin, this.SRMYAxisMax, proteomicData);
}
});
@@ -145,7 +139,7 @@ export class GeneEvidenceProteomicsComponent {
this.SRMYAxisMax += 0.2;
}
- this.SRMData = SRMData;
+ this.SRMData = proteomicData;
});
}
@@ -158,7 +152,7 @@ export class GeneEvidenceProteomicsComponent {
return item.uniprotid === this.selectedUniProtId;
}) || [];
- const LFQData: any = [];
+ const proteomicData: any = [];
differentialExpression.forEach((item: any) => {
const data: any = distribution.find((d: any) => {
@@ -166,39 +160,7 @@ export class GeneEvidenceProteomicsComponent {
});
if (data) {
- const yAxisMin = item.log2_fc < data.min ? item.log2_fc : data.min;
- const yAxisMax = item.log2_fc > data.max ? item.log2_fc : data.max;
-
- if (this.LFQYAxisMin == undefined || yAxisMin < this.LFQYAxisMin) {
- this.LFQYAxisMin = yAxisMin;
- }
-
- if (this.LFQYAxisMax == undefined || yAxisMax > this.LFQYAxisMax) {
- this.LFQYAxisMax = yAxisMax;
- }
-
- LFQData.push({
- key: data.tissue,
- value: [data.min, data.median, data.max],
- circle: {
- value: item.log2_fc,
- tooltip:
- (item.hgnc_symbol || item.ensembl_gene_id) +
- ' is ' +
- (item.cor_pval <= 0.05 ? ' ' : 'not ') +
- 'significantly differentially expressed in ' +
- item.tissue +
- ' with a log fold change value of ' +
- this.helperService.getSignificantFigures(item.log2_fc, 3) +
- ' and an adjusted p-value of ' +
- this.helperService.getSignificantFigures(item.cor_pval, 3) +
- '.',
- },
- quartiles:
- data.first_quartile > data.third_quartile
- ? [data.third_quartile, data.median, data.first_quartile]
- : [data.first_quartile, data.median, data.third_quartile],
- });
+ this.processDifferentialExpressionData(item, data, this.LFQYAxisMin, this.LFQYAxisMax, proteomicData);
}
});
@@ -210,7 +172,7 @@ export class GeneEvidenceProteomicsComponent {
this.LFQYAxisMax += 0.2;
}
- this.LFQData = LFQData;
+ this.LFQData = proteomicData;
});
}
@@ -223,7 +185,7 @@ export class GeneEvidenceProteomicsComponent {
return item.uniprotid === this.selectedUniProtId;
}) || [];
- const TMTData: any = [];
+ const proteomicData: any = [];
differentialExpression.forEach((item: any) => {
const data: any = distribution.find((d: any) => {
@@ -231,39 +193,7 @@ export class GeneEvidenceProteomicsComponent {
});
if (data) {
- const yAxisMin = item.log2_fc < data.min ? item.log2_fc : data.min;
- const yAxisMax = item.log2_fc > data.max ? item.log2_fc : data.max;
-
- if (this.TMTYAxisMin == undefined || yAxisMin < this.TMTYAxisMin) {
- this.TMTYAxisMin = yAxisMin;
- }
-
- if (this.TMTYAxisMax == undefined || yAxisMax > this.TMTYAxisMax) {
- this.TMTYAxisMax = yAxisMax;
- }
-
- TMTData.push({
- key: data.tissue,
- value: [data.min, data.median, data.max],
- circle: {
- value: item.log2_fc,
- tooltip:
- (item.hgnc_symbol || item.ensembl_gene_id) +
- ' is ' +
- (item.cor_pval <= 0.05 ? ' ' : 'not ') +
- 'significantly differentially expressed in ' +
- item.tissue +
- ' with a log fold change value of ' +
- this.helperService.getSignificantFigures(item.log2_fc, 3) +
- ' and an adjusted p-value of ' +
- this.helperService.getSignificantFigures(item.cor_pval, 3) +
- '.',
- },
- quartiles:
- data.first_quartile > data.third_quartile
- ? [data.third_quartile, data.median, data.first_quartile]
- : [data.first_quartile, data.median, data.third_quartile],
- });
+ this.processDifferentialExpressionData(item, data, this.TMTYAxisMin, this.TMTYAxisMax, proteomicData);
}
});
@@ -275,7 +205,7 @@ export class GeneEvidenceProteomicsComponent {
this.TMTYAxisMax += 0.2;
}
- this.TMTData = TMTData;
+ this.TMTData = proteomicData;
});
}
@@ -287,4 +217,9 @@ export class GeneEvidenceProteomicsComponent {
this.initLFQ();
this.initTMT();
}
+
+ getTooltipText(item: any) {
+ const tooltipText = `${ item.hgnc_symbol || item.ensembl_gene_id } is${ item.cor_pval <= 0.05 ? '' : ' not' } significantly differentially expressed in ${ item.tissue } with a log fold change value of ${ this.helperService.getSignificantFigures(item.log2_fc, 3) } and an adjusted p-value of ${ this.helperService.getSignificantFigures(item.cor_pval, 3) }.`;
+ return tooltipText;
+ }
}