Data Analysis
The GDC DAVE tools use the same API as the rest of the Data Portal and takes advantage of several new endpoints. Similar to the GDC Data Portal Exploration feature, the GDC data analysis endpoints allow API users to programmatically explore data in the GDC using advanced filters at a gene and mutation level. Survival analysis data is also available.
Endpoints
The following data analysis endpoints are available from the GDC API:
| Endpoint | Description |
|---|---|
| /genes | Allows users to access summary information about each gene using its Ensembl ID. |
| /ssms | Allows users to access information about each somatic mutation. For example, a ssm would represent the transition of C to T at position 52000 of chromosome 1. |
| /ssm_occurrences | A ssm entity as applied to a single instance (case). An example of a ssm occurrence would be that the transition of C to T at position 52000 of chromosome 1 occurred in patient TCGA-XX-XXXX. |
| /analysis/top_cases_counts_by_genes | Returns the number of cases with a mutation in each gene listed in the gene_ids parameter for each project. Note that this endpoint cannot be used with the format or fields parameters. |
| /analysis/top_mutated_genes_by_project | Returns a list of genes that have the most mutations within a given project. |
| /analysis/top_mutated_cases_by_gene | Generates information about the cases that are most affected by mutations in a given number of genes |
| /analysis/mutated_cases_count_by_project | Returns counts for the number of cases that have associated ssm data in each project. The number of affected cases can be found under "case_with_ssm": {"doc_count": $case_count}. |
| /analysis/survival | Survival plots can be generated in the Data Portal for different subsets of data, based upon many query factors such as variants, disease type and projects. This endpoint can be used to programmatically retrieve the raw data to generate these plots and apply different filters to the data. (see Survival Example) |
The methods for retrieving information from these endpoints are very similar to those used for the cases and files endpoints. These methods are explored in depth in the API Search and Retrieval documentation. The _mapping parameter can also be used with each of these endpoints to generate a list of potential fields. For example:
https://api.gdc.cancer.gov/ssms/_mapping
Note: While it is not an endpoint, the observation entity is featured in the visualization section of the API. The observation entity provides information from the MAF file, such as read depth and normal genotype, that supports the validity of the associated ssm. An example is demonstrated below:
curl "https://api.gdc.cancer.gov/ssms/57bb3f2e-ec05-52c2-ab02-7065b7d24849?expand=occurrence.case.observation.read_depth&pretty=true"
{
"data": {
"ncbi_build": "GRCh38",
"occurrence": [
{
"case": {
"observation": [
{
"read_depth": {
"t_ref_count": 321,
"t_alt_count": 14,
"t_depth": 335,
"n_depth": 115
}
}
]
}
}
],
"tumor_allele": "G",
"mutation_type": "Simple Somatic Mutation",
"end_position": 14304578,
"reference_allele": "C",
"ssm_id": "57bb3f2e-ec05-52c2-ab02-7065b7d24849",
"start_position": 14304578,
"mutation_subtype": "Single base substitution",
"cosmic_id": null,
"genomic_dna_change": "chr5:g.14304578C>G",
"gene_aa_change": [
"TRIO L229V",
"TRIO L437V",
"TRIO L447V",
"TRIO L496V"
],
"chromosome": "chr5"
},
"warnings": {}
}
Genes Endpoint Examples
Example 1: A user would like to access information about the gene ZMPSTE24, which has an Ensembl gene ID of ENSG00000084073. This would be accomplished by appending ENSG00000084073 (gene_id) to the genes endpoint.
curl "https://api.gdc.cancer.gov/genes/ENSG00000084073?pretty=true"
{
"data": {
"canonical_transcript_length": 3108,
"description": "This gene encodes a member of the peptidase M48A family. The encoded protein is a zinc metalloproteinase involved in the two step post-translational proteolytic cleavage of carboxy terminal residues of farnesylated prelamin A to form mature lamin A. Mutations in this gene have been associated with mandibuloacral dysplasia and restrictive dermopathy. [provided by RefSeq, Jul 2008]",
"cytoband": [
"1p34.2"
],
"gene_start": 40258107,
"canonical_transcript_length_genomic": 36078,
"gene_id": "ENSG00000084073",
"gene_strand": 1,
"canonical_transcript_length_cds": 1425,
"gene_chromosome": "1",
"synonyms": [
"FACE-1",
"HGPS",
"PRO1",
"STE24",
"Ste24p"
],
"is_cancer_gene_census": null,
"biotype": "protein_coding",
"gene_end": 40294184,
"canonical_transcript_id": "ENST00000372759",
"symbol": "ZMPSTE24",
"name": "zinc metallopeptidase STE24"
},
"warnings": {}
}
curl "https://api.gdc.cancer.gov/genes?pretty=true&fields=gene_id,symbol,gene_start,gene_end&format=tsv&size=2000&filters=%7B%0D%0A%22op%22%3A%22in%22%2C%0D%0A%22content%22%3A%7B%0D%0A%22field%22%3A%22gene_chromosome%22%2C%0D%0A%22value%22%3A%5B%0D%0A%227%22%0D%0A%5D%0D%0A%7D%0D%0A%7D"
gene_start gene_end symbol id
28995231 29195451 CPVL ENSG00000106066
33014114 33062797 NT5C3A ENSG00000122643
143052320 143053347 OR6V1 ENSG00000225781
100400826 100428992 ZCWPW1 ENSG00000078487
73861159 73865893 WBSCR28 ENSG00000175877
64862999 64864370 EEF1DP4 ENSG00000213640
159231435 159233377 PIP5K1P2 ENSG00000229435
141972631 141973773 TAS2R38 ENSG00000257138
16646131 16706523 BZW2 ENSG00000136261
149239651 149255609 ZNF212 ENSG00000170260
57405025 57405090 MIR3147 ENSG00000266168
130393771 130442433 CEP41 ENSG00000106477
150800403 150805120 TMEM176A ENSG00000002933
93591573 93911265 GNGT1 ENSG00000127928
117465784 117715971 CFTR ENSG00000001626
5879827 5886362 OCM ENSG00000122543
144118461 144119360 OR2A15P ENSG00000239981
30424527 30478784 NOD1 ENSG00000106100
137227341 137343865 PTN ENSG00000105894
84876554 84876956 HMGN2P11 ENSG00000232605
107470018 107475659 GPR22 ENSG00000172209
31330711 31330896 RP11-463M14.1 ENSG00000271027
78017057 79453574 MAGI2 ENSG00000187391
55736779 55739605 CICP11 ENSG00000237799
142111749 142222324 RP11-1220K2.2 ENSG00000257743
(truncated)
Simple Somatic Mutation Endpoint Examples
Example 1: Similar to the /genes endpoint, a user would like to retrieve information about the mutation based on its COSMIC ID. This would be accomplished by creating a JSON filter such as:
{
"op":"in",
"content":{
"field":"cosmic_id",
"value":[
"COSM4860838"
]
}
}
curl 'https://api.gdc.cancer.gov/ssms?pretty=true&filters=%7B%0A%22op%22%3A%22in%22%2C%0A%22content%22%3A%7B%0A%22field%22%3A%22cosmic_id%22%2C%0A%22value%22%3A%5B%0A%22COSM4860838%22%0A%5D%0A%7D%0A%7D%0A'
{
"data": {
"hits": [
{
"ncbi_build": "GRCh38",
"mutation_type": "Simple Somatic Mutation",
"mutation_subtype": "Single base substitution",
"end_position": 62438203,
"reference_allele": "C",
"ssm_id": "8b3c1a7a-e4e0-5200-9d46-5767c2982145",
"start_position": 62438203,
"cosmic_id": [
"COSM4860838",
"COSM731764",
"COSM731765"
],
"id": "8b3c1a7a-e4e0-5200-9d46-5767c2982145",
"tumor_allele": "T",
"gene_aa_change": [
"CADPS G1147G",
"CADPS G1187G",
"CADPS G1217G",
"CADPS G1226G",
"CADPS G127G",
"CADPS G218G",
"CADPS G95G"
],
"chromosome": "chr3",
"genomic_dna_change": "chr3:g.62438203C>T"
}
],
"pagination": {
"count": 1,
"sort": "",
"from": 0,
"page": 1,
"total": 1,
"pages": 1,
"size": 10
}
},
"warnings": {}
}
Simple Somatic Mutation Occurrence Endpoint Examples
Example 1: A user wants to determine the chromosome in case TCGA-DU-6407 that contains the greatest number of ssms. As this relates to mutations that are observed in a case, the ssm_occurrences endpoint is used.
{
"op":"in",
"content":{
"field":"case.submitter_id",
"value":["TCGA-DU-6407"]
}
}
curl "https://api.gdc.cancer.gov/ssm_occurrences?format=tsv&fields=ssm.chromosome&size=5000&filters=%7B%0D%0A%22op%22%3A%22in%22%2C%0D%0A%22content%22%3A%7B%0D%0A%22field%22%3A%22case.submitter_id%22%2C%0D%0A%22value%22%3A%5B%0D%0A%22TCGA-DU-6407%22%0D%0A%5D%0D%0A%7D%0D%0A%7D"
ssm.chromosome id
chr3 552c09d1-69b1-5c04-b543-524a6feae3eb
chr10 391011ff-c1fd-5e2a-a128-652bc660f64c
chr10 1378cbc4-af88-55bb-b2e5-185bb4246d7a
chr10 3a2b3870-a395-5bc3-8c8f-0d40b0f2202c
chr1 4a93d7a5-988d-5055-80da-999dc3b45d80
chrX 22a07c7c-16ba-51df-a9a9-1e41e2a45225
chr12 dbc5eafa-ea26-5f1c-946c-b6974a345b69
chr11 02ae553d-1f27-565d-96c5-2c3cfca7264a
chr2 faee73a9-4804-58ea-a91f-18c3d901774f
chr6 97c5b38b-fc96-57f5-8517-cc702b3aa70a
chr17 0010a89d-9434-5d97-8672-36ee394767d0
chr19 f08dcc53-eadc-5ceb-bf31-f6b38629e4cb
chrX 19ca262d-b354-54a0-b582-c4719e37e91d
chr19 c44a93a1-5c73-5cff-b40e-98ce7e5fe57b
chr3 b67f31b5-0341-518e-8fcc-811cd2e36af1
chr1 94abd5fd-d539-5a4a-8719-9615cf7cec5d
chr17 1476a543-2951-5ec4-b165-67551b47d810
chr2 b4822fc9-f0cc-56fd-9d97-f916234e309d
chr2 3548ecfe-5186-51e7-8f40-37f4654cd260
chr16 105e7811-4601-5ccb-ae93-e7107923599e
chr2 99b3aad4-d368-506d-99d6-047cbe5dff0f
chr13 9dc3f7cd-9efa-530a-8524-30d067e49d54
chr21 1267330b-ae6d-5e25-b19e-34e98523679e
chr16 c77f7ce5-fbe6-5da4-9a7b-b528f8e530cb
chr10 2cb06277-993e-5502-b2c5-263037c45d18
chr17 d25129ad-3ad7-584f-bdeb-fba5c3881d32
chr17 a76469cb-973c-5d4d-bf82-7cf4e8f6c129
chr10 727c9d57-7b74-556f-aa5b-e1ca1f76d119
chr15 b4a86ffd-e60c-5c9c-aaa1-9e9f02d86116
chr5 3a023e72-da92-54f7-aa18-502c1076b2b0
Analysis Endpoints
In addition to the ssms, ssm_occurrences, and genes endpoints mentioned previously, several /analysis endpoints were designed to quickly retrieve specific datasets used for visualization display.
Example 1: The /analysis/top_cases_counts_by_genes endpoint gives the number of cases with a mutation in each gene listed in the gene_ids parameter for each project. Note that this endpoint cannot be used with the format or fields parameters. In this instance, the query will produce the number of cases in each projects with mutations in the gene ENSG00000155657.
curl "https://api.gdc.cancer.gov/analysis/top_cases_counts_by_genes?gene_ids=ENSG00000155657&pretty=true"
"genes": {
"my_genes": {
"gene_id": {
"buckets": [
{
"key": "ENSG00000155657",
"doc_count": 45
}
],
"sum_other_doc_count": 0,
"doc_count_error_upper_bound": 0
},
"doc_count": 45
},
"doc_count": 12305
},
"key": "TCGA-GBM",
"doc_count": 45
}
ssms in the gene ENSG00000155657.
Example 2: The following demonstrates a use of the /analysis/top_mutated_genes_by_project endpoint. This will output the genes that are mutated in the most cases in "TCGA-DLBC" and will count the mutations that have a HIGH or MODERATE impact on gene function. Note that the score field does not represent the number of mutations in a given gene, but a calculation that is used to determine which genes have the greatest number of unique mutations.
{
"op":"AND",
"content":[
{
"op":"in",
"content":{
"field":"case.project.project_id",
"value":[
"TCGA-DLBC"
]
}
},
{
"op":"in",
"content":{
"field":"case.ssm.consequence.transcript.annotation.impact",
"value":[
"HIGH",
"MODERATE"
]
}
}
]
}
curl "https://api.gdc.cancer.gov/analysis/top_mutated_genes_by_project?fields=gene_id,symbol&filters=%7B%22op%22%3A%22AND%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22case.project.project_id%22%2C%22value%22%3A%5B%22TCGA-DLBC%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22case.ssm.consequence.transcript.annotation.impact%22%2C%22value%22%3A%5B%22HIGH%22%2C%22MODERATE%22%5D%7D%7D%5D%7D&pretty=true"
{
"data": {
"hits": [
{
"_score": 14.0,
"symbol": "IGHV2-70",
"gene_id": "ENSG00000274576"
},
{
"_score": 14.0,
"symbol": "IGLV3-1",
"gene_id": "ENSG00000211673"
},
{
"_score": 14.0,
"symbol": "IGHM",
"gene_id": "ENSG00000211899"
},
{
"_score": 11.0,
"symbol": "KMT2D",
"gene_id": "ENSG00000167548"
},
{
"_score": 11.0,
"symbol": "IGLL5",
"gene_id": "ENSG00000254709"
},
{
"_score": 11.0,
"symbol": "BTG2",
"gene_id": "ENSG00000159388"
},
{
"_score": 9.0,
"symbol": "CARD11",
"gene_id": "ENSG00000198286"
},
{
"_score": 9.0,
"symbol": "IGHG1",
"gene_id": "ENSG00000211896"
},
{
"_score": 9.0,
"symbol": "IGLC2",
"gene_id": "ENSG00000211677"
},
{
"_score": 9.0,
"symbol": "LRP1B",
"gene_id": "ENSG00000168702"
}
],
"pagination": {
"count": 10,
"sort": "None",
"from": 0,
"page": 1,
"total": 3214,
"pages": 322,
"size": 10
}
},
"warnings": {}
}
/analysis/top_mutated_cases_by_gene endpoint will generate information about the cases that are most affected by mutations in a given number of genes. Below, the file count for each category is given for the cases most affected by mutations in these 50 genes. The size of the output is limited to two cases with the size=2 parameter, but a higher value can be set by the user.
curl "https://api.gdc.cancer.gov/analysis/top_mutated_cases_by_gene?fields=diagnoses.days_to_death,diagnoses.age_at_diagnosis,diagnoses.vital_status,diagnoses.primary_diagnosis,demographic.gender,demographic.race,demographic.ethnicity,case_id,summary.data_categories.file_count,summary.data_categories.data_category&filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22%3D%22%2C%22content%22%3A%7B%22field%22%3A%22cases.project.project_id%22%2C%22value%22%3A%22TCGA-DLBC%22%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22genes.gene_id%22%2C%22value%22%3A%5B%22ENSG00000166710%22%2C%22ENSG00000005339%22%2C%22ENSG00000083857%22%2C%22ENSG00000168769%22%2C%22ENSG00000100906%22%2C%22ENSG00000184677%22%2C%22ENSG00000101680%22%2C%22ENSG00000101266%22%2C%22ENSG00000028277%22%2C%22ENSG00000140968%22%2C%22ENSG00000181827%22%2C%22ENSG00000116815%22%2C%22ENSG00000275221%22%2C%22ENSG00000139083%22%2C%22ENSG00000112851%22%2C%22ENSG00000112697%22%2C%22ENSG00000164134%22%2C%22ENSG00000009413%22%2C%22ENSG00000071626%22%2C%22ENSG00000135407%22%2C%22ENSG00000101825%22%2C%22ENSG00000104814%22%2C%22ENSG00000166415%22%2C%22ENSG00000142867%22%2C%22ENSG00000254585%22%2C%22ENSG00000139718%22%2C%22ENSG00000077721%22%2C%22ENSG00000130294%22%2C%22ENSG00000117245%22%2C%22ENSG00000117318%22%2C%22ENSG00000270550%22%2C%22ENSG00000163637%22%2C%22ENSG00000166575%22%2C%22ENSG00000065526%22%2C%22ENSG00000156453%22%2C%22ENSG00000128191%22%2C%22ENSG00000055609%22%2C%22ENSG00000204469%22%2C%22ENSG00000187605%22%2C%22ENSG00000185875%22%2C%22ENSG00000110888%22%2C%22ENSG00000007341%22%2C%22ENSG00000173198%22%2C%22ENSG00000115568%22%2C%22ENSG00000163714%22%2C%22ENSG00000125772%22%2C%22ENSG00000080815%22%2C%22ENSG00000189079%22%2C%22ENSG00000120837%22%2C%22ENSG00000143951%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22ssms.consequence.transcript.annotation.impact%22%2C%22value%22%3A%5B%22HIGH%22%5D%7D%7D%5D%7D&pretty=true&size=2"
{
"data": {
"hits": [
{
"_score": 7.0,
"diagnoses": [
{
"days_to_death": null,
"vital_status": "alive",
"age_at_diagnosis": 18691,
"primary_diagnosis": "c83.3"
}
],
"case_id": "eda9496e-be80-4a13-bf06-89f0cc9e937f",
"demographic": {
"gender": "male",
"race": "white",
"ethnicity": "hispanic or latino"
},
"summary": {
"data_categories": [
{
"file_count": 1,
"data_category": "DNA Methylation"
},
{
"file_count": 5,
"data_category": "Transcriptome Profiling"
},
{
"file_count": 1,
"data_category": "Biospecimen"
},
{
"file_count": 16,
"data_category": "Simple Nucleotide Variation"
},
{
"file_count": 1,
"data_category": "Clinical"
},
{
"file_count": 4,
"data_category": "Copy Number Variation"
},
{
"file_count": 4,
"data_category": "Raw Sequencing Data"
}
]
}
},
{
"_score": 4.0,
"diagnoses": [
{
"days_to_death": null,
"vital_status": "alive",
"age_at_diagnosis": 27468,
"primary_diagnosis": "c83.3"
}
],
"case_id": "a43e5f0e-a21f-48d8-97e0-084d413680b7",
"demographic": {
"gender": "male",
"race": "white",
"ethnicity": "not hispanic or latino"
},
"summary": {
"data_categories": [
{
"file_count": 1,
"data_category": "DNA Methylation"
},
{
"file_count": 5,
"data_category": "Transcriptome Profiling"
},
{
"file_count": 1,
"data_category": "Biospecimen"
},
{
"file_count": 16,
"data_category": "Simple Nucleotide Variation"
},
{
"file_count": 1,
"data_category": "Clinical"
},
{
"file_count": 4,
"data_category": "Copy Number Variation"
},
{
"file_count": 4,
"data_category": "Raw Sequencing Data"
}
]
}
}
],
"pagination": {
"count": 2,
"sort": "None",
"from": 0,
"page": 1,
"total": 27,
"pages": 14,
"size": 2
}
},
"warnings": {}
}
/analysis/mutated_cases_count_by_project endpoint produces counts for the number of cases that have associated ssm data in each project. The number of affected cases can be found under "case_with_ssm": {"doc_count": $case_count}.
curl "https://api.gdc.cancer.gov/analysis/mutated_cases_count_by_project?size=0&pretty=true"
{
"hits": {
"hits": [],
"total": 14551,
"max_score": 0.0
},
"_shards": {
"successful": 9,
"failed": 0,
"total": 9
},
"took": 4,
"aggregations": {
"projects": {
"buckets": [
{
"case_summary": {
"case_with_ssm": {
"doc_count": 216
},
"doc_count": 637
},
"key": "TARGET-NBL",
"doc_count": 1127
},
{
"case_summary": {
"case_with_ssm": {
"doc_count": 1044
},
"doc_count": 7625
},
"key": "TCGA-BRCA",
"doc_count": 1098
},
{
"case_summary": {
"case_with_ssm": {
"doc_count": 8
},
"doc_count": 579
},
"key": "TARGET-AML",
"doc_count": 988
},
{
"case_summary": {
"case_with_ssm": {
"doc_count": 34
},
"doc_count": 290
},
"key": "TARGET-WT",
"doc_count": 652
},
{
"case_summary": {
"case_with_ssm": {
"doc_count": 396
},
"doc_count": 3197
},
"key": "TCGA-GBM",
"doc_count": 617
},
{
"case_summary": {
"case_with_ssm": {
"doc_count": 443
},
"doc_count": 3880
},
"key": "TCGA-OV",
"doc_count": 608
},
{
"case_summary": {
"case_with_ssm": {
"doc_count": 569
},
"doc_count": 3874
},
"key": "TCGA-LUAD",
"doc_count": 585
},
{
"case_summary": {
"case_with_ssm": {
"doc_count": 542
},
"doc_count": 3874
},
"key": "TCGA-UCEC",
"doc_count": 560
},
{
"case_summary": {
"case_with_ssm": {
"doc_count": 339
},
"doc_count": 3547
},
"key": "TCGA-KIRC",
"doc_count": 537
},
{
"case_summary": {
"case_with_ssm": {
"doc_count": 510
},
"doc_count": 3671
},
"key": "TCGA-HNSC",
"doc_count": 528
},
{
"case_summary": {
"case_with_ssm": {
"doc_count": 513
},
"doc_count": 3606
},
"key": "TCGA-LGG",
"doc_count": 516
},
{
"case_summary": {
"case_with_ssm": {
"doc_count": 496
},
"doc_count": 3536
},
"key": "TCGA-THCA",
"doc_count": 507
},
{
"case_summary": {
"case_with_ssm": {
"doc_count": 497
},
"doc_count": 3520
},
"key": "TCGA-LUSC",
"doc_count": 504
},
{
"case_summary": {
"case_with_ssm": {
"doc_count": 498
},
"doc_count": 3490
},
"key": "TCGA-PRAD",
"doc_count": 500
},
{
"case_summary": {
"case_with_ssm": {
"doc_count": 470
},
"doc_count": 3289
},
"key": "TCGA-SKCM",
"doc_count": 470
},
{
"case_summary": {
"case_with_ssm": {
"doc_count": 433
},
"doc_count": 3188
},
"key": "TCGA-COAD",
"doc_count": 461
},
{
"case_summary": {
"case_with_ssm": {
"doc_count": 441
},
"doc_count": 3095
},
"key": "TCGA-STAD",
"doc_count": 443
},
{
"case_summary": {
"case_with_ssm": {
"doc_count": 412
},
"doc_count": 2884
},
"key": "TCGA-BLCA",
"doc_count": 412
},
{
"case_summary": {
"case_with_ssm": {
"doc_count": 0
},
"doc_count": 0
},
"key": "TARGET-OS",
"doc_count": 381
},
{
"case_summary": {
"case_with_ssm": {
"doc_count": 375
},
"doc_count": 2635
},
"key": "TCGA-LIHC",
"doc_count": 377
},
{
"case_summary": {
"case_with_ssm": {
"doc_count": 305
},
"doc_count": 2142
},
"key": "TCGA-CESC",
"doc_count": 307
},
{
"case_summary": {
"case_with_ssm": {
"doc_count": 288
},
"doc_count": 2033
},
"key": "TCGA-KIRP",
"doc_count": 291
},
{
"case_summary": {
"case_with_ssm": {
"doc_count": 255
},
"doc_count": 1821
},
"key": "TCGA-SARC",
"doc_count": 261
},
{
"case_summary": {
"case_with_ssm": {
"doc_count": 149
},
"doc_count": 1192
},
"key": "TCGA-LAML",
"doc_count": 200
},
{
"case_summary": {
"case_with_ssm": {
"doc_count": 184
},
"doc_count": 1293
},
"key": "TCGA-ESCA",
"doc_count": 185
},
{
"case_summary": {
"case_with_ssm": {
"doc_count": 183
},
"doc_count": 1285
},
"key": "TCGA-PAAD",
"doc_count": 185
},
{
"case_summary": {
"case_with_ssm": {
"doc_count": 179
},
"doc_count": 1253
},
"key": "TCGA-PCPG",
"doc_count": 179
},
{
"case_summary": {
"case_with_ssm": {
"doc_count": 158
},
"doc_count": 1169
},
"key": "TCGA-READ",
"doc_count": 172
},
{
"case_summary": {
"case_with_ssm": {
"doc_count": 150
},
"doc_count": 1018
},
"key": "TCGA-TGCT",
"doc_count": 150
},
{
"case_summary": {
"case_with_ssm": {
"doc_count": 123
},
"doc_count": 867
},
"key": "TCGA-THYM",
"doc_count": 124
},
{
"case_summary": {
"case_with_ssm": {
"doc_count": 66
},
"doc_count": 556
},
"key": "TCGA-KICH",
"doc_count": 113
},
{
"case_summary": {
"case_with_ssm": {
"doc_count": 92
},
"doc_count": 620
},
"key": "TCGA-ACC",
"doc_count": 92
},
{
"case_summary": {
"case_with_ssm": {
"doc_count": 83
},
"doc_count": 605
},
"key": "TCGA-MESO",
"doc_count": 87
},
{
"case_summary": {
"case_with_ssm": {
"doc_count": 80
},
"doc_count": 560
},
"key": "TCGA-UVM",
"doc_count": 80
},
{
"case_summary": {
"case_with_ssm": {
"doc_count": 0
},
"doc_count": 163
},
"key": "TARGET-RT",
"doc_count": 75
},
{
"case_summary": {
"case_with_ssm": {
"doc_count": 48
},
"doc_count": 346
},
"key": "TCGA-DLBC",
"doc_count": 58
},
{
"case_summary": {
"case_with_ssm": {
"doc_count": 57
},
"doc_count": 399
},
"key": "TCGA-UCS",
"doc_count": 57
},
{
"case_summary": {
"case_with_ssm": {
"doc_count": 51
},
"doc_count": 306
},
"key": "TCGA-CHOL",
"doc_count": 51
},
{
"case_summary": {
"case_with_ssm": {
"doc_count": 0
},
"doc_count": 13
},
"key": "TARGET-CCSK",
"doc_count": 13
}
],
"sum_other_doc_count": 0,
"doc_count_error_upper_bound": 0
}
},
"timed_out": false
}
Survival Analysis Endpoint
Survival plots are generated for different subsets of data, based on variants or projects, in the GDC Data Portal. The /analysis/survival endpoint can be used to programmatically retrieve the raw data used to generate these plots and apply different filters. Note that the fields and format parameters cannot be modified.
Example 1: A user wants to download data to generate a survival plot for cases from the project TCGA-DLBC.
curl "https://api.gdc.cancer.gov/analysis/survival?filters=%5B%7B%22op%22%3A%22%3D%22%2C%22content%22%3A%7B%22field%22%3A%22cases.project.project_id%22%2C%22value%22%3A%22TCGA-DLBC%22%7D%7D%5D&pretty=true"
{
"overallStats": {},
"results": [
{
"donors": [
{
"survivalEstimate": 1,
"id": "dc87a809-95de-4eb7-a1c2-2650475f2d7e",
"censored": true,
"time": 1
},
{
"survivalEstimate": 1,
"id": "4dd86ebd-ef16-4b2b-9ea0-5d1d7afef257",
"censored": true,
"time": 17
},
{
"survivalEstimate": 1,
"id": "0bf573ac-cd1e-42d8-90cf-b30d7b08679c",
"censored": false,
"time": 58
},
{
"survivalEstimate": 0.9777777777777777,
"id": "f978cb0f-d319-4c01-b4c5-23ae1403a106",
"censored": true,
"time": 126
},
{
"survivalEstimate": 0.9777777777777777,
"id": "a43e5f0e-a21f-48d8-97e0-084d413680b7",
"censored": true,
"time": 132
},
{
"survivalEstimate": 0.9777777777777777,
"id": "1843c82e-7a35-474f-9f79-c0a9af9aa09c",
"censored": true,
"time": 132
},
{
"survivalEstimate": 0.9777777777777777,
"id": "0030a28c-81aa-44b0-8be0-b35e1dcbf98c",
"censored": false,
"time": 248
},
{
"survivalEstimate": 0.9539295392953929,
"id": "f553f1a9-ecf2-4783-a609-6adca7c4c597",
"censored": true,
"time": 298
},
{
"survivalEstimate": 0.9539295392953929,
"id": "f784bc3a-751b-4025-aab2-0af2f6f24266",
"censored": false,
"time": 313
},
{
"survivalEstimate": 0.929469807518588,
"id": "29e3d122-15a1-4235-a356-b1a9f94ceb39",
"censored": true,
"time": 385
},
{
"survivalEstimate": 0.929469807518588,
"id": "0e251c03-bf86-4ed8-b45d-3cbc97160502",
"censored": false,
"time": 391
},
{
"survivalEstimate": 0.9043490019099776,
"id": "e6365b38-bc44-400c-b4aa-18ce8ff5bfce",
"censored": true,
"time": 427
},
{
"survivalEstimate": 0.9043490019099776,
"id": "b56bdbdb-43af-4a03-a072-54dd22d7550c",
"censored": true,
"time": 553
},
{
"survivalEstimate": 0.9043490019099776,
"id": "31bbad4e-3789-42ec-9faa-1cb86970f723",
"censored": false,
"time": 595
},
{
"survivalEstimate": 0.8777505018538018,
"id": "0e9fcccc-0630-408d-a121-2c6413824cb7",
"censored": true,
"time": 679
},
{
"survivalEstimate": 0.8777505018538018,
"id": "a5b188f0-a6d3-4d4a-b04f-36d47ec05338",
"censored": false,
"time": 708
},
{
"survivalEstimate": 0.8503207986708705,
"id": "ed746cb9-0f2f-48ce-923a-3a9f9f00b331",
"censored": true,
"time": 719
},
{
"survivalEstimate": 0.8503207986708705,
"id": "c85f340e-584b-4f3b-b6a5-540491fc8ad2",
"censored": true,
"time": 730
},
{
"survivalEstimate": 0.8503207986708705,
"id": "69f23725-adca-48ac-9b33-80a7aae24cfe",
"censored": true,
"time": 749
},
{
"survivalEstimate": 0.8503207986708705,
"id": "67325322-483f-443f-9ffa-2a20d108a2fb",
"censored": true,
"time": 751
},
{
"survivalEstimate": 0.8503207986708705,
"id": "eda9496e-be80-4a13-bf06-89f0cc9e937f",
"censored": true,
"time": 765
},
{
"survivalEstimate": 0.8503207986708705,
"id": "25ff86af-beb4-480c-b706-f3fe0306f7cf",
"censored": true,
"time": 788
},
{
"survivalEstimate": 0.8503207986708705,
"id": "1d0db5d7-39ca-466d-96b3-0d278c5ea768",
"censored": true,
"time": 791
},
{
"survivalEstimate": 0.8503207986708705,
"id": "c8cde9ea-89e9-4ee8-8a46-417a48f6d3ab",
"censored": true,
"time": 832
},
{
"survivalEstimate": 0.8503207986708705,
"id": "f0a326d2-1f3e-4a5d-bca8-32aaccc52338",
"censored": true,
"time": 946
},
{
"survivalEstimate": 0.8503207986708705,
"id": "a8e2df1e-4042-42af-9231-3a00e83489f0",
"censored": true,
"time": 965
},
{
"survivalEstimate": 0.8503207986708705,
"id": "e56e4d9c-052e-4ec6-a81b-dbd53e9c8ffe",
"censored": true,
"time": 972
},
{
"survivalEstimate": 0.8503207986708705,
"id": "45b0cf9f-a879-417f-8f39-7770552252c0",
"censored": true,
"time": 982
},
{
"survivalEstimate": 0.8503207986708705,
"id": "1f971af1-6772-4fe6-8d35-bbe527a037fe",
"censored": true,
"time": 1081
},
{
"survivalEstimate": 0.8503207986708705,
"id": "33365d22-cb83-4d8e-a2d1-06b675f75f6e",
"censored": true,
"time": 1163
},
{
"survivalEstimate": 0.8503207986708705,
"id": "6a21c948-cd85-4150-8c01-83017d7dc1ed",
"censored": false,
"time": 1252
},
{
"survivalEstimate": 0.8003019281608192,
"id": "f855dad1-6ffc-493e-ba6c-970874bc9210",
"censored": true,
"time": 1299
},
{
"survivalEstimate": 0.8003019281608192,
"id": "c1c06604-5ae2-4a53-b9c0-eb210d38e3f0",
"censored": true,
"time": 1334
},
{
"survivalEstimate": 0.8003019281608192,
"id": "58e66976-4507-4552-ac53-83a49a142dde",
"censored": true,
"time": 1373
},
{
"survivalEstimate": 0.8003019281608192,
"id": "ea54dbad-1b23-41cc-9378-d4002a8fca51",
"censored": true,
"time": 1581
},
{
"survivalEstimate": 0.8003019281608192,
"id": "d7df78b5-24f1-4ff4-bd9b-f0e6bec8289a",
"censored": true,
"time": 1581
},
{
"survivalEstimate": 0.8003019281608192,
"id": "29aff186-c321-4ff9-b81b-105e27e620ff",
"censored": true,
"time": 1617
},
{
"survivalEstimate": 0.8003019281608192,
"id": "5eff68ff-f6c3-40c9-9fc8-00e684a7b712",
"censored": true,
"time": 1739
},
{
"survivalEstimate": 0.8003019281608192,
"id": "f8cf647b-1447-4ac3-8c43-bef07765cabf",
"censored": true,
"time": 2131
},
{
"survivalEstimate": 0.8003019281608192,
"id": "c3d662ee-48d0-454a-bb0c-77d3338d3747",
"censored": true,
"time": 2983
},
{
"survivalEstimate": 0.8003019281608192,
"id": "6e9437f0-a4ed-475c-ab0e-bf1431c70a90",
"censored": true,
"time": 3333
},
{
"survivalEstimate": 0.8003019281608192,
"id": "fdecb74f-ac4e-46b1-b23a-5f7fde96ef9f",
"censored": true,
"time": 3394
},
{
"survivalEstimate": 0.8003019281608192,
"id": "a468e725-ad4b-411d-ac5c-2eacc68ec580",
"censored": false,
"time": 3553
},
{
"survivalEstimate": 0.6402415425286554,
"id": "1ea575f1-f731-408b-a629-f5f4abab569e",
"censored": true,
"time": 3897
},
{
"survivalEstimate": 0.6402415425286554,
"id": "7a589441-11ef-4158-87e7-3951d86bc2aa",
"censored": true,
"time": 4578
},
{
"survivalEstimate": 0.6402415425286554,
"id": "3622cf29-600f-4410-84d4-a9afeb41c475",
"censored": true,
"time": 5980
},
{
"survivalEstimate": 0.6402415425286554,
"id": "3f5a897d-1eaa-4d4c-8324-27ac07c90927",
"censored": false,
"time": 6425
}
],
"meta": {
"id": 140429063094496
}
}
]
}
chr3:g.179234297A>G) and the other plot will display information about cases without that mutation. This type of query will also print the results of a chi-squared analysis between the two subsets of cases.
[
{
"op":"and",
"content":[
{
"op":"=",
"content":{
"field":"cases.project.project_id",
"value":"TCGA-BRCA"
}
},
{
"op":"=",
"content":{
"field":"gene.ssm.ssm_id",
"value":"edd1ae2c-3ca9-52bd-a124-b09ed304fcc2"
}
}
]
},
{
"op":"and",
"content":[
{
"op":"=",
"content":{
"field":"cases.project.project_id",
"value":"TCGA-BRCA"
}
},
{
"op":"excludeifany",
"content":{
"field":"gene.ssm.ssm_id",
"value":"edd1ae2c-3ca9-52bd-a124-b09ed304fcc2"
}
}
]
}
]
curl "https://api.gdc.cancer.gov/analysis/survival?filters=%5B%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22%3D%22%2C%22content%22%3A%7B%22field%22%3A%22cases.project.project_id%22%2C%22value%22%3A%22TCGA-BRCA%22%7D%7D%2C%7B%22op%22%3A%22%3D%22%2C%22content%22%3A%7B%22field%22%3A%22gene.ssm.ssm_id%22%2C%22value%22%3A%22edd1ae2c-3ca9-52bd-a124-b09ed304fcc2%22%7D%7D%5D%7D%2C%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22%3D%22%2C%22content%22%3A%7B%22field%22%3A%22cases.project.project_id%22%2C%22value%22%3A%22TCGA-BRCA%22%7D%7D%2C%7B%22op%22%3A%22excludeifany%22%2C%22content%22%3A%7B%22field%22%3A%22gene.ssm.ssm_id%22%2C%22value%22%3A%22edd1ae2c-3ca9-52bd-a124-b09ed304fcc2%22%7D%7D%5D%7D%5D&pretty=true"
{
"overallStats": {
"degreesFreedom": 1,
"chiSquared": 0.8577589072612264,
"pValue": 0.35436660628146011
},
"results": [
{
"donors": [
{
"survivalEstimate": 1,
"id": "a991644b-3ee6-4cda-acf0-e37de48a49fc",
"censored": true,
"time": 10
},
{
"survivalEstimate": 1,
"id": "2e1e3bf0-1708-4b65-936c-48b89eb8966a",
"censored": true,
"time": 19
},
(truncated)
],
"meta": {
"id": 140055251282040
}
},
{
"donors": [
{
"survivalEstimate": 1,
"id": "5e4187c9-98f8-4bdb-a8da-6a914e96f47a",
"censored": true,
"time": -31
},
(truncated)
donors tag. One set of coordinates will generate a survival plot representing TCGA-BRCA cases that have the mutation of interest and the other will generate a survival plot for the remaining cases in TCGA-BRCA.
Example 3: Custom survival plots can be generated using the GDC API. For example, a user could generate survival plot data comparing patients with a mutation in genes associated with a biological pathway with patients without mutations in that pathway. The following example compares a patient with at least one mutation in either gene ENSG00000141510 or ENSG00000155657 with patients that do not have mutations in these genes.
[
{
"op":"and",
"content":[
{
"op":"=",
"content":{
"field":"cases.project.project_id",
"value":"TCGA-BRCA"
}
},
{
"op":"=",
"content":{
"field":"gene.gene_id",
"value":["ENSG00000141510","ENSG00000155657"]
}
}
]
},
{
"op":"and",
"content":[
{
"op":"=",
"content":{
"field":"cases.project.project_id",
"value":"TCGA-BRCA"
}
},
{
"op":"excludeifany",
"content":{
"field":"gene.gene_id",
"value":["ENSG00000141510","ENSG00000155657"]
}
}
]
}
]
curl "https://api.gdc.cancer.gov/analysis/survival?filters=%5B%0D%0A%7B%0D%0A%22op%22%3A%22and%22%2C%0D%0A%22content%22%3A%5B%0D%0A%7B%0D%0A%22op%22%3A%22%3D%22%2C%0D%0A%22content%22%3A%7B%0D%0A%22field%22%3A%22cases.project.project_id%22%2C%0D%0A%22value%22%3A%22TCGA-BRCA%22%0D%0A%7D%0D%0A%7D%2C%0D%0A%7B%0D%0A%22op%22%3A%22%3D%22%2C%0D%0A%22content%22%3A%7B%0D%0A%22field%22%3A%22gene.gene_id%22%2C%0D%0A%22value%22%3A%5B%22ENSG00000141510%22%2C%22ENSG00000155657%22%5D%0D%0A%7D%0D%0A%7D%0D%0A%5D%0D%0A%7D%2C%0D%0A%7B%0D%0A%22op%22%3A%22and%22%2C%0D%0A%22content%22%3A%5B%0D%0A%7B%0D%0A%22op%22%3A%22%3D%22%2C%0D%0A%22content%22%3A%7B%0D%0A%22field%22%3A%22cases.project.project_id%22%2C%0D%0A%22value%22%3A%22TCGA-BRCA%22%0D%0A%7D%0D%0A%7D%2C%0D%0A%7B%0D%0A%22op%22%3A%22excludeifany%22%2C%0D%0A%22content%22%3A%7B%0D%0A%22field%22%3A%22gene.gene_id%22%2C%0D%0A%22value%22%3A%5B%22ENSG00000141510%22%2C%22ENSG00000155657%22%5D%0D%0A%7D%0D%0A%7D%0D%0A%5D%0D%0A%7D%0D%0A%5D&pretty=true"
[{
"op":"=",
"content":{
"field":"cases.submitter_id",
"value":["TCGA-HT-A74J","TCGA-43-A56U","TCGA-GM-A3XL","TCGA-A1-A0SQ","TCGA-K1-A6RV","TCGA-J2-A4AD","TCGA-XR-A8TE"]
}
},
{
"op":"=",
"content":{
"field":"cases.submitter_id",
"value":["TCGA-55-5899","TCGA-55-6642","TCGA-55-7907","TCGA-67-6216","TCGA-75-5146","TCGA-49-4510","TCGA-78-7159"]
}
}]
curl "https://api.gdc.cancer.gov/analysis/survival?filters=%5B%7B%22op%22%3A%22%3D%22%2C%22content%22%3A%7B%22field%22%3A%22cases.submitter_id%22%2C%22value%22%3A%5B%22TCGA-HT-A74J%22%2C%22TCGA-43-A56U%22%2C%22TCGA-GM-A3XL%22%2C%22TCGA-A1-A0SQ%22%2C%22TCGA-K1-A6RV%22%2C%22TCGA-J2-A4AD%22%2C%22TCGA-XR-A8TE%22%5D%7D%7D%2C%7B%22op%22%3A%22%3D%22%2C%22content%22%3A%7B%22field%22%3A%22cases.submitter_id%22%2C%22value%22%3A%5B%22TCGA-55-5899%22%2C%22TCGA-55-6642%22%2C%22TCGA-55-7907%22%2C%22TCGA-67-6216%22%2C%22TCGA-75-5146%22%2C%22TCGA-49-4510%22%2C%22TCGA-78-7159%22%5D%7D%7D%5D"