PubMed:16358311
Annnotations
DisGeNET5_gene_disease
{"project":"DisGeNET5_gene_disease","denotations":[{"id":"16358311-10#133#138#gene4297","span":{"begin":1521,"end":1526},"obj":"gene4297"},{"id":"16358311-10#181#185#gene961","span":{"begin":1569,"end":1573},"obj":"gene961"},{"id":"16358311-10#133#138#gene4297","span":{"begin":1521,"end":1526},"obj":"gene4297"},{"id":"16358311-10#181#185#gene961","span":{"begin":1569,"end":1573},"obj":"gene961"},{"id":"16358311-10#142#146#diseaseC0079748","span":{"begin":1530,"end":1534},"obj":"diseaseC0079748"},{"id":"16358311-10#142#146#diseaseC1961102","span":{"begin":1530,"end":1534},"obj":"diseaseC1961102"},{"id":"16358311-10#142#146#diseaseC0079748","span":{"begin":1530,"end":1534},"obj":"diseaseC0079748"},{"id":"16358311-10#142#146#diseaseC1961102","span":{"begin":1530,"end":1534},"obj":"diseaseC1961102"},{"id":"16358311-10#171#176#diseaseC1961099","span":{"begin":1559,"end":1564},"obj":"diseaseC1961099"},{"id":"16358311-10#189#194#diseaseC1961099","span":{"begin":1577,"end":1582},"obj":"diseaseC1961099"},{"id":"16358311-10#171#176#diseaseC1961099","span":{"begin":1559,"end":1564},"obj":"diseaseC1961099"},{"id":"16358311-10#189#194#diseaseC1961099","span":{"begin":1577,"end":1582},"obj":"diseaseC1961099"}],"relations":[{"id":"133#138#gene4297142#146#diseaseC0079748","pred":"associated_with","subj":"16358311-10#133#138#gene4297","obj":"16358311-10#142#146#diseaseC0079748"},{"id":"133#138#gene4297142#146#diseaseC1961102","pred":"associated_with","subj":"16358311-10#133#138#gene4297","obj":"16358311-10#142#146#diseaseC1961102"},{"id":"133#138#gene4297142#146#diseaseC0079748","pred":"associated_with","subj":"16358311-10#133#138#gene4297","obj":"16358311-10#142#146#diseaseC0079748"},{"id":"133#138#gene4297142#146#diseaseC1961102","pred":"associated_with","subj":"16358311-10#133#138#gene4297","obj":"16358311-10#142#146#diseaseC1961102"},{"id":"133#138#gene4297171#176#diseaseC1961099","pred":"associated_with","subj":"16358311-10#133#138#gene4297","obj":"16358311-10#171#176#diseaseC1961099"},{"id":"133#138#gene4297189#194#diseaseC1961099","pred":"associated_with","subj":"16358311-10#133#138#gene4297","obj":"16358311-10#189#194#diseaseC1961099"},{"id":"133#138#gene4297171#176#diseaseC1961099","pred":"associated_with","subj":"16358311-10#133#138#gene4297","obj":"16358311-10#171#176#diseaseC1961099"},{"id":"133#138#gene4297189#194#diseaseC1961099","pred":"associated_with","subj":"16358311-10#133#138#gene4297","obj":"16358311-10#189#194#diseaseC1961099"},{"id":"181#185#gene961142#146#diseaseC0079748","pred":"associated_with","subj":"16358311-10#181#185#gene961","obj":"16358311-10#142#146#diseaseC0079748"},{"id":"181#185#gene961142#146#diseaseC1961102","pred":"associated_with","subj":"16358311-10#181#185#gene961","obj":"16358311-10#142#146#diseaseC1961102"},{"id":"181#185#gene961142#146#diseaseC0079748","pred":"associated_with","subj":"16358311-10#181#185#gene961","obj":"16358311-10#142#146#diseaseC0079748"},{"id":"181#185#gene961142#146#diseaseC1961102","pred":"associated_with","subj":"16358311-10#181#185#gene961","obj":"16358311-10#142#146#diseaseC1961102"},{"id":"181#185#gene961171#176#diseaseC1961099","pred":"associated_with","subj":"16358311-10#181#185#gene961","obj":"16358311-10#171#176#diseaseC1961099"},{"id":"181#185#gene961189#194#diseaseC1961099","pred":"associated_with","subj":"16358311-10#181#185#gene961","obj":"16358311-10#189#194#diseaseC1961099"},{"id":"181#185#gene961171#176#diseaseC1961099","pred":"associated_with","subj":"16358311-10#181#185#gene961","obj":"16358311-10#171#176#diseaseC1961099"},{"id":"181#185#gene961189#194#diseaseC1961099","pred":"associated_with","subj":"16358311-10#181#185#gene961","obj":"16358311-10#189#194#diseaseC1961099"},{"id":"133#138#gene4297142#146#diseaseC0079748","pred":"associated_with","subj":"16358311-10#133#138#gene4297","obj":"16358311-10#142#146#diseaseC0079748"},{"id":"133#138#gene4297142#146#diseaseC1961102","pred":"associated_with","subj":"16358311-10#133#138#gene4297","obj":"16358311-10#142#146#diseaseC1961102"},{"id":"133#138#gene4297142#146#diseaseC0079748","pred":"associated_with","subj":"16358311-10#133#138#gene4297","obj":"16358311-10#142#146#diseaseC0079748"},{"id":"133#138#gene4297142#146#diseaseC1961102","pred":"associated_with","subj":"16358311-10#133#138#gene4297","obj":"16358311-10#142#146#diseaseC1961102"},{"id":"133#138#gene4297171#176#diseaseC1961099","pred":"associated_with","subj":"16358311-10#133#138#gene4297","obj":"16358311-10#171#176#diseaseC1961099"},{"id":"133#138#gene4297189#194#diseaseC1961099","pred":"associated_with","subj":"16358311-10#133#138#gene4297","obj":"16358311-10#189#194#diseaseC1961099"},{"id":"133#138#gene4297171#176#diseaseC1961099","pred":"associated_with","subj":"16358311-10#133#138#gene4297","obj":"16358311-10#171#176#diseaseC1961099"},{"id":"133#138#gene4297189#194#diseaseC1961099","pred":"associated_with","subj":"16358311-10#133#138#gene4297","obj":"16358311-10#189#194#diseaseC1961099"},{"id":"181#185#gene961142#146#diseaseC0079748","pred":"associated_with","subj":"16358311-10#181#185#gene961","obj":"16358311-10#142#146#diseaseC0079748"},{"id":"181#185#gene961142#146#diseaseC1961102","pred":"associated_with","subj":"16358311-10#181#185#gene961","obj":"16358311-10#142#146#diseaseC1961102"},{"id":"181#185#gene961142#146#diseaseC0079748","pred":"associated_with","subj":"16358311-10#181#185#gene961","obj":"16358311-10#142#146#diseaseC0079748"},{"id":"181#185#gene961142#146#diseaseC1961102","pred":"associated_with","subj":"16358311-10#181#185#gene961","obj":"16358311-10#142#146#diseaseC1961102"},{"id":"181#185#gene961171#176#diseaseC1961099","pred":"associated_with","subj":"16358311-10#181#185#gene961","obj":"16358311-10#171#176#diseaseC1961099"},{"id":"181#185#gene961189#194#diseaseC1961099","pred":"associated_with","subj":"16358311-10#181#185#gene961","obj":"16358311-10#189#194#diseaseC1961099"},{"id":"181#185#gene961171#176#diseaseC1961099","pred":"associated_with","subj":"16358311-10#181#185#gene961","obj":"16358311-10#171#176#diseaseC1961099"},{"id":"181#185#gene961189#194#diseaseC1961099","pred":"associated_with","subj":"16358311-10#181#185#gene961","obj":"16358311-10#189#194#diseaseC1961099"}],"text":"Gene expression profiling reveals intrinsic differences between T-cell acute lymphoblastic leukemia and T-cell lymphoblastic lymphoma.\nBACKGROUND: T-cell acute lymphoblastic leukemia (T-ALL) and T-cell lymphoblastic lymphoma (T-LL) and are often thought to represent a spectrum of a single disease. The malignant cells in T-ALL and T-LL are morphologically indistinguishable, and they share the expression of common cell surface antigens and cytogenetic characteristics. However, despite these similarities, differences in the clinical behavior of T-ALL and T-LL are observed.\nPROCEDURE: We analyzed the gene expression profiles of T-ALL and T-LL samples obtained from Children's Oncology Group (COG) tumor banks using DNA arrays. Immunohistochemistry was also performed to validate the expression of selected targets.\nRESULTS: Unsupervised hierarchical clustering of all samples showed complete segregation of T-ALL and T-LL into distinct clusters. Next, we identified the top 201 genes that best differentiated T-ALL from T-LL using significance analysis of microarrays (SAM), a supervised statistical approach. Genes representing several functional groups were differentially expressed in T-LL and T-ALL. Prediction analysis of microarrays (PAM) identified a subset of genes, which accurately classified all 19 T-ALL and T-LL samples with an overall misclassification error rate of 0. Immunohistochemical validation of protein expression of selected genes identified by microarray analysis confirmed overexpression of MLL-1 in T-LL tumor cells compared to T-ALL and CD47 in T-ALL tumors cells when compared to T-LL.\nCONCLUSIONS: Despite significant similarities between the malignant T-cell precursors, clear differences in the gene expression profiles were observed between T-ALL and T-LL implying underlying differences in the biology of the two entities."}
DisGeNet-2017-sample
{"project":"DisGeNet-2017-sample","denotations":[{"id":"T1539","span":{"begin":1521,"end":1526},"obj":"gene:4297"},{"id":"T1540","span":{"begin":1530,"end":1534},"obj":"disease:C0079748"},{"id":"T1541","span":{"begin":1569,"end":1573},"obj":"gene:961"}],"relations":[{"id":"R1","pred":"associated_with","subj":"T1539","obj":"T1540"},{"id":"R2","pred":"associated_with","subj":"T1539","obj":"T1540"},{"id":"R3","pred":"associated_with","subj":"T1541","obj":"T1540"},{"id":"R4","pred":"associated_with","subj":"T1541","obj":"T1540"}],"namespaces":[{"prefix":"gene","uri":"http://www.ncbi.nlm.nih.gov/gene/"},{"prefix":"disease","uri":"http://purl.bioontology.org/ontology/MEDLINEPLUS/"}],"text":"Gene expression profiling reveals intrinsic differences between T-cell acute lymphoblastic leukemia and T-cell lymphoblastic lymphoma.\nBACKGROUND: T-cell acute lymphoblastic leukemia (T-ALL) and T-cell lymphoblastic lymphoma (T-LL) and are often thought to represent a spectrum of a single disease. The malignant cells in T-ALL and T-LL are morphologically indistinguishable, and they share the expression of common cell surface antigens and cytogenetic characteristics. However, despite these similarities, differences in the clinical behavior of T-ALL and T-LL are observed.\nPROCEDURE: We analyzed the gene expression profiles of T-ALL and T-LL samples obtained from Children's Oncology Group (COG) tumor banks using DNA arrays. Immunohistochemistry was also performed to validate the expression of selected targets.\nRESULTS: Unsupervised hierarchical clustering of all samples showed complete segregation of T-ALL and T-LL into distinct clusters. Next, we identified the top 201 genes that best differentiated T-ALL from T-LL using significance analysis of microarrays (SAM), a supervised statistical approach. Genes representing several functional groups were differentially expressed in T-LL and T-ALL. Prediction analysis of microarrays (PAM) identified a subset of genes, which accurately classified all 19 T-ALL and T-LL samples with an overall misclassification error rate of 0. Immunohistochemical validation of protein expression of selected genes identified by microarray analysis confirmed overexpression of MLL-1 in T-LL tumor cells compared to T-ALL and CD47 in T-ALL tumors cells when compared to T-LL.\nCONCLUSIONS: Despite significant similarities between the malignant T-cell precursors, clear differences in the gene expression profiles were observed between T-ALL and T-LL implying underlying differences in the biology of the two entities."}
sentences
{"project":"sentences","denotations":[{"id":"TextSentencer_T1","span":{"begin":0,"end":134},"obj":"Sentence"},{"id":"TextSentencer_T2","span":{"begin":135,"end":298},"obj":"Sentence"},{"id":"TextSentencer_T3","span":{"begin":299,"end":470},"obj":"Sentence"},{"id":"TextSentencer_T4","span":{"begin":471,"end":576},"obj":"Sentence"},{"id":"TextSentencer_T5","span":{"begin":577,"end":587},"obj":"Sentence"},{"id":"TextSentencer_T6","span":{"begin":588,"end":730},"obj":"Sentence"},{"id":"TextSentencer_T7","span":{"begin":731,"end":818},"obj":"Sentence"},{"id":"TextSentencer_T8","span":{"begin":819,"end":827},"obj":"Sentence"},{"id":"TextSentencer_T9","span":{"begin":828,"end":949},"obj":"Sentence"},{"id":"TextSentencer_T10","span":{"begin":950,"end":1113},"obj":"Sentence"},{"id":"TextSentencer_T11","span":{"begin":1114,"end":1207},"obj":"Sentence"},{"id":"TextSentencer_T12","span":{"begin":1208,"end":1387},"obj":"Sentence"},{"id":"TextSentencer_T13","span":{"begin":1388,"end":1618},"obj":"Sentence"},{"id":"TextSentencer_T14","span":{"begin":1619,"end":1631},"obj":"Sentence"},{"id":"TextSentencer_T15","span":{"begin":1632,"end":1860},"obj":"Sentence"},{"id":"T1","span":{"begin":0,"end":134},"obj":"Sentence"},{"id":"T2","span":{"begin":135,"end":298},"obj":"Sentence"},{"id":"T3","span":{"begin":299,"end":470},"obj":"Sentence"},{"id":"T4","span":{"begin":471,"end":576},"obj":"Sentence"},{"id":"T5","span":{"begin":577,"end":587},"obj":"Sentence"},{"id":"T6","span":{"begin":588,"end":730},"obj":"Sentence"},{"id":"T7","span":{"begin":731,"end":818},"obj":"Sentence"},{"id":"T8","span":{"begin":819,"end":827},"obj":"Sentence"},{"id":"T9","span":{"begin":828,"end":949},"obj":"Sentence"},{"id":"T10","span":{"begin":950,"end":1113},"obj":"Sentence"},{"id":"T11","span":{"begin":1114,"end":1207},"obj":"Sentence"},{"id":"T12","span":{"begin":1208,"end":1387},"obj":"Sentence"},{"id":"T13","span":{"begin":1388,"end":1618},"obj":"Sentence"},{"id":"T14","span":{"begin":1619,"end":1631},"obj":"Sentence"},{"id":"T15","span":{"begin":1632,"end":1860},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Gene expression profiling reveals intrinsic differences between T-cell acute lymphoblastic leukemia and T-cell lymphoblastic lymphoma.\nBACKGROUND: T-cell acute lymphoblastic leukemia (T-ALL) and T-cell lymphoblastic lymphoma (T-LL) and are often thought to represent a spectrum of a single disease. The malignant cells in T-ALL and T-LL are morphologically indistinguishable, and they share the expression of common cell surface antigens and cytogenetic characteristics. However, despite these similarities, differences in the clinical behavior of T-ALL and T-LL are observed.\nPROCEDURE: We analyzed the gene expression profiles of T-ALL and T-LL samples obtained from Children's Oncology Group (COG) tumor banks using DNA arrays. Immunohistochemistry was also performed to validate the expression of selected targets.\nRESULTS: Unsupervised hierarchical clustering of all samples showed complete segregation of T-ALL and T-LL into distinct clusters. Next, we identified the top 201 genes that best differentiated T-ALL from T-LL using significance analysis of microarrays (SAM), a supervised statistical approach. Genes representing several functional groups were differentially expressed in T-LL and T-ALL. Prediction analysis of microarrays (PAM) identified a subset of genes, which accurately classified all 19 T-ALL and T-LL samples with an overall misclassification error rate of 0. Immunohistochemical validation of protein expression of selected genes identified by microarray analysis confirmed overexpression of MLL-1 in T-LL tumor cells compared to T-ALL and CD47 in T-ALL tumors cells when compared to T-LL.\nCONCLUSIONS: Despite significant similarities between the malignant T-cell precursors, clear differences in the gene expression profiles were observed between T-ALL and T-LL implying underlying differences in the biology of the two entities."}
DisGeNET
{"project":"DisGeNET","denotations":[{"id":"T0","span":{"begin":1521,"end":1526},"obj":"gene:4297"},{"id":"T1","span":{"begin":1530,"end":1534},"obj":"disease:C0079748"},{"id":"T2","span":{"begin":1521,"end":1526},"obj":"gene:4297"},{"id":"T3","span":{"begin":1530,"end":1534},"obj":"disease:C1961102"},{"id":"T4","span":{"begin":1521,"end":1526},"obj":"gene:4297"},{"id":"T5","span":{"begin":1559,"end":1564},"obj":"disease:C1961099"},{"id":"T6","span":{"begin":1569,"end":1573},"obj":"gene:961"},{"id":"T7","span":{"begin":1530,"end":1534},"obj":"disease:C0079748"},{"id":"T8","span":{"begin":1569,"end":1573},"obj":"gene:961"},{"id":"T9","span":{"begin":1530,"end":1534},"obj":"disease:C1961102"},{"id":"T10","span":{"begin":1569,"end":1573},"obj":"gene:961"},{"id":"T11","span":{"begin":1559,"end":1564},"obj":"disease:C1961099"},{"id":"T12","span":{"begin":1569,"end":1573},"obj":"gene:961"},{"id":"T13","span":{"begin":1577,"end":1582},"obj":"disease:C1961099"}],"relations":[{"id":"R1","pred":"associated_with","subj":"T0","obj":"T1"},{"id":"R2","pred":"associated_with","subj":"T2","obj":"T3"},{"id":"R3","pred":"associated_with","subj":"T4","obj":"T5"},{"id":"R4","pred":"associated_with","subj":"T6","obj":"T7"},{"id":"R5","pred":"associated_with","subj":"T8","obj":"T9"},{"id":"R6","pred":"associated_with","subj":"T10","obj":"T11"},{"id":"R7","pred":"associated_with","subj":"T12","obj":"T13"}],"namespaces":[{"prefix":"gene","uri":"http://www.ncbi.nlm.nih.gov/gene/"},{"prefix":"disease","uri":"http://purl.bioontology.org/ontology/MEDLINEPLUS/"}],"text":"Gene expression profiling reveals intrinsic differences between T-cell acute lymphoblastic leukemia and T-cell lymphoblastic lymphoma.\nBACKGROUND: T-cell acute lymphoblastic leukemia (T-ALL) and T-cell lymphoblastic lymphoma (T-LL) and are often thought to represent a spectrum of a single disease. The malignant cells in T-ALL and T-LL are morphologically indistinguishable, and they share the expression of common cell surface antigens and cytogenetic characteristics. However, despite these similarities, differences in the clinical behavior of T-ALL and T-LL are observed.\nPROCEDURE: We analyzed the gene expression profiles of T-ALL and T-LL samples obtained from Children's Oncology Group (COG) tumor banks using DNA arrays. Immunohistochemistry was also performed to validate the expression of selected targets.\nRESULTS: Unsupervised hierarchical clustering of all samples showed complete segregation of T-ALL and T-LL into distinct clusters. Next, we identified the top 201 genes that best differentiated T-ALL from T-LL using significance analysis of microarrays (SAM), a supervised statistical approach. Genes representing several functional groups were differentially expressed in T-LL and T-ALL. Prediction analysis of microarrays (PAM) identified a subset of genes, which accurately classified all 19 T-ALL and T-LL samples with an overall misclassification error rate of 0. Immunohistochemical validation of protein expression of selected genes identified by microarray analysis confirmed overexpression of MLL-1 in T-LL tumor cells compared to T-ALL and CD47 in T-ALL tumors cells when compared to T-LL.\nCONCLUSIONS: Despite significant similarities between the malignant T-cell precursors, clear differences in the gene expression profiles were observed between T-ALL and T-LL implying underlying differences in the biology of the two entities."}