mutLBSgeneDB

mutLBSgeneDB
mutated Ligand Binding Site gene DataBase

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	Gene Summary
	Ligand Binding Site Mutation Information
	Protein Structure Related Information
	Gene Expression and Gene-Gene Network
	Phenotype Information
	Pharmacological Information
	Conservation Information for LBS

Gene summary for TBP

Gene summary

Basic gene Info.	Gene symbol	TBP
	Gene name	TATA box binding protein
	Synonyms	GTF2D\|GTF2D1\|HDL4\|SCA17\|TFIID
	Cytomap	UCSC genome browser: 6q27
	Type of gene	protein-coding
	RefGenes	NM_001172085.1, NM_003194.4,
	Description	TATA sequence-binding proteinTATA-box binding protein N-terminal domainTATA-box factorTATA-box-binding proteintranscription initiation factor TFIID TBP subunit
	Modification date	20141219
dbXrefs	MIM : 600075
	HGNC : HGNC
	Ensembl : ENSG00000112592
	HPRD : 02511
	Vega : OTTHUMG00000016084
Protein	UniProt: P20226 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_TBP
	BioGPS: 6908
Pathway	NCI Pathway Interaction Database: TBP
	KEGG: TBP
	REACTOME: TBP
	Pathway Commons: TBP
Context	iHOP: TBP
	ligand binding site mutation search in PubMed: TBP
	UCL Cancer Institute: TBP
Assigned class in mutLBSgeneDB	B: This gene belongs to targetable_mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez

GO ID	GO Term	PubMed ID
GO:0006366	transcription from RNA polymerase II promoter	7724559
GO:0006383	transcription from RNA polymerase III promoter	9027316

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Ligand binding site mutations for TBP

Lollipop-style diagram of mutations at LBS in amino-acid sequence.
We represented ligand binding site mutations only. (You can see big image via clicking.)

: non-synonymous mutation on LBS, Circle size denotes number of samples.

Cancer type specific mutLBS sorted by frequency

LBS	AAchange of nsSNV	Cancer type	# samples
K225,G223	A224V	COAD	1
T171,V169	S170F	SKCM	1
R196	R196Q	UCEC	1
T210,L212	A211T	UCEC	1

cf) Cancer type abbreviation. BLCA: Bladder urothelial carcinoma, BRCA: Breast invasive carcinoma, CESC: Cervical squamous cell carcinoma and endocervical adenocarcinoma, COAD: Colon adenocarcinoma, GBM: Glioblastoma multiforme, LGG: Brain lower grade glioma, 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, LUAD: Lung adenocarcinoma, LUSC: Lung squamous cell carcinoma, OV: Ovarian serous cystadenocarcinoma, PAAD: Pancreatic adenocarcinoma, PRAD: Prostate adenocarcinoma, SKCM: Skin cutaneous melanoma, STAD: Stomach adenocarcinoma, THCA: Thyroid carcinoma, UCEC: Uterine corpus endometrial carcinoma.

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Protein structure related information for TBP

Relative protein structure stability change (ΔΔE) using Mupro 1.1
Mupro score denotes assessment of the effect of mutations on thermodynamic stability.
(ΔΔE<0: mutation decreases stability, ΔΔE>0: mutation increases stability)

: nsSNV at non-LBS

: nsSNV at LBS

nsSNVs sorted by the relative stability change of protein structure by each mutation
Blue: mutations of positive stability change. and red : the most recurrent mutation for this gene.

LBS	AAchange of nsSNV	Relative stability change
R196	R196Q	-1.1497506
K225	A224V	-0.8687637
G223	A224V	-0.8687637
L212	A211T	-0.68731417
T210	A211T	-0.68731417
T171	S170F	-0.58792241
V169	S170F	-0.58792241

(MuPro1.1: Jianlin Cheng et al., Prediction of Protein Stability Changes for Single-Site Mutations Using Support Vector Machines, PROTEINS: Structure, Function, and Bioinformatics. 2006, 62:1125-1132)

Structure image for TBP from PDB

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Differential gene expression and gene-gene network for TBP

Differential gene expression between mutated and non-mutated LBS samples in all 16 major cancer types

Differential co-expressed gene network based on protein-protein interaction data (CePIN)

* Left PPI network was created from samples with mutations in the LBS of TBP and the right PPI network was created from samples without mutations in the LBS of TBP. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.

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Phenotype information for TBP

Gene level disease information (DisGeNet)

Disease ID	Disease name	# PubMed	Association type
umls:C1846707	Spinocerebellar Ataxia 17	5	Biomarker, GeneticVariation

Mutation level pathogenic information (ClinVar annotation)

Allele ID

AA change

Clinical significance

Origin

Phenotype IDs

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Pharmacological information for TBP

Gene expression profile of anticancer drug treated cell-lines (CCLE)
Heatmap showing the correlation between gene expression and drug response across all the cell-lines. We chose the top 20 among 138 drugs.We used Pearson's correlation coefficient.

Drug information targeting mutLBSgene (Approved drugs only)

Drug status

DrugBank ID

Name

Type

Drug structure

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of TBP go to BioLip

Ligand ID	Ligand short name	Ligand long name	PDB ID	PDB name	mutLBS
NUC		Nucleic Acids	1c9b	F	V169 L212
NUC		Nucleic Acids	1c9b	B	V169 R196 T210 L212 G223
NUC		Nucleic Acids	1c9b	F	V169 R196 T210 L212 G223
NUC		Nucleic Acids	1c9b	J	V169 R196 T210 L212 G223
NUC		Nucleic Acids	1c9b	R	V169 R196 T210 L212 G223
NUC		Nucleic Acids	1nvp	A	V169 R196 T210 L212 G223
NUC		Nucleic Acids	4roc	B	V169 R196 T210 L212 G223
NUC		Nucleic Acids	4rod	B	V169 R196 T210 L212 G223
NUC		Nucleic Acids	4roe	B	V169 R196 T210 L212 G223
NUC		Nucleic Acids	1c9b	R	V169 T171
NUC		Nucleic Acids	4roc	B	V169 T171
NUC		Nucleic Acids	4rod	B	V169 T171
NUC		Nucleic Acids	1c9b	B	V169 T171 L212
NUC		Nucleic Acids	1c9b	J	V169 T171 L212
NUC		Nucleic Acids	1c9b	N	V169 T171 L212
NUC		Nucleic Acids	1nvp	A	V169 T171 L212
NUC		Nucleic Acids	4roe	B	V169 T171 L212
NUC		Nucleic Acids	1c9b	N	V169 T210 L212

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Conservation information for LBS of TBP

Multiple alignments for P20226 in multiple species

LBS	AA sequence	# species	Species
A198	NPKRFAAVIMR	8	Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus, Gallus gallus, Bos taurus, Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Schizosaccharomyces pombe (strain 972 / ATCC 24843)
F197	YNPKRFAAVIM	8	Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus, Gallus gallus, Bos taurus, Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Schizosaccharomyces pombe (strain 972 / ATCC 24843)
F214	TTALIFSSGKM	6	Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus, Gallus gallus, Bos taurus
F214	TTALIFASGKM	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
F214	STALIFASGKM	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
F288	YEPELFPGLIY	8	Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus, Gallus gallus, Bos taurus, Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Schizosaccharomyces pombe (strain 972 / ATCC 24843)
F305	IVLLIFVSGKV	6	Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus, Gallus gallus, Bos taurus
F305	IVLLIFVSGKI	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
F305	VVLLIFVSGKI	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G223	KMVCTGAKSEE	6	Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus, Gallus gallus, Bos taurus
G223	KMVVTGAKSED	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
G223	KMVVLGGKSED	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G314	KVVLTGAKVRA	5	Homo sapiens, Xenopus tropicalis, Mus musculus, Gallus gallus, Bos taurus
G314	KVVLTGAKVRG	1	Danio rerio
G314	KIVLTGAKQRE	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
G314	KIVLTGAKVRE	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
I201	RFAAVIMRIRE	8	Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus, Gallus gallus, Bos taurus, Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Schizosaccharomyces pombe (strain 972 / ATCC 24843)
I292	LFPGLIYRMIK	6	Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus, Gallus gallus, Bos taurus
I292	LFPGLIYRMVK	2	Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Schizosaccharomyces pombe (strain 972 / ATCC 24843)
K218	IFSSGKMVCTG	6	Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus, Gallus gallus, Bos taurus
K218	IFASGKMVVTG	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
K218	IFASGKMVVLG	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
K225	VCTGAKSEEQS	6	Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus, Gallus gallus, Bos taurus
K225	VVTGAKSEDDS	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
K225	VVLGGKSEDDS	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
K309	IFVSGKVVLTG	6	Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus, Gallus gallus, Bos taurus
K309	IFVSGKIVLTG	2	Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L212	PRTTALIFSSG	6	Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus, Gallus gallus, Bos taurus
L212	PKTTALIFASG	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
L212	PKSTALIFASG	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L287	SYEPELFPGLI	8	Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus, Gallus gallus, Bos taurus, Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L303	PRIVLLIFVSG	6	Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus, Gallus gallus, Bos taurus
L303	PKIVLLIFVSG	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
L303	PKVVLLIFVSG	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
N167	VPQLQNIVSTV	6	Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus, Gallus gallus, Bos taurus
N167	VPTLQNIVATV	2	Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Schizosaccharomyces pombe (strain 972 / ATCC 24843)
N257	DFKIQNMVGSC	6	Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus, Gallus gallus, Bos taurus
N257	DFKIQNIVGSC	2	Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Schizosaccharomyces pombe (strain 972 / ATCC 24843)
P289	EPELFPGLIYR	8	Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus, Gallus gallus, Bos taurus, Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Q166	IVPQLQNIVST	6	Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus, Gallus gallus, Bos taurus
Q166	IVPTLQNIVAT	2	Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Q256	LDFKIQNMVGS	6	Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus, Gallus gallus, Bos taurus
Q256	TDFKIQNIVGS	2	Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R196	EYNPKRFAAVI	8	Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus, Gallus gallus, Bos taurus, Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R203	AAVIMRIREPR	6	Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus, Gallus gallus, Bos taurus
R203	AAVIMRIREPK	2	Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R208	RIREPRTTALI	6	Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus, Gallus gallus, Bos taurus
R208	RIREPKTTALI	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
R208	RIREPKSTALI	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R294	PGLIYRMIKPR	6	Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus, Gallus gallus, Bos taurus
R294	PGLIYRMVKPK	2	Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R299	RMIKPRIVLLI	6	Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus, Gallus gallus, Bos taurus
R299	RMVKPKIVLLI	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
R299	RMVKPKVVLLI	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S216	ALIFSSGKMVC	6	Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus, Gallus gallus, Bos taurus
S216	ALIFASGKMVV	2	Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S261	QNMVGSCDVKF	6	Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus, Gallus gallus, Bos taurus
S261	QNIVGSCDVKF	2	Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S307	LLIFVSGKVVL	6	Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus, Gallus gallus, Bos taurus
S307	LLIFVSGKIVL	2	Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Schizosaccharomyces pombe (strain 972 / ATCC 24843)
T171	QNIVSTVNLGC	6	Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus, Gallus gallus, Bos taurus
T171	QNIVATVTLGC	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
T171	QNIVATVNLDC	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
T210	REPRTTALIFS	6	Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus, Gallus gallus, Bos taurus
T210	REPKTTALIFA	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
T210	REPKSTALIFA	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
T222	GKMVCTGAKSE	6	Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus, Gallus gallus, Bos taurus
T222	GKMVVTGAKSE	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
T222	GKMVVLGGKSE	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
T313	GKVVLTGAKVR	6	Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus, Gallus gallus, Bos taurus
T313	GKIVLTGAKQR	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
T313	GKIVLTGAKVR	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
V169	QLQNIVSTVNL	6	Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus, Gallus gallus, Bos taurus
V169	TLQNIVATVTL	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
V169	TLQNIVATVNL	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
V220	SSGKMVCTGAK	6	Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus, Gallus gallus, Bos taurus
V220	ASGKMVVTGAK	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
V220	ASGKMVVLGGK	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
V259	KIQNMVGSCDV	6	Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus, Gallus gallus, Bos taurus
V259	KIQNIVGSCDV	2	Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Schizosaccharomyces pombe (strain 972 / ATCC 24843)
V301	IKPRIVLLIFV	6	Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus, Gallus gallus, Bos taurus
V301	VKPKIVLLIFV	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
V301	VKPKVVLLIFV	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
V311	VSGKVVLTGAK	6	Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus, Gallus gallus, Bos taurus
V311	VSGKIVLTGAK	2	Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Schizosaccharomyces pombe (strain 972 / ATCC 24843)