生物信息學(xué)第四講基因調(diào)節(jié)網(wǎng)絡(luò)分析

基因調(diào)節(jié)網(wǎng)絡(luò)分析廖

奇寧波大學(xué)醫(yī)學(xué)院主要內(nèi)容蛋白互作、轉(zhuǎn)錄因子調(diào)節(jié)關(guān)系數(shù)據(jù)庫的介紹和使用非編碼RNA調(diào)節(jié)網(wǎng)絡(luò)數(shù)據(jù)庫的介紹和使用基因網(wǎng)絡(luò)圖的展示、Cytoscape軟件的介紹和使用蛋白蛋白相互作用STRINGMIPSBioGRIDIntActHPRDSTRING輸入蛋白名、蛋白描述、基因名選擇物種/名字序列多個蛋白名字多個蛋白序列顯示物種信息蛋白家族（家族名、單個或多個蛋白名、序列等）網(wǎng)絡(luò)節(jié)點、邊顏色的意義Input

protein預(yù)測的相

互作用蛋白線的顏色、粗細、形狀代表

不同意思，選擇其中一種展示相互作用的來源預(yù)測相互作用的最低分值相互作用蛋白的個數(shù)圖形類型圖顯示參數(shù)基因功能富集網(wǎng)絡(luò)基本信息基因功能富集計算富集功能的背景輸出結(jié)果相互作用關(guān)系MIPSMIPS收集由專業(yè)審核者從文獻中手動核對的高質(zhì)量的哺乳動物蛋白蛋白相互作用。只選取單通量實驗驗證的數(shù)據(jù)，因為更可靠。http://mips.gsf.de/proj/ppi/蛋白1的信息蛋白2的信息相互作用的信息BioGRID目前版本：3.4.163，搜索了65590篇發(fā)表的文獻，收錄了來自主要模式物種的1591402個蛋白和遺傳相互作用，27785個化學(xué)反應(yīng)和39028個轉(zhuǎn)錄后修飾/…

…目前收錄的統(tǒng)計信息1）基因名、基因ID、關(guān)鍵詞2）Pubmed

ID3）3個字符+*，如MYC*多個關(guān)鍵詞搜索,

AND,

ORSH2

OR

Domainprotein

AND

kinase

ANDadapter

(+protein

+kinase+adapter)c.

+protein

+kinase–yeastd.+“proteinkinasedomain”

-“SH2Domain”e.+(proteinkinasedomain)

+(sh2domain)數(shù)據(jù)下載相互作用的分子信息富集的GO功能相互作用的信息化合物信息組蛋白修飾位點未知特定位點的關(guān)聯(lián)的蛋白網(wǎng)絡(luò)展示IntAct比如輸入MYC基因相互作用自定義顯示條目下載相互作用分子不同種類的分子HPRD/查詢?yōu)g覽比對輸入MYC功能表達定位相互作用序列比對轉(zhuǎn)錄因子調(diào)節(jié)關(guān)系TRRUSTCistromeTRRUST/trrustHuman:

800

TFs

8,444

TF-target

regulatory

relationshipsMouse:

828

TFs

6,552

TF-target

regulatory來源于11,237

pubmed

文獻。輸入一個基因名，如BRCA1、MYC等輸入基因列表，用逗號分隔調(diào)節(jié)的靶基因上游調(diào)節(jié)的TFs共有靶基因的TF查詢高通量數(shù)據(jù)檢測的轉(zhuǎn)錄因子靶基因數(shù)據(jù)庫（高通量數(shù)據(jù)來源，具有一定的可信度）/Cistrome/Cistrome_Project.htmlCistrome轉(zhuǎn)錄因子靶基因輸入關(guān)鍵詞，如轉(zhuǎn)錄因子名字選擇物種選擇細胞系選擇轉(zhuǎn)錄因子搜索人CEPBP在不同生物過程下的靶基因選擇其中1個，得到如下基本信息GEO數(shù)據(jù)庫的ID生物過程或細胞系信息ChIP-seq數(shù)據(jù)基本信息，可忽略靶基因點擊putative

targets下載選擇排序靠前的靶基因較為可信，若想進一步提高可靠性：多個同個轉(zhuǎn)錄因子不同細胞系（或相同細胞系）的靶基因取交集與共表達的蛋白編碼基因取交集轉(zhuǎn)錄因子在癌癥中的靶基因轉(zhuǎn)錄因子選擇轉(zhuǎn)錄因子和癌癥類型miRNA

target

database（實驗驗證）miRTarBaseTarBasemiRTarBase靶基因Tarbasehttp://carolina.imis.athena-

innovation.gr/diana_tools/web/index.php?r=tarbasev8%2Findex比如，輸入hsa-let-7b-3p靶基因miRNA

target

database（預(yù)測）TargetScanmiRDBmiRcodeTargetScan/vert_72/比如輸入MYC調(diào)節(jié)的miRNAsmiRDB由軟件MirTarget預(yù)測而來的結(jié)果。MirTarget基于高通量檢測的miIRNA-靶基因關(guān)系，提取相關(guān)特征，構(gòu)建機器學(xué)習方法，從而獲得預(yù)測模型。包含5個物種，

human,

mouse,

rat,

dog

和

chicken.比如輸入MYC/index.html查詢的結(jié)果miRNA信息miRcode輸入MYC或者ENSG00000136997.9/index.phpSearch

MYCSearch

miR-155Search

linc00472非編碼RNA綜合數(shù)據(jù)庫starBasemiRNA-ncRNA,miRNA-mRNA,ncRNA-RNA,RBP-

ncRNA

and

RBP-mRNA

interactions1.1millionmiRNA-ncRNA,

2.5millionmiRNA-mRNA,0.9millionRBP-ncRNAand1.1

millionRBP-mRNA

interactionsgeneexpressiondataof32typesofcancerswhich

arederivedfrom10,159RNA-seqand9,925miRNA-

seqdata/點擊更換參數(shù)后，點擊√，再點擊Quick

Search更換參數(shù)對特定列進行篩查ceRNA調(diào)節(jié)關(guān)系RNA結(jié)合蛋白相互作用預(yù)測catPARID/page/catrapid_group/update_submission/143562/31bb002528選擇物種輸入蛋白序列基于蛋白序列進行預(yù)測基于RNA序列進行預(yù)測/update_submission/143563/73bf419b9e調(diào)節(jié)網(wǎng)絡(luò)綜合數(shù)據(jù)庫RegNetworkTF→TFTF→geneTF→miRNAmiRNA→TFmiRNA→gene/DATABASEDESCRIPTIONSPECIESWEBSITEBioGridBioGRID

is

an

online

interaction

repository

with

data

compiled

through

comprehensive

curationeffortsMouse/EnsemblEnsembl

is

to

provide

a

centralized

resource

for

geneticists,

molecular

biologists

and

other

researchers

studying

the

genomes

of

our

own

species

and

other

vertebrates

and

model

organismsHuman

and

mouseHPRDHPRD

is

a

curated

human

protein-protein

interaction

databaseHumanIntActIntAct

is

a

database

system

of

molecular

interaction

data.

All

interactions

are

derived

from

literature

curation

or

direct

user

submissionsMousehttp://www.ebi.ac.uk/intact/KEGGKEGG

is

a

widely

used

pathway

database

resource

for

understanding

high-level

linkage

functionsand

utilitiesof

biological

systemHuman

and

mousehttp://www.genome.jp/kegg/MicroTDIANA-microT

is

a

combined

computational-experimental

approach

predicts

mouse

microRNAtargetsHuman

and

mousehttp://www.microrna.gr/microTmiRandamiRanda

is

a

miRNA

target

prediction

method

based

on

dynamic

programming

algorithmHuman

and

mousemiRBasemiRBase

database

is

a

searchable

database

of

published

miRNA

sequences

and

annotationHuman

and

mouse/miRecordsmiRecords

is

a

resource

for

animal

miRNA-target

interactions.

The

validated

targets

component

is

used,

which

is

a

large,

high-quality

database

of

experimentally

validated

miRNAtargetsHuman

and

mousehttp://miR/miRecordsmiRTarBasemiRTarBase

is

a

database

which

curates

experimentally

validated

microRNA-targetinteractionsHuman

and

mousehttp://miRTarB.tw/PicTarPicTar

is

a

computational

method

for

identifying

common

targets

of

microRNAsHuman

and

mousehttp://pictar.mdc-berlin.de/STRINGSTRING

is

a

database

of

known

and

predicted

protein

interactionsMouseTarbaseTarbase

collectes

available

miRNA

targets

derived

from

all

contemporary

experimental

techniques(gene

specific

and

high-throughput)Human

and

mousehttp://www.microrna.gr/tarbaseTargetScanTargetScan

is

an

algorithm

to

predict

biological

targets

of

miRNAs

by

searching

for

the

presence

of

conserved

8mer

and

7mer

sites

that

match

the

seed

region

of

each

miRNAHuman

and

mouse/TransmiRTransmiR

is

a

transcription

factor-microRNA

regulation

databaseHuman

and

mouse51/hmdd/mirna/tf/TREDTranscriptional

Regulatory

Element

Database

(TRED)

is

an

integrated

repository

repository

for

both

cis-

and

trans-

regulatory

elements

in

mammals.

It

contains

the