Mutation Analysis (MutSig v2.0)

Lung Adenocarcinoma (Primary solid tumor)

23 May 2013 | analyses__2013_05_23

Maintainer Information

Citation Information

Maintained by Dan DiCara (Broad Institute)

Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Mutation Analysis (MutSig v2.0). Broad Institute of MIT and Harvard. doi:10.7908/C1VD6WHQ

- Overview

+ Introduction

- Summary

MAF used for this analysis:LUAD-TP.final_analysis_set.maf
Significantly mutated genes (q ≤ 0.1): 129
Mutations seen in COSMIC: 516
Significantly mutated genes in COSMIC territory: 23
Genes with clustered mutations (≤ 3 aa apart): 385
Significantly mutated genesets: 16
Significantly mutated genesets: (excluding sig. mutated genes):0

Mutation Preprocessing

Read 229 MAFs of type "Broad"
Total number of mutations in input MAFs: 251233
After removing 79 mutations outside chr1-24: 251154
After removing 1211 blacklisted mutations: 249943
After removing 144408 noncoding mutations: 105535
After collapsing adjacent/redundant mutations: 94095

Mutation Filtering

Number of mutations before filtering: 94095
After removing 1293 mutations outside gene set: 92802
After removing 182 mutations outside category set: 92620

- Results

+ Breakdown of Mutations by Type

type	count
Frame_Shift_Del	1515
Frame_Shift_Ins	584
In_Frame_Del	183
In_Frame_Ins	22
Missense_Mutation	60561
Nonsense_Mutation	4805
Nonstop_Mutation	58
Silent	22884
Splice_Site	1874
Translation_Start_Site	134
Total	92620

+ Breakdown of Mutation Rates by Category Type

category	n	N	rate	rate_per_mb	relative_rate	exp_ns_s_ratio
*CpG->A	8888	379287204	0.000023	23	2.3	2.1
*Cp(A/C/T)->A	22068	3108508517	7.1e-06	7.1	0.7	5
C->(T/G)	18984	3487795721	5.4e-06	5.4	0.53	2.8
A->mut	10752	3354933814	3.2e-06	3.2	0.31	3.9
indel+null	8896	6842729535	1.3e-06	1.3	0.13	NaN
double_null	148	6842729535	2.2e-08	0.022	0.0021	NaN
Total	69736	6842729535	1e-05	10	1	3.5

+ Target Coverage for Each Individual

+ Distribution of Mutation Counts, Coverage, and Mutation Rates Across Samples

+ CoMut Plot

+ Significantly Mutated Genes

Column Descriptions:

N = number of sequenced bases in this gene across the individual set
n = number of (nonsilent) mutations in this gene across the individual set
npat = number of patients (individuals) with at least one nonsilent mutation
nsite = number of unique sites having a non-silent mutation
nsil = number of silent mutations in this gene across the individual set
n1 = number of nonsilent mutations of type: *CpG->A
n2 = number of nonsilent mutations of type: *Cp(A/C/T)->A
n3 = number of nonsilent mutations of type: C->(T/G)
n4 = number of nonsilent mutations of type: A->mut
n5 = number of nonsilent mutations of type: indel+null
n6 = number of nonsilent mutations of type: double_null
p_classic = p-value for the observed amount of nonsilent mutations being elevated in this gene
p_ns_s = p-value for the observed nonsilent/silent ratio being elevated in this gene
p_cons = p-value for enrichment of mutations at evolutionarily most-conserved sites in gene
p_joint = p-value for clustering + conservation
p = p-value (overall)
q = q-value, False Discovery Rate (Benjamini-Hochberg procedure)

Table 3. Get Full Table A Ranked List of Significantly Mutated Genes. Number of significant genes found: 129. Number of genes displayed: 35. Click on a gene name to display its stick figure depicting the distribution of mutations and mutation types across the chosen gene (this feature may not be available for all significant genes).

rank	gene	description	N	n	npat	nsite	nsil	n1	n2	n3	n4	n5	n6	p_classic	p_ns_s	p_cons	p_joint	p	q
1	STK11	serine/threonine kinase 11	199230	21	20	20	0	0	4	2	4	11	0	9.44e-15	0.01	0.037	0.0023	8.88e-16	3.62e-12
2	TP53	tumor protein p53	288082	128	119	106	2	8	22	31	18	49	0	2.11e-15	1.2e-10	9.2e-06	0	<1.00e-15	<3.62e-12
3	KRAS	v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog	161903	60	60	6	0	0	47	10	3	0	0	<1.00e-15	0.002	0	0	<1.00e-15	<3.62e-12
4	EGFR	epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)	918061	33	27	19	7	2	5	4	13	9	0	0.00150	0.65	0.0029	0	<1.00e-15	<3.62e-12
5	CDKN2A	cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4)	226023	14	14	14	1	0	1	4	4	5	0	5.30e-09	0.26	4e-07	0	<1.00e-15	<3.62e-12
6	KEAP1	kelch-like ECH-associated protein 1	418841	39	39	37	0	4	8	13	10	4	0	7.55e-15	0.000026	0.026	0.021	5.77e-15	1.74e-11
7	NAV3	neuron navigator 3	1659792	67	52	67	4	4	36	16	6	4	1	9.77e-14	0.0026	0.75	0.6	1.85e-12	4.78e-09
8	MAGEC1	melanoma antigen family C, 1	774020	39	33	38	2	2	14	13	7	3	0	9.86e-13	0.0051	0.57	1	2.82e-11	6.39e-08
9	CDH10	cadherin 10, type 2 (T2-cadherin)	552119	52	41	52	8	4	27	12	1	8	0	3.19e-12	0.27	0.73	1	8.77e-11	1.76e-07
10	MUC7	mucin 7, secreted	261518	19	17	19	1	0	8	3	5	3	0	2.79e-10	0.091	0.66	0.11	7.76e-10	1.30e-06
11	TMTC1	transmembrane and tetratricopeptide repeat containing 1	543417	32	26	30	3	3	17	7	3	2	0	4.86e-11	0.055	0.19	0.64	7.88e-10	1.30e-06
12	OR4C16	olfactory receptor, family 4, subfamily C, member 16	214115	16	15	15	0	0	9	2	3	2	0	1.74e-09	0.035	0.28	0.021	9.10e-10	1.37e-06
13	ZNF676	zinc finger protein 676	407391	21	20	20	2	0	9	9	0	3	0	2.03e-08	0.27	0.25	0.016	7.54e-09	1.05e-05
14	EPHA6	EPH receptor A6	755242	33	30	33	4	3	17	7	3	3	0	7.56e-09	0.17	0.02	0.071	1.20e-08	1.55e-05
15	RIMS2	regulating synaptic membrane exocytosis 2	994318	45	39	45	4	4	16	10	8	7	0	3.46e-09	0.051	0.24	0.26	1.96e-08	2.37e-05
16	OR2L3	olfactory receptor, family 2, subfamily L, member 3	215947	16	15	16	2	1	9	2	4	0	0	1.81e-09	0.19	0.76	0.6	2.34e-08	2.64e-05
17	ELTD1	EGF, latrophilin and seven transmembrane domain containing 1	482503	20	20	20	0	0	4	4	8	4	0	1.36e-09	0.015	0.64	0.86	2.51e-08	2.67e-05
18	REG3A	regenerating islet-derived 3 alpha	125492	15	14	14	2	0	4	7	2	2	0	4.14e-09	0.25	0.63	0.53	4.57e-08	4.15e-05
19	CNBD1	cyclic nucleotide binding domain containing 1	238160	14	14	14	1	0	5	3	4	2	0	8.04e-09	0.32	0.071	0.28	4.66e-08	4.15e-05
20	REG1B	regenerating islet-derived 1 beta (pancreatic stone protein, pancreatic thread protein)	119309	15	14	15	2	1	7	1	3	3	0	1.22e-08	0.39	0.064	0.18	4.68e-08	4.15e-05
21	CD5L	CD5 molecule-like	244572	15	15	15	1	3	3	0	5	4	0	1.26e-08	0.1	0.11	0.18	4.82e-08	4.15e-05
22	OR2T4	olfactory receptor, family 2, subfamily T, member 4	240679	18	17	18	2	1	7	8	2	0	0	1.02e-08	0.071	0.92	0.28	5.90e-08	4.86e-05
23	GABRB3	gamma-aminobutyric acid (GABA) A receptor, beta 3	314646	18	17	18	1	3	6	4	4	1	0	1.64e-08	0.038	0.75	0.2	6.65e-08	5.23e-05
24	TRIM58	tripartite motif-containing 58	254648	15	15	15	2	1	3	3	5	3	0	5.26e-08	0.19	0.26	0.18	1.79e-07	0.000135
25	BAGE2	B melanoma antigen family, member 2	79234	9	9	9	0	0	4	2	1	2	0	2.07e-08	0.12	0.48	0.89	3.45e-07	0.000243
26	OR4A5	olfactory receptor, family 4, subfamily A, member 5	218008	13	12	13	0	1	4	3	4	1	0	3.65e-08	0.035	0.72	0.52	3.54e-07	0.000243
27	NRAS	neuroblastoma RAS viral (v-ras) oncogene homolog	134194	4	4	2	1	0	1	0	3	0	0	0.0161	0.71	0.21	1.2e-06	3.62e-07	0.000243
28	SPRR3	small proline-rich protein 3	117706	7	7	4	0	0	1	0	1	5	0	1.17e-05	0.62	0.074	0.0019	4.08e-07	0.000264
29	BRAF	v-raf murine sarcoma viral oncogene homolog B1	510899	17	17	12	1	1	7	2	5	2	0	5.89e-07	0.096	0.43	0.061	6.56e-07	0.000409
30	OR2L8	olfactory receptor, family 2, subfamily L, member 8	215947	15	13	13	2	1	8	3	2	1	0	3.09e-07	0.23	0.26	0.12	6.89e-07	0.000415
31	CRIPAK	cysteine-rich PAK1 inhibitor	280983	15	13	8	4	2	1	3	0	9	0	4.34e-05	0.9	0.13	0.0015	1.16e-06	0.000676
32	PABPC3	poly(A) binding protein, cytoplasmic 3	435100	12	12	12	1	1	5	1	5	0	0	0.000125	0.22	0.18	0.00068	1.47e-06	0.000829
33	LRRIQ3	leucine-rich repeats and IQ motif containing 3	435787	17	15	16	1	1	3	3	5	5	0	1.75e-07	0.26	0.92	1	2.89e-06	0.00158
34	ZNF804A	zinc finger protein 804A	834934	44	38	44	5	0	26	8	4	6	0	1.79e-07	0.31	0.7	1	2.96e-06	0.00158
35	C18orf34	chromosome 18 open reading frame 34	606392	23	21	23	2	0	11	4	6	2	0	2.68e-07	0.27	0.64	1	4.33e-06	0.00224

+ COSMIC analyses

In this analysis, COSMIC is used as a filter to increase power by restricting the territory of each gene. Cosmic version: v48.

Table 4. Get Full Table Significantly mutated genes (COSMIC territory only). To access the database please go to: COSMIC. Number of significant genes found: 23. Number of genes displayed: 10

rank	gene	description	n	cos	n_cos	N_cos	cos_ev	p	q
1	LRP1B	low density lipoprotein-related protein 1B (deleted in tumors)	148	18	8	4122	8	1.8e-13	8e-10
2	KRAS	v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog	60	52	60	11908	797017	4.7e-13	1.1e-09
3	BRAF	v-raf murine sarcoma viral oncogene homolog B1	17	89	12	20381	28944	7.4e-13	1.1e-09
4	STK11	serine/threonine kinase 11	21	130	14	29770	27	9.9e-13	1.1e-09
5	EGFR	epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)	33	293	29	67097	10294	1.5e-12	1.1e-09
6	TP53	tumor protein p53	128	356	122	81524	18207	1.6e-12	1.1e-09
7	CDKN2A	cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4)	14	332	14	76028	259	1.7e-12	1.1e-09
8	MET	met proto-oncogene (hepatocyte growth factor receptor)	12	34	6	7786	64	3.2e-10	1.8e-07
9	PIK3CA	phosphoinositide-3-kinase, catalytic, alpha polypeptide	11	220	9	50380	3946	4.3e-09	2.2e-06
10	NF1	neurofibromin 1 (neurofibromatosis, von Recklinghausen disease, Watson disease)	30	285	9	65265	13	3.9e-08	0.000017

Note:

n - number of (nonsilent) mutations in this gene across the individual set.

cos = number of unique mutated sites in this gene in COSMIC

n_cos = overlap between n and cos.

N_cos = number of individuals times cos.

cos_ev = total evidence: number of reports in COSMIC for mutations seen in this gene.

p = p-value for seeing the observed amount of overlap in this gene)

q = q-value, False Discovery Rate (Benjamini-Hochberg procedure)

+ Clustered Mutations

num	gene	desc	n	nmuts0	nmuts3	nmuts12	npairs0	npairs3	npairs12
6691	KRAS	v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog	60	1382	1488	1488	1382	1488	1488
13095	TP53	tumor protein p53	128	53	200	636	53	200	636
3863	EGFR	epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)	33	39	60	60	39	60	60
9562	PIK3CA	phosphoinositide-3-kinase, catalytic, alpha polypeptide	11	6	10	11	6	10	11
8466	NRAS	neuroblastoma RAS viral (v-ras) oncogene homolog	4	6	6	6	6	6	6
13299	TSHZ3	teashirt zinc finger homeobox 3	39	5	14	29	5	14	29
1224	BRAF	v-raf murine sarcoma viral oncogene homolog B1	17	5	9	13	5	9	13
6429	KEAP1	kelch-like ECH-associated protein 1	39	4	17	44	4	17	44
14417	ZNF536	zinc finger protein 536	54	4	11	28	4	11	28
2388	CDH18	cadherin 18, type 2	32	4	11	23	4	11	23

+ Geneset Analyses

Table 6. Get Full Table A Ranked List of Significantly Mutated Genesets. (Source: MSigDB GSEA Cannonical Pathway Set).Number of significant genesets found: 16. Number of genesets displayed: 10

rank	geneset	description	genes	N_genes	mut_tally	N	n	npat	nsite	nsil	n1	n2	n3	n4	n5	p_ns_s	p	q
1	P53PATHWAY	p53 induces cell cycle arrest or apoptosis under conditions of DNA damage.	APAF1, ATM, BAX, BCL2, CCND1, CCNE1, CDK2, CDK4, CDKN1A, E2F1, GADD45A, MDM2, PCNA, RB1, TIMP3, TP53	16	APAF1(8), ATM(22), BAX(1), BCL2(1), CCND1(2), CCNE1(3), CDK2(4), CDK4(2), CDKN1A(1), E2F1(3), GADD45A(1), MDM2(2), PCNA(1), RB1(13), TP53(128)	6266585	192	143	169	16	16	37	42	29	68	1.9e-06	<1.00e-15	<1.54e-13
2	P53HYPOXIAPATHWAY	Hypoxia induces p53 accumulation and consequent apoptosis with p53-mediated cell cycle arrest, which is present under conditions of DNA damage.	ABCB1, AKT1, ATM, BAX, CDKN1A, CPB2, CSNK1A1, CSNK1D, FHL2, GADD45A, HIC1, HIF1A, HSPA1A, HSPCA, IGFBP3, MAPK8, MDM2, NFKBIB, NQO1, TP53	19	ABCB1(20), ATM(22), BAX(1), CDKN1A(1), CPB2(4), CSNK1A1(1), CSNK1D(2), GADD45A(1), HIF1A(1), IGFBP3(2), MAPK8(3), MDM2(2), NQO1(3), TP53(128)	7172280	191	138	167	18	17	40	45	27	62	0.000012	<1.00e-15	<1.54e-13
3	PLK3PATHWAY	Active Plk3 phosphorylates CDC25c, blocking the G2/M transition, and phosphorylates p53 to induce apoptosis.	ATM, ATR, CDC25C, CHEK1, CHEK2, CNK, TP53, YWHAH	7	ATM(22), ATR(17), CDC25C(3), CHEK1(6), CHEK2(2), TP53(128)	5517526	178	136	155	7	10	35	48	28	57	1e-08	<1.00e-15	<1.54e-13
4	TERTPATHWAY	hTERC, the RNA subunit of telomerase, and hTERT, the catalytic protein subunit, are required for telomerase activity and are overexpressed in many cancers.	HDAC1, MAX, MYC, SP1, SP3, TP53, WT1, ZNF42	7	HDAC1(3), MAX(3), SP1(1), SP3(4), TP53(128), WT1(8)	2427858	147	122	125	10	9	29	35	21	53	1.2e-06	<1.00e-15	<1.54e-13
5	SA_G1_AND_S_PHASES	Cdk2, 4, and 6 bind cyclin D in G1, while cdk2/cyclin E promotes the G1/S transition.	ARF1, ARF3, CCND1, CDK2, CDK4, CDKN1A, CDKN1B, CDKN2A, CFL1, E2F1, E2F2, MDM2, NXT1, PRB1, TP53	15	ARF3(1), CCND1(2), CDK2(4), CDK4(2), CDKN1A(1), CDKN1B(3), CDKN2A(14), E2F1(3), MDM2(2), NXT1(1), PRB1(3), TP53(128)	2958909	164	125	142	8	15	29	38	24	58	1.1e-09	1.44e-15	1.78e-13
6	RNAPATHWAY	dsRNA-activated protein kinase phosphorylates elF2a, which generally inhibits translation, and activates NF-kB to provoke inflammation.	CHUK, DNAJC3, EIF2S1, EIF2S2, MAP3K14, NFKB1, NFKBIA, PRKR, RELA, TP53	9	CHUK(3), DNAJC3(3), MAP3K14(1), NFKB1(3), NFKBIA(1), TP53(128)	3372941	139	121	117	9	9	23	36	18	53	2.2e-06	2.44e-15	2.51e-13
7	ATMPATHWAY	The tumor-suppressing protein kinase ATM responds to radiation-induced DNA damage by blocking cell-cycle progression and activating DNA repair.	ABL1, ATM, BRCA1, CDKN1A, CHEK1, CHEK2, GADD45A, JUN, MAPK8, MDM2, MRE11A, NBS1, NFKB1, NFKBIA, RAD50, RAD51, RBBP8, RELA, TP53, TP73	19	ABL1(2), ATM(22), BRCA1(9), CDKN1A(1), CHEK1(6), CHEK2(2), GADD45A(1), JUN(1), MAPK8(3), MDM2(2), MRE11A(6), NFKB1(3), NFKBIA(1), RAD50(3), RAD51(1), RBBP8(3), TP53(128), TP73(4)	10278207	198	140	175	16	15	41	53	28	61	1.7e-06	3.11e-15	2.61e-13
8	RBPATHWAY	The ATM protein kinase recognizes DNA damage and blocks cell cycle progression by phosphorylating chk1 and p53, which normally inhibits Rb to allow G1/S transitions.	ATM, CDC2, CDC25A, CDC25B, CDC25C, CDK2, CDK4, CHEK1, MYT1, RB1, TP53, WEE1, YWHAH	12	ATM(22), CDC25A(4), CDC25B(1), CDC25C(3), CDK2(4), CDK4(2), CHEK1(6), MYT1(6), RB1(13), TP53(128), WEE1(3)	6070332	192	140	169	13	15	37	43	29	68	1.6e-07	3.66e-15	2.61e-13
9	TIDPATHWAY	On ligand binding, interferon gamma receptors stimulate JAK2 kinase to phosphorylate STAT transcription factors, which promote expression of interferon responsive genes.	DNAJA3, HSPA1A, IFNG, IFNGR1, IFNGR2, IKBKB, JAK2, LIN7A, NFKB1, NFKBIA, RB1, RELA, TIP-1, TNF, TNFRSF1A, TNFRSF1B, TP53, USH1C, WT1	18	IFNG(4), IFNGR1(3), IFNGR2(3), IKBKB(3), JAK2(4), LIN7A(2), NFKB1(3), NFKBIA(1), RB1(13), TNFRSF1B(1), TP53(128), USH1C(4), WT1(8)	6332308	177	133	155	16	15	35	41	21	65	1.8e-06	3.89e-15	2.61e-13
10	PMLPATHWAY	Ring-shaped PML nuclear bodies regulate transcription and are required co-activators in p53- and DAXX-mediated apoptosis.	CREBBP, DAXX, HRAS, PAX3, PML, PRAM-1, RARA, RB1, SIRT1, SP100, TNF, TNFRSF1A, TNFRSF1B, TNFRSF6, TNFSF6, TP53, UBL1	13	CREBBP(4), DAXX(6), HRAS(1), PAX3(6), PML(7), RARA(3), RB1(13), SIRT1(1), SP100(9), TNFRSF1B(1), TP53(128)	6622222	179	131	157	15	14	30	47	25	63	3.8e-07	4.33e-15	2.61e-13

Table 7. Get Full Table A Ranked List of Significantly Mutated Genesets (Excluding Significantly Mutated Genes). Number of significant genesets found: 0. Number of genesets displayed: 10

rank	geneset	description	genes	N_genes	mut_tally	N	n	npat	nsite	nsil	n1	n2	n3	n4	n5	n6	p_ns_s	p	q
1	FBW7PATHWAY	Cyclin E interacts with cell cycle checkpoint kinase cdk2 to allow transcription of genes required for S phase, including transcription of additional cyclin E.	CCNE1, CDC34, CDK2, CUL1, E2F1, FBXW7, RB1, SKP1A, TFDP1	8	CCNE1(3), CDC34(1), CDK2(4), CUL1(6), E2F1(3), FBXW7(4), RB1(13), TFDP1(3)	2895018	37	30	37	3	5	8	9	6	9	0	0.023	0.061	1
2	P27PATHWAY	p27 blocks the G1/S transition by inhibiting the checkpoint kinase cdk2/cyclin E and is inhibited by cdk2-mediated ubiquitination.	CCNE1, CDK2, CDKN1B, CKS1B, CUL1, E2F1, NEDD8, RB1, RBX1, SKP1A, SKP2, TFDP1, UBE2M	12	CCNE1(3), CDK2(4), CDKN1B(3), CUL1(6), E2F1(3), NEDD8(2), RB1(13), SKP2(4), TFDP1(3), UBE2M(1)	2978832	42	33	42	5	5	8	11	7	11	0	0.051	0.1	1
3	IL18PATHWAY	Pro-inflammatory IL-18 is activated in macrophages by caspase-1 cleavage and, in conjunction with IL-12, stimulates Th1 cell differentiation.	CASP1, IFNG, IL12A, IL12B, IL18, IL2	6	CASP1(2), IFNG(4), IL12A(3), IL2(5)	1033019	14	12	13	1	2	7	2	2	1	0	0.15	0.24	1
4	HSA00130_UBIQUINONE_BIOSYNTHESIS	Genes involved in ubiquinone biosynthesis	COQ2, COQ3, COQ5, COQ6, COQ7, ND1, ND2, ND3, ND4, ND4L, ND5, ND6, NDUFA12, NDUFA13, NDUFB11	8	COQ3(4), COQ5(5), COQ6(3), COQ7(1), NDUFA12(2), NDUFA13(4), NDUFB11(1)	1380412	20	14	20	2	5	5	5	1	4	0	0.082	0.32	1
5	BOTULINPATHWAY	Blockade of Neurotransmitter Relase by Botulinum Toxin	CHRM1, CHRNA1, SNAP25, STX1A, VAMP2	5	CHRM1(2), CHRNA1(7), SNAP25(4), STX1A(3)	1118665	16	13	16	3	5	3	5	1	2	0	0.2	0.35	1
6	HSA00902_MONOTERPENOID_BIOSYNTHESIS	Genes involved in monoterpenoid biosynthesis	CYP2C19, CYP2C9	2	CYP2C19(9), CYP2C9(3)	690893	12	11	12	3	2	3	3	2	2	0	0.54	0.4	1
7	SKP2E2FPATHWAY	E2F-1, a transcription factor that promotes the G1/S transition, is repressed by Rb and activated by cdk2/cyclin E.	CCNA1, CCNE1, CDC34, CDK2, CUL1, E2F1, RB1, SKP1A, SKP2, TFDP1	9	CCNA1(2), CCNE1(3), CDC34(1), CDK2(4), CUL1(6), E2F1(3), RB1(13), SKP2(4), TFDP1(3)	2974481	39	31	39	6	6	9	9	6	9	0	0.12	0.41	1
8	HSA00730_THIAMINE_METABOLISM	Genes involved in thiamine metabolism	LHPP, MTMR1, MTMR2, MTMR6, NFS1, PHPT1, THTPA, TPK1	8	LHPP(2), MTMR1(5), MTMR2(2), MTMR6(6), NFS1(4), PHPT1(1), TPK1(5)	2218323	25	20	25	3	1	9	6	7	1	1	0.15	0.55	1
9	HSA00031_INOSITOL_METABOLISM	Genes involved in inositol metabolism	ALDH6A1, TPI1	2	TPI1(6)	566088	6	5	6	0	0	3	2	1	0	0	0.24	0.6	1
10	HSA00830_RETINOL_METABOLISM	Genes involved in retinol metabolism	ALDH1A1, ALDH1A2, BCMO1, RDH5	4	ALDH1A1(3), ALDH1A2(9), BCMO1(4)	1334612	16	14	16	3	2	4	5	1	4	0	0.33	0.64	1

+ Methods & Data

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