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PubMed:28100567 JSON TXT

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CL-cell

Id	Subject	Object	Predicate	Lexical cue	cl_id
T1	80-92	Cell	denotes	cancer cells	http://purl.obolibrary.org/obo/CL:0001064

GlyCosmos6-Glycan-Motif-Image

Id	Subject	Object	Predicate	Lexical cue	image
T1	942-953	Glycan_Motif	denotes	Tn antigens	https://api.glycosmos.org/wurcs2image/0.10.0/png/binary/G57321FI
T2	1023-1039	Glycan_Motif	denotes	lactosylceramide	https://api.glycosmos.org/wurcs2image/0.10.0/png/binary/G84224TW\|https://api.glycosmos.org/wurcs2image/0.10.0/png/binary/G74621DY\|https://api.glycosmos.org/wurcs2image/0.10.0/png/binary/G20420WT

GlyCosmos6-Glycan-Motif-Structure

Id	Subject	Object	Predicate	Lexical cue
T1	942-953	https://glytoucan.org/Structures/Glycans/G57321FI	denotes	Tn antigens
T2	1023-1039	https://glytoucan.org/Structures/Glycans/G20420WT	denotes	lactosylceramide
T3	1023-1039	https://glytoucan.org/Structures/Glycans/G74621DY	denotes	lactosylceramide
T4	1023-1039	https://glytoucan.org/Structures/Glycans/G84224TW	denotes	lactosylceramide

Glycosmos6-GlycoEpitope

Id	Subject	Object	Predicate	Lexical cue
T1	1023-1039	http://www.glycoepitope.jp/epitopes/EP0078	denotes	lactosylceramide

sentences

Id	Subject	Object	Predicate	Lexical cue
TextSentencer_T1	0-93	Sentence	denotes	MeCP2 regulated glycogenes contribute to proliferation and apoptosis of gastric cancer cells.
TextSentencer_T2	94-306	Sentence	denotes	Aberrant glycogene and glycan expression is intimately associated with carcinogenesis, invasion, and metastasis of gastric cancer (GC); however the regulatory mechanisms for glycogenes in GC cells remain unclear.
TextSentencer_T3	307-512	Sentence	denotes	Methyl-CpG-binding protein 2 (MeCP2) regulates genes by binding to methylated promoters, and in our previous work we found that it is overexpressed in GC cell lines and tissues, functioning as an oncogene.
TextSentencer_T4	513-713	Sentence	denotes	In this study we detected the expression of 212 glycogenes in MeCP2 silenced GC cells versus control using the Agilent Whole Human Genome Microarray and mining the data through bioinformatic analysis.
TextSentencer_T5	714-1082	Sentence	denotes	A total of 10 glycogenes exhibited increased expression (FC ≥ 2, P < 0.05), while 16 showed decreased expression (FC ≤ 2, P < 0.05) in the MeCP2 silenced cells, which corresponded to down-regulation of Lewis antigens (UEA-I), T/Tn antigens (PNA), and mature N-glycans (PHA-E and PHA-E+L) and up-regulation of lactosylceramide, a precursor oligosaccharide of N-glycans.
TextSentencer_T6	1083-1331	Sentence	denotes	Examination of the TCGA Gastric Cancer databases demonstrated that nine glycogenes (24.6%) were oppositely regulated by MeCP2 in MeCP2 knockdown BGC-823 cells relative to their expression level in GC tissues, and might be downstream genes of MeCP2.
TextSentencer_T7	1332-1478	Sentence	denotes	Individual gene analysis suggested that neutral alpha-glucosidase AB (GANAB) knockdown can rescue the effects of MeCP2 overexpression on GC cells.
TextSentencer_T8	1479-1596	Sentence	denotes	MeCP2 promotes GANAB by binding to the second methylated CpG island (206 bp, -12916 to -13122) of the GANAB promoter.
TextSentencer_T9	1597-1775	Sentence	denotes	In conclusion, glycogenes can be either up- or down-regulated by MeCP2 directly or indirectly to alter the glycopatterning and affect the proliferation and apoptosis of GC cells.
T1	0-93	Sentence	denotes	MeCP2 regulated glycogenes contribute to proliferation and apoptosis of gastric cancer cells.
T2	94-306	Sentence	denotes	Aberrant glycogene and glycan expression is intimately associated with carcinogenesis, invasion, and metastasis of gastric cancer (GC); however the regulatory mechanisms for glycogenes in GC cells remain unclear.
T3	307-512	Sentence	denotes	Methyl-CpG-binding protein 2 (MeCP2) regulates genes by binding to methylated promoters, and in our previous work we found that it is overexpressed in GC cell lines and tissues, functioning as an oncogene.
T4	513-713	Sentence	denotes	In this study we detected the expression of 212 glycogenes in MeCP2 silenced GC cells versus control using the Agilent Whole Human Genome Microarray and mining the data through bioinformatic analysis.
T5	714-1082	Sentence	denotes	A total of 10 glycogenes exhibited increased expression (FC ≥ 2, P < 0.05), while 16 showed decreased expression (FC ≤ 2, P < 0.05) in the MeCP2 silenced cells, which corresponded to down-regulation of Lewis antigens (UEA-I), T/Tn antigens (PNA), and mature N-glycans (PHA-E and PHA-E+L) and up-regulation of lactosylceramide, a precursor oligosaccharide of N-glycans.
T6	1083-1331	Sentence	denotes	Examination of the TCGA Gastric Cancer databases demonstrated that nine glycogenes (24.6%) were oppositely regulated by MeCP2 in MeCP2 knockdown BGC-823 cells relative to their expression level in GC tissues, and might be downstream genes of MeCP2.
T7	1332-1478	Sentence	denotes	Individual gene analysis suggested that neutral alpha-glucosidase AB (GANAB) knockdown can rescue the effects of MeCP2 overexpression on GC cells.
T8	1479-1596	Sentence	denotes	MeCP2 promotes GANAB by binding to the second methylated CpG island (206 bp, -12916 to -13122) of the GANAB promoter.
T9	1597-1775	Sentence	denotes	In conclusion, glycogenes can be either up- or down-regulated by MeCP2 directly or indirectly to alter the glycopatterning and affect the proliferation and apoptosis of GC cells.

mondo_disease

Id	Subject	Object	Predicate	Lexical cue	mondo_id
T1	72-86	Disease	denotes	gastric cancer	http://purl.obolibrary.org/obo/MONDO_0001056
T2	209-223	Disease	denotes	gastric cancer	http://purl.obolibrary.org/obo/MONDO_0001056
T3	225-227	Disease	denotes	GC	http://purl.obolibrary.org/obo/MONDO_0001056
T4	282-284	Disease	denotes	GC	http://purl.obolibrary.org/obo/MONDO_0001056
T5	458-460	Disease	denotes	GC	http://purl.obolibrary.org/obo/MONDO_0001056
T6	590-592	Disease	denotes	GC	http://purl.obolibrary.org/obo/MONDO_0001056
T7	983-986	Disease	denotes	PHA	http://purl.obolibrary.org/obo/MONDO_0007710\|http://purl.obolibrary.org/obo/MONDO_0008214
T9	993-996	Disease	denotes	PHA	http://purl.obolibrary.org/obo/MONDO_0007710\|http://purl.obolibrary.org/obo/MONDO_0008214
T11	1107-1121	Disease	denotes	Gastric Cancer	http://purl.obolibrary.org/obo/MONDO_0001056
T12	1280-1282	Disease	denotes	GC	http://purl.obolibrary.org/obo/MONDO_0001056
T13	1469-1471	Disease	denotes	GC	http://purl.obolibrary.org/obo/MONDO_0001056
T14	1766-1768	Disease	denotes	GC	http://purl.obolibrary.org/obo/MONDO_0001056

HP-phenotype

Id	Subject	Object	Predicate	Lexical cue	hp_id
T1	72-86	Phenotype	denotes	gastric cancer	HP:0012126
T2	209-223	Phenotype	denotes	gastric cancer	HP:0012126
T3	225-227	Phenotype	denotes	GC	HP:0012126
T4	282-284	Phenotype	denotes	GC	HP:0012126
T5	458-460	Phenotype	denotes	GC	HP:0012126
T6	590-592	Phenotype	denotes	GC	HP:0012126
T7	1107-1121	Phenotype	denotes	Gastric Cancer	HP:0012126
T8	1280-1282	Phenotype	denotes	GC	HP:0012126
T9	1469-1471	Phenotype	denotes	GC	HP:0012126
T10	1766-1768	Phenotype	denotes	GC	HP:0012126

Glycan-GlyCosmos

Id	Subject	Object	Predicate	Lexical cue	image
T1	1023-1039	Glycan	denotes	lactosylceramide	https://api.glycosmos.org/wurcs2image/latest/png/binary/G84224TW

GlyCosmos15-HP

Id	Subject	Object	Predicate	Lexical cue	hp_id
T1	72-86	Phenotype	denotes	gastric cancer	HP:0012126
T2	209-223	Phenotype	denotes	gastric cancer	HP:0012126
T3	225-227	Phenotype	denotes	GC	HP:0012126
T4	282-284	Phenotype	denotes	GC	HP:0012126
T5	458-460	Phenotype	denotes	GC	HP:0012126
T6	590-592	Phenotype	denotes	GC	HP:0012126
T7	1107-1121	Phenotype	denotes	Gastric Cancer	HP:0012126
T8	1280-1282	Phenotype	denotes	GC	HP:0012126
T9	1469-1471	Phenotype	denotes	GC	HP:0012126
T10	1766-1768	Phenotype	denotes	GC	HP:0012126

GlyCosmos15-NCBITAXON

Id	Subject	Object	Predicate	Lexical cue	db_id
T1	638-643	OrganismTaxon	denotes	Human	9606

GlyCosmos15-CL

Id	Subject	Object	Predicate	Lexical cue	cl_id
T1	80-92	Cell	denotes	cancer cells	http://purl.obolibrary.org/obo/CL:0001064

sentences

Id	Subject	Object	Predicate	Lexical cue
TextSentencer_T1	0-93	Sentence	denotes	MeCP2 regulated glycogenes contribute to proliferation and apoptosis of gastric cancer cells.
TextSentencer_T2	94-306	Sentence	denotes	Aberrant glycogene and glycan expression is intimately associated with carcinogenesis, invasion, and metastasis of gastric cancer (GC); however the regulatory mechanisms for glycogenes in GC cells remain unclear.
TextSentencer_T3	307-512	Sentence	denotes	Methyl-CpG-binding protein 2 (MeCP2) regulates genes by binding to methylated promoters, and in our previous work we found that it is overexpressed in GC cell lines and tissues, functioning as an oncogene.
TextSentencer_T4	513-713	Sentence	denotes	In this study we detected the expression of 212 glycogenes in MeCP2 silenced GC cells versus control using the Agilent Whole Human Genome Microarray and mining the data through bioinformatic analysis.
TextSentencer_T5	714-1082	Sentence	denotes	A total of 10 glycogenes exhibited increased expression (FC ≥ 2, P < 0.05), while 16 showed decreased expression (FC ≤ 2, P < 0.05) in the MeCP2 silenced cells, which corresponded to down-regulation of Lewis antigens (UEA-I), T/Tn antigens (PNA), and mature N-glycans (PHA-E and PHA-E+L) and up-regulation of lactosylceramide, a precursor oligosaccharide of N-glycans.
TextSentencer_T6	1083-1331	Sentence	denotes	Examination of the TCGA Gastric Cancer databases demonstrated that nine glycogenes (24.6%) were oppositely regulated by MeCP2 in MeCP2 knockdown BGC-823 cells relative to their expression level in GC tissues, and might be downstream genes of MeCP2.
TextSentencer_T7	1332-1478	Sentence	denotes	Individual gene analysis suggested that neutral alpha-glucosidase AB (GANAB) knockdown can rescue the effects of MeCP2 overexpression on GC cells.
TextSentencer_T8	1479-1596	Sentence	denotes	MeCP2 promotes GANAB by binding to the second methylated CpG island (206 bp, -12916 to -13122) of the GANAB promoter.
TextSentencer_T9	1597-1775	Sentence	denotes	In conclusion, glycogenes can be either up- or down-regulated by MeCP2 directly or indirectly to alter the glycopatterning and affect the proliferation and apoptosis of GC cells.
T1	0-93	Sentence	denotes	MeCP2 regulated glycogenes contribute to proliferation and apoptosis of gastric cancer cells.
T2	94-306	Sentence	denotes	Aberrant glycogene and glycan expression is intimately associated with carcinogenesis, invasion, and metastasis of gastric cancer (GC); however the regulatory mechanisms for glycogenes in GC cells remain unclear.
T3	307-512	Sentence	denotes	Methyl-CpG-binding protein 2 (MeCP2) regulates genes by binding to methylated promoters, and in our previous work we found that it is overexpressed in GC cell lines and tissues, functioning as an oncogene.
T4	513-713	Sentence	denotes	In this study we detected the expression of 212 glycogenes in MeCP2 silenced GC cells versus control using the Agilent Whole Human Genome Microarray and mining the data through bioinformatic analysis.
T5	714-1082	Sentence	denotes	A total of 10 glycogenes exhibited increased expression (FC ≥ 2, P < 0.05), while 16 showed decreased expression (FC ≤ 2, P < 0.05) in the MeCP2 silenced cells, which corresponded to down-regulation of Lewis antigens (UEA-I), T/Tn antigens (PNA), and mature N-glycans (PHA-E and PHA-E+L) and up-regulation of lactosylceramide, a precursor oligosaccharide of N-glycans.
T6	1083-1331	Sentence	denotes	Examination of the TCGA Gastric Cancer databases demonstrated that nine glycogenes (24.6%) were oppositely regulated by MeCP2 in MeCP2 knockdown BGC-823 cells relative to their expression level in GC tissues, and might be downstream genes of MeCP2.
T7	1332-1478	Sentence	denotes	Individual gene analysis suggested that neutral alpha-glucosidase AB (GANAB) knockdown can rescue the effects of MeCP2 overexpression on GC cells.
T8	1479-1596	Sentence	denotes	MeCP2 promotes GANAB by binding to the second methylated CpG island (206 bp, -12916 to -13122) of the GANAB promoter.
T9	1597-1775	Sentence	denotes	In conclusion, glycogenes can be either up- or down-regulated by MeCP2 directly or indirectly to alter the glycopatterning and affect the proliferation and apoptosis of GC cells.

GlyCosmos15-Sentences

Id	Subject	Object	Predicate	Lexical cue
T1	0-93	Sentence	denotes	MeCP2 regulated glycogenes contribute to proliferation and apoptosis of gastric cancer cells.
T2	94-306	Sentence	denotes	Aberrant glycogene and glycan expression is intimately associated with carcinogenesis, invasion, and metastasis of gastric cancer (GC); however the regulatory mechanisms for glycogenes in GC cells remain unclear.
T3	307-512	Sentence	denotes	Methyl-CpG-binding protein 2 (MeCP2) regulates genes by binding to methylated promoters, and in our previous work we found that it is overexpressed in GC cell lines and tissues, functioning as an oncogene.
T4	513-713	Sentence	denotes	In this study we detected the expression of 212 glycogenes in MeCP2 silenced GC cells versus control using the Agilent Whole Human Genome Microarray and mining the data through bioinformatic analysis.
T5	714-1082	Sentence	denotes	A total of 10 glycogenes exhibited increased expression (FC ≥ 2, P < 0.05), while 16 showed decreased expression (FC ≤ 2, P < 0.05) in the MeCP2 silenced cells, which corresponded to down-regulation of Lewis antigens (UEA-I), T/Tn antigens (PNA), and mature N-glycans (PHA-E and PHA-E+L) and up-regulation of lactosylceramide, a precursor oligosaccharide of N-glycans.
T6	1083-1331	Sentence	denotes	Examination of the TCGA Gastric Cancer databases demonstrated that nine glycogenes (24.6%) were oppositely regulated by MeCP2 in MeCP2 knockdown BGC-823 cells relative to their expression level in GC tissues, and might be downstream genes of MeCP2.
T7	1332-1478	Sentence	denotes	Individual gene analysis suggested that neutral alpha-glucosidase AB (GANAB) knockdown can rescue the effects of MeCP2 overexpression on GC cells.
T8	1479-1596	Sentence	denotes	MeCP2 promotes GANAB by binding to the second methylated CpG island (206 bp, -12916 to -13122) of the GANAB promoter.
T9	1597-1775	Sentence	denotes	In conclusion, glycogenes can be either up- or down-regulated by MeCP2 directly or indirectly to alter the glycopatterning and affect the proliferation and apoptosis of GC cells.

GlyCosmos15-GlycoEpitope

Id	Subject	Object	Predicate	Lexical cue	glycoepitope_id
T1	1023-1039	http://purl.jp/bio/12/glyco/glycan#Glycan_epitope	denotes	lactosylceramide	http://www.glycoepitope.jp/epitopes/EP0078

GlyCosmos15-Lectin-Jamboree

Id	Subject	Object	Predicate	Lexical cue	glycosmos_id
T1	955-958	Lectin	denotes	PNA	GL_003655
T2	983-988	Lectin	denotes	PHA-E	GL_002666
T3	993-998	Lectin	denotes	PHA-E	GL_002666

GlyCosmos15-MONDO

Id	Subject	Object	Predicate	Lexical cue	mondo_id
T1	72-86	Disease	denotes	gastric cancer	MONDO:0001056\|MONDO:0004950
T3	209-223	Disease	denotes	gastric cancer	MONDO:0001056\|MONDO:0004950
T5	225-227	Disease	denotes	GC	MONDO:0001056
T6	282-284	Disease	denotes	GC	MONDO:0001056
T7	458-460	Disease	denotes	GC	MONDO:0001056
T8	590-592	Disease	denotes	GC	MONDO:0001056
T9	1107-1121	Disease	denotes	Gastric Cancer	MONDO:0001056\|MONDO:0004950
T11	1280-1282	Disease	denotes	GC	MONDO:0001056
T12	1469-1471	Disease	denotes	GC	MONDO:0001056
T13	1766-1768	Disease	denotes	GC	MONDO:0001056

GlyCosmos15-FMA

Id	Subject	Object	Predicate	Lexical cue	db_id
T1	476-483	Body_part	denotes	tissues	FMA:9637
T2	644-650	Body_part	denotes	Genome	FMA:84116
T3	1283-1290	Body_part	denotes	tissues	FMA:9637

GlyCosmos15-Glycan

Id	Subject	Object	Predicate	Lexical cue	image
T1	1023-1039	Glycan	denotes	lactosylceramide	https://api.glycosmos.org/wurcs2image/latest/png/binary/G84224TW

NCBITAXON

Id	Subject	Object	Predicate	Lexical cue	db_id
T1	638-643	OrganismTaxon	denotes	Human	9606

GlyCosmos-GlycoEpitope

Id	Subject	Object	Predicate	Lexical cue	glycoepitope_id
T1	1023-1039	http://purl.jp/bio/12/glyco/glycan#Glycan_epitope	denotes	lactosylceramide	http://www.glycoepitope.jp/epitopes/EP0078