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- Introduced a comprehensive RNA velocity analysis pipeline using scVelo, including data loading, preprocessing, velocity estimation, and visualization. - Added a script for running RNA velocity analysis with customizable parameters and output options. - Created detailed documentation for IQ-TREE 2 phylogenetic inference, covering command syntax, model selection, bootstrapping methods, and output interpretation. - Included references for velocity models and their mathematical framework, along with a comparison of different models. - Enhanced the scVelo skill documentation with installation instructions, use cases, and best practices for RNA velocity analysis.
129 lines
4.3 KiB
Markdown
129 lines
4.3 KiB
Markdown
# cBioPortal Study Exploration Reference
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## Major Study Collections
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### TCGA (The Cancer Genome Atlas)
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| Study ID | Cancer Type | Samples |
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|----------|-------------|---------|
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| `brca_tcga` | Breast Cancer | ~1,000 |
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| `luad_tcga` | Lung Adenocarcinoma | ~500 |
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| `lusc_tcga` | Lung Squamous Cell Carcinoma | ~500 |
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| `coadread_tcga` | Colorectal Cancer | ~600 |
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| `gbm_tcga` | Glioblastoma | ~600 |
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| `prad_tcga` | Prostate Cancer | ~500 |
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| `skcm_tcga` | Skin Cutaneous Melanoma | ~450 |
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| `blca_tcga` | Bladder Urothelial Carcinoma | ~400 |
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| `hnsc_tcga` | Head and Neck Squamous | ~500 |
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| `lihc_tcga` | Liver Hepatocellular Carcinoma | ~370 |
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| `stad_tcga` | Stomach Adenocarcinoma | ~440 |
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| `ucec_tcga` | Uterine Endometrial Carcinoma | ~550 |
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| `ov_tcga` | Ovarian Serous Carcinoma | ~580 |
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| `kirc_tcga` | Kidney Renal Clear Cell Carcinoma | ~530 |
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| `thca_tcga` | Thyroid Cancer | ~500 |
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| `paad_tcga` | Pancreatic Adenocarcinoma | ~180 |
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| `laml_tcga` | Acute Myeloid Leukemia | ~200 |
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| `acc_tcga` | Adrenocortical Carcinoma | ~90 |
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### TCGA Pan-Cancer
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| Study ID | Description |
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|----------|-------------|
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| `tcga_pan_can_atlas_2018` | TCGA Pan-Cancer Atlas (32 cancer types, ~10K samples) |
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### MSK-IMPACT (Memorial Sloan Kettering)
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| Study ID | Description |
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|----------|-------------|
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| `msk_impact_2017` | MSK-IMPACT clinical sequencing |
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| `mskcc_pd` | MSK pediatric solid tumors |
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### AACR Project GENIE
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| Study ID | Description |
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|----------|-------------|
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| `genie_14_1_public` | GENIE v14.1 (multi-center clinical sequencing) |
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## Molecular Profile ID Naming Conventions
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Molecular profile IDs are structured as `{studyId}_{type}`:
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| Type Suffix | Alteration Type |
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|-------------|----------------|
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| `_mutations` | Somatic mutations (MAF) |
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| `_gistic` | Copy number (GISTIC discrete: -2, -1, 0, 1, 2) |
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| `_cna` | Copy number (continuous log2 ratio) |
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| `_mrna` | mRNA expression (z-scores or log2) |
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| `_rna_seq_v2_mrna` | RNA-seq (RSEM) |
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| `_rna_seq_v2_mrna_median_Zscores` | RNA-seq z-scores relative to normals |
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| `_rppa` | RPPA protein expression |
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| `_rppa_Zscores` | RPPA z-scores |
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| `_sv` | Structural variants/fusions |
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| `_methylation_hm450` | DNA methylation (450K array) |
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**Example:** For `brca_tcga`:
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- `brca_tcga_mutations` — mutation data
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- `brca_tcga_gistic` — CNA data
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- `brca_tcga_rna_seq_v2_mrna` — RNA-seq expression
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## Sample List Categories
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Each study has sample lists of different subsets:
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| Category | sampleListId Pattern | Contents |
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|----------|---------------------|----------|
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| `all_cases_in_study` | `{studyId}_all` | All samples |
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| `all_cases_with_mutation_data` | `{studyId}_sequenced` | Sequenced samples only |
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| `all_cases_with_cna_data` | `{studyId}_cna` | Samples with CNA data |
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| `all_cases_with_mrna_data` | `{studyId}_mrna` | Samples with expression |
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| `all_cases_with_rppa_data` | `{studyId}_rppa` | Samples with RPPA |
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| `all_complete_cases` | `{studyId}_complete` | Complete multiplatform data |
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## Common Gene Entrez IDs
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| Gene | Entrez ID | Role |
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|------|-----------|------|
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| TP53 | 7157 | Tumor suppressor |
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| PIK3CA | 5290 | Oncogene |
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| KRAS | 3845 | Oncogene |
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| BRCA1 | 672 | Tumor suppressor |
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| BRCA2 | 675 | Tumor suppressor |
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| PTEN | 5728 | Tumor suppressor |
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| EGFR | 1956 | Oncogene |
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| MYC | 4609 | Oncogene |
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| RB1 | 5925 | Tumor suppressor |
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| APC | 324 | Tumor suppressor |
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| CDKN2A | 1029 | Tumor suppressor |
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| IDH1 | 3417 | Oncogene (mutant) |
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| BRAF | 673 | Oncogene |
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| CDH1 | 999 | Tumor suppressor |
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| VHL | 7428 | Tumor suppressor |
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## Mutation Type Classifications
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| mutationType | Description |
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|-------------|-------------|
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| `Missense_Mutation` | Amino acid change |
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| `Nonsense_Mutation` | Premature stop codon |
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| `Frame_Shift_Del` | Frameshift deletion |
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| `Frame_Shift_Ins` | Frameshift insertion |
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| `Splice_Site` | Splice site mutation |
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| `In_Frame_Del` | In-frame deletion |
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| `In_Frame_Ins` | In-frame insertion |
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| `Translation_Start_Site` | Start codon mutation |
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| `Nonstop_Mutation` | Stop codon mutation |
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| `Silent` | Synonymous |
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| `5'Flank` | 5' flanking |
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| `3'UTR` | 3' UTR |
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## OncoPrint Color Legend
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cBioPortal uses consistent colors in OncoPrint:
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- **Red**: Amplification
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- **Blue (dark)**: Deep deletion
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- **Green**: Missense mutation
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- **Black**: Truncating mutation
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- **Purple**: Fusion
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- **Orange**: mRNA upregulation
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- **Teal**: mRNA downregulation
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