Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

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	Gene Summary
	Phenotypic Information (metabolism pathway, cancer, disease, phenome)
	Mutations : SVs, CNVs, SNVs
	Gene expression: GE, Protein, DEGE, CNV vs GE
	Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG
	Pharmacological Information: Drug-Gene Network
	Cross referenced IDs

Gene Summary for EIF3H

Basic gene info.	Gene symbol	EIF3H
	Gene name	eukaryotic translation initiation factor 3, subunit H
	Synonyms	EIF3S3\|eIF3-gamma\|eIF3-p40
	Cytomap	UCSC genome browser: 8q24.11
	Genomic location	chr8 :117657054-117768062
	Type of gene	protein-coding
	RefGenes	NM_003756.2,
	Ensembl id	ENSG00000147677
	Description	eIF-3-gammaeIF3 p40 subuniteukaryotic translation initiation factor 3 subunit 3eukaryotic translation initiation factor 3 subunit Heukaryotic translation initiation factor 3, subunit 2 (beta, 36kD)eukaryotic translation initiation factor 3, subunit 3
	Modification date	20141207
dbXrefs	MIM : 603912
	HGNC : HGNC
	Ensembl : ENSG00000147677
	HPRD : 04885
Protein	UniProt: O15372 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_EIF3H
	BioGPS: 8667
	Gene Expression Atlas: ENSG00000147677
	The Human Protein Atlas: ENSG00000147677
Pathway	NCI Pathway Interaction Database: EIF3H
	KEGG: EIF3H
	REACTOME: EIF3H
	ConsensusPathDB
	Pathway Commons: EIF3H
Metabolism	MetaCyc: EIF3H
	HUMANCyc: EIF3H
Regulation	Ensembl's Regulation: ENSG00000147677
	miRBase: chr8 :117,657,054-117,768,062
	TargetScan: NM_003756
	cisRED: ENSG00000147677
Context	iHOP: EIF3H
	cancer metabolism search in PubMed: EIF3H
	UCL Cancer Institute: EIF3H
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of EIF3H in cancer cell metabolism	1. Pittman AM, Naranjo S, Jalava SE, Twiss P, Ma Y, et al. (2010) Allelic variation at the 8q23.3 colorectal cancer risk locus functions as a cis-acting regulator of EIF3H. PLoS Genet 6: e1001126. doi: 10.1371/journal.pgen.1001126. pmid: 2940760. go to article 2. Lee JP, Brauweiler A, Rudolph M, Hooper JE, Drabkin HA, et al. (2010) The TRC8 ubiquitin ligase is sterol regulated and interacts with lipid and protein biosynthetic pathways. Mol Cancer Res 8: 93-106. doi: 10.1158/1541-7786.MCR-08-0491. pmid: 3086825. go to article 3. Zhang L, Smit-McBride Z, Pan X, Rheinhardt J, Hershey JW (2008) An oncogenic role for the phosphorylated h-subunit of human translation initiation factor eIF3. J Biol Chem 283: 24047-24060. doi: 10.1074/jbc.M800956200. pmid: 2527115. go to article

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Phenotypic Information for EIF3H(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: EIF3H
	Familial Cancer Database: EIF3H

* This gene is included in those cancer gene databases.

						.
Oncogene ¹	Tumor Suppressor gene ²	Cancer Gene Census ³	CancerGenes ⁴	Network of Cancer Gene ⁵	Significant driver gene in	Therapeutic Vulnerabilities in Cancer¹

cf) number; DB name
1 Oncogene; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
2 Tumor Suppressor gene; https://bioinfo.uth.edu/TSGene/,
3 Cancer Gene Census; http://www.nature.com/nrc/journal/v4/n3/abs/nrc1299.html,
4 CancerGenes; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
5 Network of Cancer Gene; http://ncg.kcl.ac.uk/index.php,
1Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_PROTEINS

Others
OMIM	603912; gene.
Orphanet
Disease	KEGG Disease: EIF3H
	MedGen: EIF3H (Human Medical Genetics with Condition)
	ClinVar: EIF3H
Phenotype	MGI: EIF3H (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: EIF3H

Mutations for EIF3H

* Under tables are showing count per each tissue to give us broad intuition about tissue specific mutation patterns.You can go to the detailed page for each mutation database's web site.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- For Inter-chromosomal Variations

* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.

- For Intra-chromosomal Variations

* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
pancreas	EIF3H	chr8	117718770	117718790	EIF3H	chr8	117725072	117725092

cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows EIF3H related fusion information.

ID	Head Gene						Tail Gene
Accession	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a
BE090337	FAM129B	12	105	9	130279206	130279301	EIF3H	105	621	8	117668154	117738411
XX000007	CYTH1	1	22	17	76778284	76778305	EIF3H	22	121	8	117767938	117768037
AI861912	EIF3H	9	115	8	117657071	117657177	NRL	114	431	14	24584067	24584383
CV398950	EIF3H	13	139	8	117723321	117723446	EIF3H	138	222	8	117723217	117723301
AW372241	EIF3H	14	222	8	117671093	117738339	EIF3H	213	277	8	117669490	117669554
AA715462	EIF3H	6	195	8	117668129	117669527	EIF3H	191	303	8	117661089	117668130
AA648095	EIF3H	1	179	8	117668129	117669516	EIF3H	175	287	8	117661089	117668130
AW965128	EIF3H	1	369	8	117658734	117668233	EIF3H	365	633	8	117668108	117671083
AI302586	EIF3H	8	324	8	117657074	117658757	ACSL5	319	428	10	114177613	114181373
DA942074	EIF3H	1	299	8	117658793	117668222	CMC1	299	525	3	28287324	28287550

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

LOSS (# sample)

cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract)

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SNV Counts per Each Loci in COSMIC data : go to COSMIC point mutation

: Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=4

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=24)	Stat. for Synonymous SNVs (# total SNVs=7)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=0)
There's no deleted snv.	There's no inserted snv.

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Top 10 SNVs Having the Most Samples in COSMIC data

* When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site,primary_histology,mutation(aa),pubmedID.

GRCh37 position	Mutation(aa)	Unique sampleID count
chr8:117738327-117738327	p.E73K	3
chr8:117658833-117658833	p.R280C	3
chr8:117671091-117671091	p.Y140N	1
chr8:117738326-117738326	p.E73A	1
chr8:117658772-117658772	p.D300V	1
chr8:117668098-117668098	p.S235I	1
chr8:117671101-117671101	p.S136S	1
chr8:117658786-117658786	p.P295P	1
chr8:117668111-117668111	p.L231I	1
chr8:117671117-117671117	p.R131L	1

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SNV Counts per Each Loci in TCGA data

: non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=2

Point Mutation/ Tissue ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample				3	1		4					3	3				1	5	1	3
# mutation				3	1		4					3	3				1	5	1	3
nonsynonymous SNV				1	1							2	2				1	3	1	3
synonymous SNV				2			4					1	1					2

cf) Tissue ID; Tissue type (1; BLCA[Bladder Urothelial Carcinoma], 2; BRCA[Breast invasive carcinoma], 3; CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], 4; COAD[Colon adenocarcinoma], 5; GBM[Glioblastoma multiforme], 6; Glioma Low Grade, 7; HNSC[Head and Neck squamous cell carcinoma], 8; KICH[Kidney Chromophobe], 9; KIRC[Kidney renal clear cell carcinoma], 10; KIRP[Kidney renal papillary cell carcinoma], 11; LAML[Acute Myeloid Leukemia], 12; LUAD[Lung adenocarcinoma], 13; LUSC[Lung squamous cell carcinoma], 14; OV[Ovarian serous cystadenocarcinoma ], 15; PAAD[Pancreatic adenocarcinoma], 16; PRAD[Prostate adenocarcinoma], 17; SKCM[Skin Cutaneous Melanoma], 18:STAD[Stomach adenocarcinoma], 19:THCA[Thyroid carcinoma], 20:UCEC[Uterine Corpus Endometrial Carcinoma])

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Top 10 SNVs Having the Most Samples in TCGA data

* We represented just top 10 SNVs. When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site, primary_histology, mutation(aa), pubmedID.

Genomic Position	Mutation(aa)	Unique sampleID count
chr8:117658786	p.P295P	2
chr8:117671117	p.S3P	1
chr8:117658799	p.R291L	1
chr8:117671153	p.N285N	1
chr8:117658816	p.Q282Q	1
chr8:117671196	p.L231I	1
chr8:117658825	p.K227K	1
chr8:117738277	p.L164L	1
chr8:117668111	p.I151M	1
chr8:117738327	p.L150L	1

Other DBs for Point Mutations

Point Mutation Table of Ensembl: go to Ensembl variation table

Mutation of cBioPortal: go to cBioPortal's Cross-cancer alteration summary

Copy Number for EIF3H in TCGA

* Copy number data were extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered on Jan-05-2015. Function ProcessCNAData in TCGA-Assembler package was used to obtain gene-level copy number value which is calculated as the average copy number of the genomic region of a gene.

cf) Tissue ID[Tissue type]: BLCA[Bladder Urothelial Carcinoma], BRCA[Breast invasive carcinoma], CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], COAD[Colon adenocarcinoma], GBM[Glioblastoma multiforme], Glioma Low Grade, 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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Gene Expression for EIF3H

Gene Expression in Cancer Cell-lines (CCLE)

* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data.

Differential Gene Expression in Primary Tumors (TCGA)

* Normalized gene expression data of RNASeqV2 was extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered at Jan-05-2015. Only eight cancer types have enough normal control samples for differential expression analysis.
(t test, adjusted p<0.05 (using Benjamini-Hochberg FDR))

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CNV vs Gene Expression Plot

* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types

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Gene-Gene Network Information

Co-Expressed gene's network Plot

* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown.
Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene

: Open all plots for all cancer types


C8orf76,COPS5,DCAF13,EBAG9,EIF3E,EIF3H,RMDN1, IGFBP5,MRPL13,MRPS28,NSMCE2,POLR2K,RAD21,TMEM70, TRPS1,EMC2,TTTY2,UTP23,WDYHV1,ZFAND1,ZNF706	BTF3,C11orf1,CCT4,DPH5,EEF1A1,EIF3H,EIF3M, RPL15,RPL22,RPL23A,RPL26,RPL30,RPL35A,RPL38, RPL41,RPL6,RPS13,RPS15A,RPS29,RPS3A,RSL24D1

ANKRD46,AZIN1,NDUFAF6,C8orf59,COPS5,DCAF13,DPY19L4, EBAG9,EIF3E,EIF3H,MED30,MTERF3,PABPC1,RPL30, RPL8,RPS20,SLC25A32,TATDN1,EMC2,UTP23,ZFAND1	ATP5G2,C6orf48,CLNS1A,EEF1A1,EEF1G,EIF3D,EIF3H, EIF3L,GNB2L1,NACA,RPL10,RPL14,RPL23A,RPL30, RPL3,RPL38,RPL6,RPS23,RPS25,RSL1D1,TOMM20

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

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Pharmacological Information for EIF3H

There's no related Drug.

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Cross referenced IDs for EIF3H

* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section

: Open all cross reference information