Metabolite page

Showing information for HMDB0000098 ('xylose')

Metabolite information
HMDB ID	HMDB0000098
Synonyms	Acquired immune deficiency syndrome Acquired immunodeficiency syndrome Bacterial overgrowth Beautification product Carcinoma of the lung Cytoplasma D Xylose D-Xylopentose D-Xylopyranose D-[+]-Xylose D-xylo-Pentose Digestion Extracellular region Faecal Faeces Fecal Flora Gramineae Granulomatous colitis Hiv Legume Lung carcinoma Nephropathy Papilionoideae Pcp Personal hygiene Regional enteritis Renal disease Sbbos Sibo Small intestinal bacterial overgrowth Small intestinal bacterial overgrowth syndrome Soy Soya Soya bean Soybean Stool Toiletries Toiletry Wood sugar Xylomed Xylopyranose Xylose Xyloside [3R,4S,5R]-tetrahydro-2H-Pyran-2,3,4,5-tetrol xylo-Pfan
Chemical formula	C5H10O5
IUPAC name	(3R,4S,5R)-oxane-2,3,4,5-tetrol
CAS registry number	58-86-6
Monisotopic molecular weight	150.05282343
Chemical taxonomy
Super class	Organic oxygen compounds
Class	Organooxygen compounds
Sub class	Carbohydrates and carbohydrate conjugates
Biological properties
Pahtways
Author-emphasized biomarker in the paper(s)	Fahrmann et al. 2015

Lung cancer metabolomics studies that identify HMDB0000098 ('xylose')

Reference	Country	Specimen	Marker function	Participants (Case)						Participants (Control)
Reference	Country	Specimen	Marker function	Cancer type	Stage	Number	Gender (M,F)	Age mean (range) (M/F)	Smoking status	Type	Number	Gender (M,F)	Age mean (range) (M/F)	Smoking status
Fahrmann et al. 2015	–	plasma	diagnosis	adenocarcinoma	I, II, III, IV	43	21, 22	67.3 ± 10.10	–	healthy	43	21, 22	65.9 ± 8.05	–
Miyamoto et al. 2015	–	blood	diagnosis	adenocarcinoma	unknown (mostly late stage)	18	10, 8	67 (50-85) / 62 (53-72)	former, current	healthy	20	8, 12	64 (49-80) / 66 (58-82)	former, current
Fahrmann et al. 2015	–	serum	diagnosis	adenocarcinoma	I, II, III, IV	43	21, 22	67.3 ± 10.10	–	healthy	43	21, 22	65.9 ± 8.05	–
Fahrmann et al. 2015	–	plasma	diagnosis	adenocarcinoma	I, II, III, IV	52	17, 35	65.9 ± 9.66	–	healthy	31	11, 20	64.1 ± 8.97	–
Mazzone et al. 2016	–	serum	–	adenocarcinoma, squamous cell carcinoma	I, II, III	94	55.3%, 44.7%	68.7	–	at-risk controls	190	50.5%, 49.5%	66.2	–
Miyamoto et al. 2015	–	blood	diagnosis	NSCLC, SCLC, mesothelioma, secondary metastasis to lung	I, II, III, IV	11	4, 7	67 (61-73) / 67 (47-76)	smoker, non-smoker	healthy	11	5, 6	69 (61-83) / 54 (44-61)	unknown
Fahrmann et al. 2015	–	serum	diagnosis	adenocarcinoma	I, II, III, IV	49	17, 32	65.9 ± 9.87	–	healthy	31	11, 20	64.1 ± 8.97	–

Reference	Chromatography	Ion source	Positive/Negative mode	Mass analyzer	Identification level
Fahrmann et al. 2015	GC	EI	–	TOF	–
Miyamoto et al. 2015	GC	EI	–	TOF	MS/MS
Fahrmann et al. 2015	GC	EI	–	TOF	–
Fahrmann et al. 2015	GC	EI	–	TOF	–
Mazzone et al. 2016	GC	EI	–	quadrupole	MS/MS
Miyamoto et al. 2015	GC	EI	–	TOF	MS/MS
Fahrmann et al. 2015	GC	EI	–	TOF	–

Reference	Data processing software	Database search
Fahrmann et al. 2015	–	UC Davis Metabolomics BinBase database
Miyamoto et al. 2015	ChromaTOF software (Leco)	UC Davis Metabolomics BinBase database
Fahrmann et al. 2015	–	UC Davis Metabolomics BinBase database
Fahrmann et al. 2015	–	UC Davis Metabolomics BinBase database
Mazzone et al. 2016	Metabolon LIMS system	Metabolon LIMS system
Miyamoto et al. 2015	ChromaTOF software (Leco)	UC Davis Metabolomics BinBase database
Fahrmann et al. 2015	–	UC Davis Metabolomics BinBase database

Differential analysis
Classification analysis

Reference	Difference method	Mean concentration (case)	Mean concentration (control)	Fold change (case/control)	P-value	FDR	VIP
Fahrmann et al. 2015	regress (by the covariates: age, gender and smoking history [packs per year]), permutation test	549 ± 386	637 ± 573	0.86	0.301	0.582	–
Miyamoto et al. 2015	Analysis of Covariance	6184.66666666667	3703.45	1.66997439324594	0.249424600772595	–	–
Fahrmann et al. 2015	regress (by the covariates: age, gender and smoking history [packs per year]), permutation test	1035 ± 792	1140 ± 729	0.908	0.164	0.439	–
Fahrmann et al. 2015	regress (by the covariates: age, gender and smoking history [packs per year]), permutation test	287 ± 616	357 ± 469	0.8	0.14	0.527	–
Mazzone et al. 2016	two- sample independent t test	0.9926883± 1.05832	1.2979132± 1.634773	0.76483411987797	0.100322	0.186508322	–
Miyamoto et al. 2015	Analysis of Covariance	3302.81818181818	6454.63636363636	0.511697018351854	0.0542660686253641	–	–
Fahrmann et al. 2015	regress (by the covariates: age, gender and smoking history [packs per year]), permutation test	215 ± 138	481 ± 558	0.45	0	0.032	–

Reference	Classification method	Cutoff value	AUROC 95%CI	Sensitivity (%)	Specificity (%)	Accuracy (%)
Fahrmann et al. 2015	random forest	–	–	–	–	–
Miyamoto et al. 2015	–	–	–	–	–	–
Fahrmann et al. 2015	random forest	–	Bin_225393+aspartate+xylose+glutamate=0.820 (0.729, 0.911) Bin_225393+aspartate+xylose=0.806 (0.711, 0.901)	76.7 Bin_225393+aspartate+xylose=74.4	23.3 Bin_225393+aspartate+xylose=53.5	50.0 Bin_225393+aspartate+xylose=67.4
Fahrmann et al. 2015	random forest	–	–	–	–	–
Mazzone et al. 2016	–	–	–	–	–	–
Miyamoto et al. 2015	–	–	–	–	–	–
Fahrmann et al. 2015	random forest	–	Bin_225393+aspartate+xylose+glutamate=0.874 (0.800, 0.947) Bin_225393+aspartate+xylose=0.864 (0.787, 0.942)	–	–	53.8 Bin_225393+aspartate+xylose=68.8