科研技能教程单元课06TCGA肿瘤数据库使用教程（一）

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2••基因 •

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Adrenocortical

carcinomaBladder

Urothelial

CarcinomaBreast

invasive

carcinomaCervical

squamous

cell

carcinoma

and

endocervical

adenocarcinomaCholangiocarcinoma •Colon

adenocarcinomaColon

adenocarcinoma/Rectum

adenocarcinomaLymphoid

Neoplasm

Diffuse

Large

B-cell

Lymphoma

( B )Esophageal

carcinomaFFPE

Pilot

Phase

II

FFPEGlioblastoma

multiformeGliomaHead

and

Neck

squamous

cell

carcinomaKidney

ChromophobePan-kidney

cohort

(KICH+KIRC+KIRP)Kidney

renal

clear

cell

carcinomaKidney

renal

papillary

cell

carcinomaAcute

Myeloid

LeukemiaBrain

Lower

Grade

GliomaLiver

hepatocellular

carcinomaLung

adenocarcinomaLung

squamous

cell

carcinomaMesotheliomaOvarian

serous

cystadenocarcinomaPancreatic

adenocarcinomaPheochromocytoma

andParagangliomaProstateadenocarcinomaRectum

adenocarcinomaSarcomaSkin

Cutaneous

MelanomaStomach

adenocarcinomaStomach

and

Esophageal

carcinomaTesticular

Germ

Cell

TumorsThyroid

carcinomaThymomaUterine

Corpus

Endometrial

CarcinomaUterine

CarcinosarcomaUveal

MelanomaData

typessupportedby

RTCGAToolbox.Data

Type

(Parameter)DescriptionOutput

Object

(FirehoseData)ClinicalProvides

clinical

information

for

each

sample.

Clinical

information

may

include

stage,

survival

time,

sex,

age

and

more.fd@Clinical

(data

frame)RNAseqGene

or/andRNAseq2GeneNormGenelevelexpressiondatafromRNA-seqplatforms.Thisparameter

providesraw

counts

and

normalized

values.

Firehose

provides2

different

algorithms

for

RNAseq

data

processing.

(Data

types

can

be

specified

by

using

RNAseqNorm

and

RNAseq2Norm

parameters)fd@

RNASeqGene,

fd@RNASeq2GeneNorm

(data

matrix)miRNASeqGenemiRNA

expression

levels

from

next

generation

sequencing

platformsfd@

miRNASeqGene

(data

matrix)CNASNPSegmented

copynumber

alterations

(in

somatic

cells)fd@

CNASNP

(dataframe)CNVSNPSegmented

copynumber

variations

(in

germline

cells)fd@CNVSNP(data

frame)CNSSeqCopy

number

alterations

provided

by

next

generation

sequencing

platformsfd@

CNAseq

(data

frame)CNACGHCopynumber

alterations

provided

byCGH

array

platformsfd@

CNACGH

(alist

of

FirehoseCGHArray

objects)MethylationMethylation

data

providedby

array

platformsfd@

Methylation

(a

list

ofFirehoseMethylationArray

object)MutationGene

level

mutation

information

matrixfa@

Mutations

(dataframe)mRNAArrayGene

level

expression

data

provided

byarray

platformsfd@

mRNAArray

(alist

of

FirehosemRNAArray

objects)miRNAArraymiRNA

expression

data

provided

byarray

platformsfd@

miRNAArray

(alist

of

FirehosemRNAArray

objects)RPPAArrayReverse

phase

protein

array

(RPPA)

expressionfd@

RPPAArray

(a

list

ofFirehosemRNAArray

objects)••••••

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