| {item.assay} |
- {pass1b06AssayTissueJson['transcriptomics'][item.id].map((tissue) => (
+ {pass1b06AssayTissueJson['metabolomics-targeted'][item.id].map((tissue) => (
{capitalize(tissue.split('-').slice(1).join('-').replace(/-/g, ' '))}
diff --git a/src/MainStudy/pass1b06AssayTissueTreeData.js b/src/MainStudy/pass1b06AssayTissueTreeData.js
index 438496cf..e48455c9 100644
--- a/src/MainStudy/pass1b06AssayTissueTreeData.js
+++ b/src/MainStudy/pass1b06AssayTissueTreeData.js
@@ -1,196 +1,215 @@
const pass1b06AssayTissueTreeData = [
- [undefined, 'Rats: Endurance Training'],
- ['Rats: Endurance Training', 'Transcriptomics'],
- ['Rats: Endurance Training', 'Untargeted Proteomics'],
- ['Rats: Endurance Training', 'Untargeted Metabolomics'],
- ['Rats: Endurance Training', 'Targeted Metabolomics'],
- ['Rats: Endurance Training', 'Epigenomics'],
- ['Epigenomics', 'RRBS'],
- ['Epigenomics', 'ATAC-seq'],
- ['Targeted Metabolomics', 'Targeted Tricarboxylic Acid Cycle'],
- ['Targeted Metabolomics', 'Targeted Oxylipins'],
- ['Targeted Metabolomics', 'Targeted Nucleotides'],
- ['Targeted Metabolomics', 'Targeted Keto Acids'],
- ['Targeted Metabolomics', 'Targeted Ethanolamides'],
- ['Targeted Metabolomics', 'Targeted Amines'],
- ['Targeted Metabolomics', 'Targeted Acyl-CoA'],
- ['Untargeted Metabolomics', 'Untargeted Reversed-Phase Positive'],
- ['Untargeted Metabolomics', 'Untargeted Reversed-Phase Negative'],
- ['Untargeted Metabolomics', 'Untargeted Lipidomics Reversed-Phase Positive'],
- ['Untargeted Metabolomics', 'Untargeted Lipidomics Reversed-Phase Negative'],
- ['Untargeted Metabolomics', 'Untargeted Ion-Pair Negative'],
- ['Untargeted Metabolomics', 'Untargeted HILIC-Positive'],
- ['Untargeted Proteomics', 'Protein Ubiquitination'],
- ['Untargeted Proteomics', 'Global Proteomics'],
- ['Untargeted Proteomics', 'Phosphoproteomics'],
- ['Untargeted Proteomics', 'Acetyl Proteomics'],
- ['Transcriptomics', 'RNA-seq'],
- ['ATAC-seq', 'White Adipose'],
- ['ATAC-seq', 'Brown Adipose'],
- ['ATAC-seq', 'Liver'],
- ['ATAC-seq', 'Lung'],
- ['ATAC-seq', 'Kidney'],
- ['ATAC-seq', 'Heart'],
- ['ATAC-seq', 'Gastrocnemius'],
- ['ATAC-seq', 'Hippocampus'],
- ['RRBS', 'White Adipose'],
- ['RRBS', 'Brown Adipose'],
- ['RRBS', 'Liver'],
- ['RRBS', 'Lung'],
- ['RRBS', 'Kidney'],
- ['RRBS', 'Heart'],
- ['RRBS', 'Gastrocnemius'],
- ['RRBS', 'Hippocampus'],
- ['Targeted Tricarboxylic Acid Cycle', 'White Adipose'],
- ['Targeted Tricarboxylic Acid Cycle', 'Brown Adipose'],
- ['Targeted Tricarboxylic Acid Cycle', 'Liver'],
- ['Targeted Tricarboxylic Acid Cycle', 'Lung'],
- ['Targeted Tricarboxylic Acid Cycle', 'Kidney'],
- ['Targeted Tricarboxylic Acid Cycle', 'Heart'],
- ['Targeted Tricarboxylic Acid Cycle', 'Gastrocnemius'],
- ['Targeted Tricarboxylic Acid Cycle', 'Hippocampus'],
- ['Targeted Tricarboxylic Acid Cycle', 'Plasma'],
- ['Targeted Oxylipins', 'White Adipose'],
- ['Targeted Oxylipins', 'Brown Adipose'],
- ['Targeted Oxylipins', 'Liver'],
- ['Targeted Oxylipins', 'Lung'],
- ['Targeted Oxylipins', 'Kidney'],
- ['Targeted Oxylipins', 'Heart'],
- ['Targeted Oxylipins', 'Gastrocnemius'],
- ['Targeted Oxylipins', 'Hippocampus'],
- ['Targeted Oxylipins', 'Plasma'],
- ['Targeted Nucleotides', 'White Adipose'],
- ['Targeted Nucleotides', 'Liver'],
- ['Targeted Nucleotides', 'Heart'],
- ['Targeted Nucleotides', 'Gastrocnemius'],
- ['Targeted Keto Acids', 'White Adipose'],
- ['Targeted Keto Acids', 'Liver'],
- ['Targeted Keto Acids', 'Heart'],
- ['Targeted Keto Acids', 'Gastrocnemius'],
- ['Targeted Keto Acids', 'Plasma'],
- ['Targeted Ethanolamides', 'White Adipose'],
- ['Targeted Ethanolamides', 'Brown Adipose'],
- ['Targeted Ethanolamides', 'Liver'],
- ['Targeted Ethanolamides', 'Lung'],
- ['Targeted Ethanolamides', 'Kidney'],
- ['Targeted Ethanolamides', 'Heart'],
- ['Targeted Ethanolamides', 'Gastrocnemius'],
- ['Targeted Ethanolamides', 'Hippocampus'],
- ['Targeted Ethanolamides', 'Plasma'],
- ['Targeted Amines', 'White Adipose'],
- ['Targeted Amines', 'Brown Adipose'],
- ['Targeted Amines', 'Liver'],
- ['Targeted Amines', 'Lung'],
- ['Targeted Amines', 'Kidney'],
- ['Targeted Amines', 'Heart'],
- ['Targeted Amines', 'Gastrocnemius'],
- ['Targeted Amines', 'Hippocampus'],
- ['Targeted Amines', 'Plasma'],
- ['Targeted Acyl-CoA', 'White Adipose'],
- ['Targeted Acyl-CoA', 'Liver'],
- ['Targeted Acyl-CoA', 'Heart'],
- ['Targeted Acyl-CoA', 'Gastrocnemius'],
- ['Untargeted Reversed-Phase Positive', 'White Adipose'],
- ['Untargeted Reversed-Phase Positive', 'Brown Adipose'],
- ['Untargeted Reversed-Phase Positive', 'Liver'],
- ['Untargeted Reversed-Phase Positive', 'Lung'],
- ['Untargeted Reversed-Phase Positive', 'Kidney'],
- ['Untargeted Reversed-Phase Positive', 'Heart'],
- ['Untargeted Reversed-Phase Positive', 'Gastrocnemius'],
- ['Untargeted Reversed-Phase Positive', 'Hippocampus'],
- ['Untargeted Reversed-Phase Positive', 'Plasma'],
- ['Untargeted Reversed-Phase Negative', 'White Adipose'],
- ['Untargeted Reversed-Phase Negative', 'Brown Adipose'],
- ['Untargeted Reversed-Phase Negative', 'Liver'],
- ['Untargeted Reversed-Phase Negative', 'Lung'],
- ['Untargeted Reversed-Phase Negative', 'Kidney'],
- ['Untargeted Reversed-Phase Negative', 'Heart'],
- ['Untargeted Reversed-Phase Negative', 'Gastrocnemius'],
- ['Untargeted Reversed-Phase Negative', 'Hippocampus'],
- ['Untargeted Reversed-Phase Negative', 'Plasma'],
- ['Untargeted Lipidomics Reversed-Phase Positive', 'White Adipose'],
- ['Untargeted Lipidomics Reversed-Phase Positive', 'Brown Adipose'],
- ['Untargeted Lipidomics Reversed-Phase Positive', 'Liver'],
- ['Untargeted Lipidomics Reversed-Phase Positive', 'Lung'],
- ['Untargeted Lipidomics Reversed-Phase Positive', 'Kidney'],
- ['Untargeted Lipidomics Reversed-Phase Positive', 'Heart'],
- ['Untargeted Lipidomics Reversed-Phase Positive', 'Gastrocnemius'],
- ['Untargeted Lipidomics Reversed-Phase Positive', 'Hippocampus'],
- ['Untargeted Lipidomics Reversed-Phase Positive', 'Plasma'],
- ['Untargeted Lipidomics Reversed-Phase Negative', 'White Adipose'],
- ['Untargeted Lipidomics Reversed-Phase Negative', 'Brown Adipose'],
- ['Untargeted Lipidomics Reversed-Phase Negative', 'Liver'],
- ['Untargeted Lipidomics Reversed-Phase Negative', 'Lung'],
- ['Untargeted Lipidomics Reversed-Phase Negative', 'Kidney'],
- ['Untargeted Lipidomics Reversed-Phase Negative', 'Heart'],
- ['Untargeted Lipidomics Reversed-Phase Negative', 'Gastrocnemius'],
- ['Untargeted Lipidomics Reversed-Phase Negative', 'Hippocampus'],
- ['Untargeted Lipidomics Reversed-Phase Negative', 'Plasma'],
- ['Untargeted Ion-Pair Negative', 'White Adipose'],
- ['Untargeted Ion-Pair Negative', 'Brown Adipose'],
- ['Untargeted Ion-Pair Negative', 'Liver'],
- ['Untargeted Ion-Pair Negative', 'Lung'],
- ['Untargeted Ion-Pair Negative', 'Kidney'],
- ['Untargeted Ion-Pair Negative', 'Heart'],
- ['Untargeted Ion-Pair Negative', 'Gastrocnemius'],
- ['Untargeted Ion-Pair Negative', 'Hippocampus'],
- ['Untargeted Ion-Pair Negative', 'Plasma'],
- ['Untargeted HILIC-Positive', 'Vena Cava'],
- ['Untargeted HILIC-Positive', 'White Adipose'],
- ['Untargeted HILIC-Positive', 'Brown Adipose'],
- ['Untargeted HILIC-Positive', 'Liver'],
- ['Untargeted HILIC-Positive', 'Small Intestine'],
- ['Untargeted HILIC-Positive', 'Lung'],
- ['Untargeted HILIC-Positive', 'Ovaries'],
- ['Untargeted HILIC-Positive', 'Testes'],
- ['Untargeted HILIC-Positive', 'Spleen'],
- ['Untargeted HILIC-Positive', 'Colon'],
- ['Untargeted HILIC-Positive', 'Adrenal'],
- ['Untargeted HILIC-Positive', 'Kidney'],
- ['Untargeted HILIC-Positive', 'Heart'],
- ['Untargeted HILIC-Positive', 'Vastus Lateralis'],
- ['Untargeted HILIC-Positive', 'Gastrocnemius'],
- ['Untargeted HILIC-Positive', 'Hypothalamus'],
- ['Untargeted HILIC-Positive', 'Cortex'],
- ['Untargeted HILIC-Positive', 'Hippocampus'],
- ['Untargeted HILIC-Positive', 'Plasma'],
- ['Protein Ubiquitination', 'Liver'],
- ['Protein Ubiquitination', 'Heart'],
- ['Global Proteomics', 'White Adipose'],
- ['Global Proteomics', 'Liver'],
- ['Global Proteomics', 'Lung'],
- ['Global Proteomics', 'Kidney'],
- ['Global Proteomics', 'Heart'],
- ['Global Proteomics', 'Gastrocnemius'],
- ['Global Proteomics', 'Cortex'],
- ['Phosphoproteomics', 'White Adipose'],
- ['Phosphoproteomics', 'Liver'],
- ['Phosphoproteomics', 'Lung'],
- ['Phosphoproteomics', 'Kidney'],
- ['Phosphoproteomics', 'Heart'],
- ['Phosphoproteomics', 'Gastrocnemius'],
- ['Phosphoproteomics', 'Cortex'],
- ['Acetyl Proteomics', 'Liver'],
- ['Acetyl Proteomics', 'Heart'],
- ['RNA-seq', 'Vena Cava'],
- ['RNA-seq', 'White Adipose'],
- ['RNA-seq', 'Brown Adipose'],
- ['RNA-seq', 'Liver'],
- ['RNA-seq', 'Small Intestine'],
- ['RNA-seq', 'Lung'],
- ['RNA-seq', 'Ovaries'],
- ['RNA-seq', 'Testes'],
- ['RNA-seq', 'Spleen'],
- ['RNA-seq', 'Colon'],
- ['RNA-seq', 'Adrenal'],
- ['RNA-seq', 'Kidney'],
- ['RNA-seq', 'Heart'],
- ['RNA-seq', 'Vastus Lateralis'],
- ['RNA-seq', 'Gastrocnemius'],
- ['RNA-seq', 'Hypothalamus'],
- ['RNA-seq', 'Cortex'],
- ['RNA-seq', 'Hippocampus'],
- ['RNA-seq', 'Blood Rna'],
+ { id: '0.0', parent: '', name: 'Rats: Endurance Training' },
+ { id: '1.0', parent: '0.0', name: 'Targeted Metabolomics', collapsed: true },
+ { id: '1.1', parent: '0.0', name: 'Untargeted Metabolomics', collapsed: true },
+ { id: '1.2', parent: '0.0', name: 'Untargeted Proteomics', collapsed: true },
+ { id: '1.3', parent: '0.0', name: 'Transcriptomics' },
+ { id: '1.4', parent: '0.0', name: 'Epigenomics', collapsed: true },
+ { id: '2.0', parent: '1.4', name: 'RRBS' },
+ { id: '2.1', parent: '1.4', name: 'ATAC-seq' },
+ { id: '2.2', parent: '1.0', name: 'Targeted Tricarboxylic Acid Cycle' },
+ { id: '2.3', parent: '1.0', name: 'Targeted Oxylipins' },
+ { id: '2.4', parent: '1.0', name: 'Targeted Nucleotides' },
+ { id: '2.5', parent: '1.0', name: 'Targeted Keto Acids' },
+ { id: '2.6', parent: '1.0', name: 'Targeted Ethanolamides' },
+ { id: '2.7', parent: '1.0', name: 'Targeted Amines' },
+ { id: '2.8', parent: '1.0', name: 'Targeted Acyl-CoA' },
+ { id: '2.9', parent: '1.1', name: 'Untargeted Reversed-Phase Positive' },
+ { id: '2.10', parent: '1.1', name: 'Untargeted Reversed-Phase Negative' },
+ { id: '2.11', parent: '1.1', name: 'Untargeted Lipidomics Reversed-Phase Positive' },
+ { id: '2.12', parent: '1.1', name: 'Untargeted Lipidomics Reversed-Phase Negative' },
+ { id: '2.13', parent: '1.1', name: 'Untargeted Ion-Pair Negative' },
+ { id: '2.14', parent: '1.1', name: 'Untargeted HILIC-Positive' },
+ { id: '2.15', parent: '1.2', name: 'Protein Ubiquitination' },
+ { id: '2.16', parent: '1.2', name: 'Global Proteomics' },
+ { id: '2.17', parent: '1.2', name: 'Phosphoproteomics' },
+ { id: '2.18', parent: '1.2', name: 'Acetyl Proteomics' },
+ { id: '2.19', parent: '1.3', name: 'RNA-seq' },
+ // RRBS tissues
+ { id: '3.0', parent: '2.0', name: 'White Adipose' },
+ { id: '3.1', parent: '2.0', name: 'Brown Adipose' },
+ { id: '3.2', parent: '2.0', name: 'Liver' },
+ { id: '3.3', parent: '2.0', name: 'Lung' },
+ { id: '3.4', parent: '2.0', name: 'Kidney' },
+ { id: '3.5', parent: '2.0', name: 'Heart' },
+ { id: '3.6', parent: '2.0', name: 'Gastrocnemius' },
+ { id: '3.7', parent: '2.0', name: 'Hippocampus' },
+ // ATAC-seq tissues
+ { id: '3.8', parent: '2.1', name: 'White Adipose' },
+ { id: '3.9', parent: '2.1', name: 'Brown Adipose' },
+ { id: '3.10', parent: '2.1', name: 'Liver' },
+ { id: '3.11', parent: '2.1', name: 'Lung' },
+ { id: '3.12', parent: '2.1', name: 'Kidney' },
+ { id: '3.13', parent: '2.1', name: 'Heart' },
+ { id: '3.14', parent: '2.1', name: 'Gastrocnemius' },
+ { id: '3.15', parent: '2.1', name: 'Hippocampus' },
+ // Targeted Tricarboxylic Acid Cycle tissues
+ { id: '3.16', parent: '2.2', name: 'White Adipose' },
+ { id: '3.17', parent: '2.2', name: 'Brown Adipose' },
+ { id: '3.18', parent: '2.2', name: 'Liver' },
+ { id: '3.19', parent: '2.2', name: 'Lung' },
+ { id: '3.20', parent: '2.2', name: 'Kidney' },
+ { id: '3.21', parent: '2.2', name: 'Heart' },
+ { id: '3.22', parent: '2.2', name: 'Gastrocnemius' },
+ { id: '3.23', parent: '2.2', name: 'Hippocampus' },
+ { id: '3.24', parent: '2.2', name: 'Plasma' },
+ // Targeted Oxylipins tissues
+ { id: '3.25', parent: '2.3', name: 'White Adipose' },
+ { id: '3.26', parent: '2.3', name: 'Brown Adipose' },
+ { id: '3.27', parent: '2.3', name: 'Liver' },
+ { id: '3.28', parent: '2.3', name: 'Lung' },
+ { id: '3.29', parent: '2.3', name: 'Kidney' },
+ { id: '3.30', parent: '2.3', name: 'Heart' },
+ { id: '3.31', parent: '2.3', name: 'Gastrocnemius' },
+ { id: '3.32', parent: '2.3', name: 'Hippocampus' },
+ { id: '3.33', parent: '2.3', name: 'Plasma' },
+ // Targeted Nucleotides tissues
+ { id: '3.34', parent: '2.4', name: 'White Adipose' },
+ { id: '3.35', parent: '2.4', name: 'Liver' },
+ { id: '3.36', parent: '2.4', name: 'Heart' },
+ { id: '3.37', parent: '2.4', name: 'Gastrocnemius' },
+ // Targeted Keto Acids tissues
+ { id: '3.38', parent: '2.5', name: 'White Adipose' },
+ { id: '3.39', parent: '2.5', name: 'Liver' },
+ { id: '3.40', parent: '2.5', name: 'Heart' },
+ { id: '3.41', parent: '2.5', name: 'Gastrocnemius' },
+ { id: '3.42', parent: '2.5', name: 'Plasma' },
+ // Targeted Ethanolamides tissues
+ { id: '3.43', parent: '2.6', name: 'White Adipose' },
+ { id: '3.44', parent: '2.6', name: 'Brown Adipose' },
+ { id: '3.45', parent: '2.6', name: 'Liver' },
+ { id: '3.46', parent: '2.6', name: 'Lung' },
+ { id: '3.47', parent: '2.6', name: 'Kidney' },
+ { id: '3.48', parent: '2.6', name: 'Heart' },
+ { id: '3.49', parent: '2.6', name: 'Gastrocnemius' },
+ { id: '3.50', parent: '2.6', name: 'Hippocampus' },
+ { id: '3.51', parent: '2.6', name: 'Plasma' },
+ // Targeted Amines tissues
+ { id: '3.52', parent: '2.7', name: 'White Adipose' },
+ { id: '3.53', parent: '2.7', name: 'Brown Adipose' },
+ { id: '3.54', parent: '2.7', name: 'Liver' },
+ { id: '3.55', parent: '2.7', name: 'Lung' },
+ { id: '3.56', parent: '2.7', name: 'Kidney' },
+ { id: '3.57', parent: '2.7', name: 'Heart' },
+ { id: '3.58', parent: '2.7', name: 'Gastrocnemius' },
+ { id: '3.59', parent: '2.7', name: 'Hippocampus' },
+ { id: '3.60', parent: '2.7', name: 'Plasma' },
+ // Targeted Acyl-CoA tissues
+ { id: '3.61', parent: '2.8', name: 'White Adipose' },
+ { id: '3.62', parent: '2.8', name: 'Liver' },
+ { id: '3.63', parent: '2.8', name: 'Heart' },
+ { id: '3.64', parent: '2.8', name: 'Gastrocnemius' },
+ // Untargeted Reversed-Phase Positive tissues
+ { id: '3.65', parent: '2.9', name: 'White Adipose' },
+ { id: '3.66', parent: '2.9', name: 'Brown Adipose' },
+ { id: '3.67', parent: '2.9', name: 'Liver' },
+ { id: '3.68', parent: '2.9', name: 'Lung' },
+ { id: '3.69', parent: '2.9', name: 'Kidney' },
+ { id: '3.70', parent: '2.9', name: 'Heart' },
+ { id: '3.71', parent: '2.9', name: 'Gastrocnemius' },
+ { id: '3.72', parent: '2.9', name: 'Hippocampus' },
+ { id: '3.73', parent: '2.9', name: 'Plasma' },
+ // Untargeted Reversed-Phase Negative tissues
+ { id: '3.74', parent: '2.10', name: 'White Adipose' },
+ { id: '3.75', parent: '2.10', name: 'Brown Adipose' },
+ { id: '3.76', parent: '2.10', name: 'Liver' },
+ { id: '3.77', parent: '2.10', name: 'Lung' },
+ { id: '3.78', parent: '2.10', name: 'Kidney' },
+ { id: '3.79', parent: '2.10', name: 'Heart' },
+ { id: '3.80', parent: '2.10', name: 'Gastrocnemius' },
+ { id: '3.81', parent: '2.10', name: 'Hippocampus' },
+ { id: '3.82', parent: '2.10', name: 'Plasma' },
+ // Untargeted Lipidomics Reversed-Phase Positive tissues
+ { id: '3.83', parent: '2.11', name: 'White Adipose' },
+ { id: '3.84', parent: '2.11', name: 'Brown Adipose' },
+ { id: '3.85', parent: '2.11', name: 'Liver' },
+ { id: '3.86', parent: '2.11', name: 'Lung' },
+ { id: '3.87', parent: '2.11', name: 'Kidney' },
+ { id: '3.88', parent: '2.11', name: 'Heart' },
+ { id: '3.89', parent: '2.11', name: 'Gastrocnemius' },
+ { id: '3.90', parent: '2.11', name: 'Hippocampus' },
+ { id: '3.91', parent: '2.11', name: 'Plasma' },
+ // Untargeted Lipidomics Reversed-Phase Negaive tissues
+ { id: '3.92', parent: '2.12', name: 'White Adipose' },
+ { id: '3.93', parent: '2.12', name: 'Brown Adipose' },
+ { id: '3.94', parent: '2.12', name: 'Liver' },
+ { id: '3.95', parent: '2.12', name: 'Lung' },
+ { id: '3.96', parent: '2.12', name: 'Kidney' },
+ { id: '3.97', parent: '2.12', name: 'Heart' },
+ { id: '3.98', parent: '2.12', name: 'Gastrocnemius' },
+ { id: '3.99', parent: '2.12', name: 'Hippocampus' },
+ { id: '4.00', parent: '2.12', name: 'Plasma' },
+ // Untargeted Ion-Pair Negative tissues
+ { id: '4.01', parent: '2.13', name: 'White Adipose' },
+ { id: '4.02', parent: '2.13', name: 'Brown Adipose' },
+ { id: '4.03', parent: '2.13', name: 'Liver' },
+ { id: '4.04', parent: '2.13', name: 'Lung' },
+ { id: '4.05', parent: '2.13', name: 'Kidney' },
+ { id: '4.06', parent: '2.13', name: 'Heart' },
+ { id: '4.07', parent: '2.13', name: 'Gastrocnemius' },
+ { id: '4.08', parent: '2.13', name: 'Hippocampus' },
+ { id: '4.09', parent: '2.13', name: 'Plasma' },
+ // Untargeted HILIC-Positive tissues
+ { id: '4.10', parent: '2.14', name: 'White Adipose' },
+ { id: '4.11', parent: '2.14', name: 'Brown Adipose' },
+ { id: '4.12', parent: '2.14', name: 'Liver' },
+ { id: '4.12', parent: '2.14', name: 'Small Intestine' },
+ { id: '4.14', parent: '2.14', name: 'Lung' },
+ { id: '4.15', parent: '2.14', name: 'Ovaries' },
+ { id: '4.16', parent: '2.14', name: 'Testes' },
+ { id: '4.17', parent: '2.14', name: 'Spleen' },
+ { id: '4.18', parent: '2.14', name: 'Colon' },
+ { id: '4.19', parent: '2.14', name: 'Adrenal' },
+ { id: '4.20', parent: '2.14', name: 'Kidney' },
+ { id: '4.21', parent: '2.14', name: 'Heart' },
+ { id: '4.22', parent: '2.14', name: 'Vastus Lateralis' },
+ { id: '4.23', parent: '2.14', name: 'Gastrocnemius' },
+ { id: '4.24', parent: '2.14', name: 'Hypothalamus' },
+ { id: '4.25', parent: '2.14', name: 'Cortex' },
+ { id: '4.26', parent: '2.14', name: 'Hippocampus' },
+ { id: '4.27', parent: '2.14', name: 'Plasma' },
+ // Protein Ubiquitination tissues
+ { id: '4.28', parent: '2.15', name: 'Liver' },
+ { id: '4.29', parent: '2.15', name: 'Heart' },
+ // Global Proteomics tissues
+ { id: '4.30', parent: '2.16', name: 'White Adipose' },
+ { id: '4.31', parent: '2.16', name: 'Liver' },
+ { id: '4.32', parent: '2.16', name: 'Lung' },
+ { id: '4.33', parent: '2.16', name: 'Kidney' },
+ { id: '4.34', parent: '2.16', name: 'Heart' },
+ { id: '4.35', parent: '2.16', name: 'Gastrocnemius' },
+ { id: '4.36', parent: '2.16', name: 'Cortex' },
+ // Phosphoproteomics tissues
+ { id: '4.37', parent: '2.17', name: 'White Adipose' },
+ { id: '4.38', parent: '2.17', name: 'Liver' },
+ { id: '4.39', parent: '2.17', name: 'Lung' },
+ { id: '4.41', parent: '2.17', name: 'Kidney' },
+ { id: '4.42', parent: '2.17', name: 'Heart' },
+ { id: '4.43', parent: '2.17', name: 'Gastrocnemius' },
+ { id: '4.44', parent: '2.17', name: 'Cortex' },
+ // Acetyl Proteomics tissues
+ { id: '4.45', parent: '2.18', name: 'Liver' },
+ { id: '4.46', parent: '2.18', name: 'Heart' },
+ // Untargeted HILIC-Positive tissues
+ { id: '4.47', parent: '2.19', name: 'Vena Cava' },
+ { id: '4.48', parent: '2.19', name: 'White Adipose' },
+ { id: '4.49', parent: '2.19', name: 'Brown Adipose' },
+ { id: '4.50', parent: '2.19', name: 'Liver' },
+ { id: '4.51', parent: '2.19', name: 'Small Intestine' },
+ { id: '4.52', parent: '2.19', name: 'Lung' },
+ { id: '4.53', parent: '2.19', name: 'Ovaries' },
+ { id: '4.54', parent: '2.19', name: 'Testes' },
+ { id: '4.55', parent: '2.19', name: 'Spleen' },
+ { id: '4.56', parent: '2.19', name: 'Colon' },
+ { id: '4.57', parent: '2.19', name: 'Adrenal' },
+ { id: '4.58', parent: '2.19', name: 'Kidney' },
+ { id: '4.59', parent: '2.19', name: 'Heart' },
+ { id: '4.60', parent: '2.19', name: 'Vastus Lateralis' },
+ { id: '4.61', parent: '2.19', name: 'Gastrocnemius' },
+ { id: '4.62', parent: '2.19', name: 'Hypothalamus' },
+ { id: '4.63', parent: '2.19', name: 'Cortex' },
+ { id: '4.64', parent: '2.19', name: 'Hippocampus' },
+ { id: '4.65', parent: '2.19', name: 'Blood Rna' },
];
export default pass1b06AssayTissueTreeData;
diff --git a/src/MainStudy/pass1b_06_assay_tissue.json b/src/MainStudy/pass1b_06_assay_tissue.json
index 1bde6e57..41d5e432 100644
--- a/src/MainStudy/pass1b_06_assay_tissue.json
+++ b/src/MainStudy/pass1b_06_assay_tissue.json
@@ -21,69 +21,55 @@
"t70-white-adipose"
]
},
- "metabolomics-targeted": {
- "metab-t-acoa": [
- "t55-gastrocnemius",
- "t58-heart",
- "t68-liver",
- "t70-white-adipose"
- ],
- "metab-t-amines": [
- "t31-plasma",
+ "transcriptomics": {
+ "transcript-rna-seq": [
+ "t30-blood-rna",
"t52-hippocampus",
+ "t53-cortex",
+ "t54-hypothalamus",
"t55-gastrocnemius",
+ "t56-vastus-lateralis",
"t58-heart",
"t59-kidney",
+ "t60-adrenal",
+ "t61-colon",
+ "t62-spleen",
+ "t63-testes",
+ "t64-ovaries",
"t66-lung",
+ "t67-small-intestine",
"t68-liver",
"t69-brown-adipose",
- "t70-white-adipose"
+ "t70-white-adipose",
+ "t99-vena-cava"
+ ]
+ },
+ "proteomics-untargeted": {
+ "prot-ac": [
+ "t58-heart",
+ "t68-liver"
],
- "metab-t-etamidpos": [
- "t31-plasma",
- "t52-hippocampus",
+ "prot-ph": [
+ "t53-cortex",
"t55-gastrocnemius",
"t58-heart",
"t59-kidney",
"t66-lung",
"t68-liver",
- "t69-brown-adipose",
- "t70-white-adipose"
- ],
- "metab-t-ka": [
- "t31-plasma",
- "t55-gastrocnemius",
- "t58-heart",
- "t68-liver",
- "t70-white-adipose"
- ],
- "metab-t-nuc": [
- "t55-gastrocnemius",
- "t58-heart",
- "t68-liver",
"t70-white-adipose"
],
- "metab-t-oxylipneg": [
- "t31-plasma",
- "t52-hippocampus",
+ "prot-pr": [
+ "t53-cortex",
"t55-gastrocnemius",
"t58-heart",
"t59-kidney",
"t66-lung",
"t68-liver",
- "t69-brown-adipose",
"t70-white-adipose"
],
- "metab-t-tca": [
- "t31-plasma",
- "t52-hippocampus",
- "t55-gastrocnemius",
+ "prot-ub": [
"t58-heart",
- "t59-kidney",
- "t66-lung",
- "t68-liver",
- "t69-brown-adipose",
- "t70-white-adipose"
+ "t68-liver"
]
},
"metabolomics-untargeted": {
@@ -164,55 +150,69 @@
"t70-white-adipose"
]
},
- "proteomics-untargeted": {
- "prot-ac": [
+ "metabolomics-targeted": {
+ "metab-t-acoa": [
+ "t55-gastrocnemius",
"t58-heart",
- "t68-liver"
+ "t68-liver",
+ "t70-white-adipose"
],
- "prot-ph": [
- "t53-cortex",
+ "metab-t-amines": [
+ "t31-plasma",
+ "t52-hippocampus",
"t55-gastrocnemius",
"t58-heart",
"t59-kidney",
"t66-lung",
"t68-liver",
+ "t69-brown-adipose",
"t70-white-adipose"
],
- "prot-pr": [
- "t53-cortex",
+ "metab-t-etamidpos": [
+ "t31-plasma",
+ "t52-hippocampus",
"t55-gastrocnemius",
"t58-heart",
"t59-kidney",
"t66-lung",
"t68-liver",
+ "t69-brown-adipose",
"t70-white-adipose"
],
- "prot-ub": [
+ "metab-t-ka": [
+ "t31-plasma",
+ "t55-gastrocnemius",
"t58-heart",
- "t68-liver"
- ]
- },
- "transcriptomics": {
- "transcript-rna-seq": [
- "t30-blood-rna",
+ "t68-liver",
+ "t70-white-adipose"
+ ],
+ "metab-t-nuc": [
+ "t55-gastrocnemius",
+ "t58-heart",
+ "t68-liver",
+ "t70-white-adipose"
+ ],
+ "metab-t-oxylipneg": [
+ "t31-plasma",
"t52-hippocampus",
- "t53-cortex",
- "t54-hypothalamus",
"t55-gastrocnemius",
- "t56-vastus-lateralis",
"t58-heart",
"t59-kidney",
- "t60-adrenal",
- "t61-colon",
- "t62-spleen",
- "t63-testes",
- "t64-ovaries",
"t66-lung",
- "t67-small-intestine",
"t68-liver",
"t69-brown-adipose",
- "t70-white-adipose",
- "t99-vena-cava"
+ "t70-white-adipose"
+ ],
+ "metab-t-tca": [
+ "t31-plasma",
+ "t52-hippocampus",
+ "t55-gastrocnemius",
+ "t58-heart",
+ "t59-kidney",
+ "t66-lung",
+ "t68-liver",
+ "t69-brown-adipose",
+ "t70-white-adipose"
]
}
}
diff --git a/src/MainStudy/studyAssays.jsx b/src/MainStudy/studyAssays.jsx
index 9c738539..a903f185 100644
--- a/src/MainStudy/studyAssays.jsx
+++ b/src/MainStudy/studyAssays.jsx
@@ -22,7 +22,6 @@ function StudyAssays() {
chart: {
spacingBottom: 30,
marginRight: 120,
- height: 2600,
},
title: {
align: 'center',
@@ -48,7 +47,7 @@ function StudyAssays() {
},
dataLabels: {
align: 'left',
- pointFormat: '{point.id}',
+ pointFormat: '{point.name}',
style: {
color: '#000000',
textOutline: '3px #ffffff',
@@ -115,7 +114,7 @@ function StudyAssays() {
-
+ pest_control_rodent diff --git a/src/Navbar/navbar.jsx b/src/Navbar/navbar.jsx index 2c1ca35e..5b383fa7 100644 --- a/src/Navbar/navbar.jsx +++ b/src/Navbar/navbar.jsx @@ -273,7 +273,7 @@ export function Navbar({ Limited Acute Exercise Data - Data Deposition + Public Data Repositories {!userType || (userType && userType !== 'internal') ? ( OmicsPipelines + + Community +
+
+ );
+}
+
+export default Phenotype;
diff --git a/src/assets/figures/vial_label_data_linkage_example.svg b/src/assets/figures/vial_label_data_linkage_example.svg
new file mode 100644
index 00000000..66e52345
--- /dev/null
+++ b/src/assets/figures/vial_label_data_linkage_example.svg
@@ -0,0 +1,189 @@
+
+
\ No newline at end of file
diff --git a/src/sass/_technicalGuides.scss b/src/sass/_technicalGuides.scss
new file mode 100644
index 00000000..1505f5c7
--- /dev/null
+++ b/src/sass/_technicalGuides.scss
@@ -0,0 +1,21 @@
+.technicalGuidesPage {
+ &.phenotype {
+ .technical-guide-content-container {
+ h3 {
+ background: -webkit-linear-gradient(45deg, #a64d79, #1c4587);
+ -webkit-background-clip: text;
+ -webkit-text-fill-color: transparent;
+
+ .study-title-species-icon {
+ font-size: 1.85rem;
+ }
+ }
+
+ table {
+ td:first-child {
+ width: 35%;
+ }
+ }
+ }
+ }
+}
\ No newline at end of file
diff --git a/src/sass/main.scss b/src/sass/main.scss
index 1c7680b5..508105ef 100644
--- a/src/sass/main.scss
+++ b/src/sass/main.scss
@@ -41,3 +41,4 @@
@import 'reactLiteYoutubeEmbed';
@import 'license';
@import 'dataDeposition';
+@import 'technicalGuides';
diff --git a/src/sass/mainStudy/_mainStudyPage.scss b/src/sass/mainStudy/_mainStudyPage.scss
index 68a11926..a391fb6a 100644
--- a/src/sass/mainStudy/_mainStudyPage.scss
+++ b/src/sass/mainStudy/_mainStudyPage.scss
@@ -106,6 +106,10 @@
padding: 0.3rem 0.65rem;
}
}
+
+ .assay-tissue-treegraph-container {
+ min-height: 70vh;
+ }
}
}
+
+
+
+ + pest_control_rodent + Endurance trained young adult rats study ++Summary++ This dataset is a complete collection of measured phenotypic variables, gathered + for a study on Endurance Training in 6-month-old rats. Specifically, male and + female Fischer 344 rats were subjected to progressive treadmill endurance + exercise training for 1, 2, 4, or 8 weeks, with tissues collected 48 hours after + the last exercise bout. Sex-matched sedentary, untrained rats were used as + controls. Whole blood, plasma, and 18 solid tissues were analyzed using + epigenomics, transcriptomics, proteomics, metabolomics, and protein immunoassay + technologies, with most assays performed in a subset of these tissues. Depending + on the assay, between 3 and 6 replicates per sex per time point were + analyzed. Although this phenotypic dataset includes 147 animals, a subset of 60 + animals was selected for the molecular assays. + +Files Overview+
+
+ |
| Variable | +Description | +
|---|---|
| viallabel | ++ Vial Label ID. A unique code given to each sample vial. This ID is + found in all related results and metadata files, serving as a key + to match the quantitative results with the phenotypic data. + | +
| pid | ++ Participant Identifier. Uniquely assigned to each animal subject + (rats in this study). Samples (“viallabel”) coming from the same animal + have the same PID. It is relevant when combining results from multiple + assays and phenotype data. + | +
| registration___sex | ++ Sex of the animal. 1 = Female, 2 = Male + | +
| study_group_timepoint | ++ It combines the intervention and sacrifice time codes into a specific + format: [study group (training|control] - [time point (1w|2w|4w|8w weeks)]. + | +
| specimen_processing___sampletypedescription | ++ Tissue name from which the sample was derived. + | +
+
+ description
+ motrpac_pass1b-06_pheno_dictionary_merged_v4.0.txt
+
+
+ + This data dictionary defines the scope and possible values of data fields present + in the phenotypic data tables. It is intended to ensure that the phenotypic data + tables are easily interpretable and usable for analysis. +
++ Key variables include: +
+
+
+
+
+
+ | Variable | +Description | +
|---|---|
| form_name | ++ Groups related variables by the Case Report Form the variable originated from. + | +
| field_name | ++ Name of specific data field. + | +
| calculated_or_created_(1=True) | ++ Flag indicating whether the field is calculated. + | +
| field_description | ++ Description of what the field represents. + | +
| data_type | +
+ Data type of the field (e.g.
+ {' '}
+ int
+ ,
+ {' '}
+ varchar
+ ,
+ {' '}
+ datetime
+ ).
+ |
+
| categorical_values | ++ Accepted values for categorical variables. + | +
| categorical_definitions | ++ Definitions of categorical values. + | +
| continuous_range_min | ++ Minimum value for continuous variables if applicable. + | +
| continuous_range_max | ++ Maximum value for continuous variables if applicable. + | +
Data Quality Notes
++ Samples from weeks 1 and 2 originating from Vena Cava tissue were excluded + from downstream molecular analysis due to contamination issues. However, + phenotypic data for these samples remains accessible. +
+Example data linkage via vial labels and pids
+
+ 
+
+