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Module:
Search for Mutations by gene
Step 1: Select Cancer
Close
ACC: Adrenocortical Carcinoma
BLCA: Bladder Urothelial Carcinoma
BRCA: Breast Invasive Carcinoma
CESC: Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma
CHOL: Cholangiocarcinoma
COAD: Colon Adenocarcinoma
DLBC: Lymphoid Neoplasm Diffuse Large B-cell Lymphoma
ESCA: Esophageal Carcinoma
GBM: Glioblastoma Multiforme
HNSC: Head and Neck Squamous Cell Carcinoma
KICH: Kidney Chromophobe
KIRC: Kidney Renal Clear Cell Carcinoma
KIRP: Kidney Renal Papillary Cell Carcinoma
LAML: Acute Myeloid Leukemia
LGG: Brain Lower Grade Glioma
LIHC: Liver Hepatocellular Carcinoma
LUAD: Lung Adenocarcinoma
LUSC: Lung Squamous Cell Carcinoma
OV: Ovarian Serous Cystadenocarcinoma
PAAD: Pancreatic Adenocarcinoma
PCPG: Pheochromocytoma and Paraganglioma
PRAD: Prostate Adenocarcinoma
READ: Rectum Adenocarcinoma
SARC: Sarcoma
SKCM: Skin Cutaneous Melanoma
STAD: Stomach Adenocarcinoma
TGCT: Testicular Germ Cell Tumors
THCA: Thyroid Carcinoma
THYM: Thymoma
UCEC: Uterine Corpus Endometrial Carcinoma
UCS: Uterine Carcinosarcoma
UVM: Uveal Melanoma
ACC
BLCA
BRCA
CESC
CHOL
COAD
DLBC
ESCA
GBM
HNSC
KICH
KIRC
KIRP
LAML
LGG
LIHC
LUAD
LUSC
MESO
OV
PAAD
PCPG
PRAD
READ
SARC
SKCM
STAD
TGCT
THCA
THYM
UCEC
UCS
UVM
Step 2: Input Genes/Chromosomes
By Genes/By Genomic Location
All genes?
OR
Upload File
OR
Cancer panel gene lists:
(runtime: ~1 min per cancer)
Foundation One
(336 genes)
ThermoFisher
(409 genes)
Step 3: Advanced Options
Variant Classification
(
One selection at least
REQUIRED
; Runtime: ~5sec per cancer for all selection
)
Classification Explanations
RNA - variant lies on one of the RNA transcripts.
Missense - the point mutation alters the protein structure by one amino acid.
Nonsense - a premature stop codon is created by the variant.
Intron - variant lies between exons within the bounds of the chosen transcript.
3'UTR - variant is on the 3'UTR for the chosen transcript.
Silent - variant is in coding region of the chosen transcript, but protein structure is identical. I.e. a synonymous mutation.
Splice - the variant is within two bases of a splice site.
5'Flank - the variant is upstream of the chosen transcript (within 3kb).
IGR - intergenic region. Does not overlap any transcript.
Nonstop - variant removes stop codon.
Indel - insertion or selection that overlaps the start codon.
SNP - point mutation that overlaps the start codon.
5'UTR - variant is on the 5'UTR for the chosen transcript
RNA
Intron
Splice
IGR
3Flank
Missense
3UTR
5Flank
Nonstop
5UTR
Nonsense
Silent
TSS
INDEL
SNP