databaseArrayExpressfile_versionsfilesTxtftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE32nnn/GSE32246/suppl/filelist.txt

Rawftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE32nnn/GSE32246/suppl/GSE32246_RAW.tar

typemirror

scores001390additionalomics_typeTranscriptomicssubmitterLars BullingerspeciesHomo Sapienssubmitter_keywordstranscription profiling by arrayfull_dataset_linkhttps://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-32246submitter_emaillars.bullinger@uniklinik-ulm.derepositoryGEOArrayExpresssample_protocolHybridization - not provided
Labeling - A universal reference RNA (pooled from 11 cell lines) was labeled identically but with Cy3-dUTP
Nucleic Acid Extraction - Normal karyotype acute myeloid leukemia (NK-AML) specimens comprise Ficoll gradient purified mononuclear cells (>80% blasts) from diagnostic peripheral blood or bone marrow. Total RNA was isolated from stored, frozen mononuclear AML-cell pellets using Trizol reagent, and RNA quality assessed by gel electrophoresis.; Protocol Type = Extract preparationdata_protocolAssay Data Transformation - ID_REF = ID_REF<br>CH1I_MEAN = Mean feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale<br>CH2I_MEAN = Mean feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale<br>CH1B_MEDIAN = The median feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel; Background<br>CH2B_MEDIAN = The median feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background<br>CH1D_MEAN = The mean feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel<br>CH2D_MEAN = .The mean feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy5 channel<br>CH1I_MEDIAN = Median feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale<br>CH2I_MEDIAN = Median feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale<br>CH1B_MEAN = The mean feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Background<br>CH2B_MEAN = The mean feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Background<br>CH1D_MEDIAN = The median feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale<br>CH2D_MEDIAN = The median feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale<br>CH1_PER_SAT = The percentage of feature pixels at wavelength 532 nm that are saturated.; Type: integer; Scale: linear_scale<br>CH2_PER_SAT = The percentage of feature pixels at wavelength 635 nm that are saturated.; Type: integer; Scale: linear_scale<br>CH1I_SD = The standard deviation of the feature intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel<br>CH2I_SD = The standard deviation of the feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel<br>CH1B_SD = The standard deviation of the feature background intensity at wavelength 532 nm.; Type: float; Scale: linear_scale; Channel: Cy3 Channel; Background<br>CH2B_SD = The standard deviation of the feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background<br>PERGTBCH1I_1SD = The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale<br>PERGTBCH2I_1SD = The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 635 nm.; Type: integer; Scale: linear_scale<br>PERGTBCH1I_2SD = The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale<br>PERGTBCH2I_2SD = The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale<br>SUM_MEAN = The sum of the arithmetic mean intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale<br>SUM_MEDIAN = The sum of the median intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale<br>RAT1_MEAN = Ratio of the arithmetic mean intensities of each spot for each wavelength, with the median background subtracted. Channel 1/Channel 2 ratio, (CH1I_MEAN - CH1B_MEDIAN)/(CH2I_MEAN - CH2B_MEDIAN) or Green/Red ratio.; Type: float; Scale: linear_scale<br>RAT2_MEAN = The ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale<br>RAT2_MEDIAN = The ratio of the median intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale<br>PIX_RAT2_MEAN = The geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale<br>PIX_RAT2_MEDIAN = The median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale<br>RAT2_SD = The geometric standard deviation of the pixel intensity ratios.; Type: float; Scale: linear_scale<br>TOT_SPIX = The total number of feature pixels.; Type: integer; Scale: linear_scale<br>TOT_BPIX = The total number of background pixels.; Type: integer; Scale: linear_scale<br>REGR = The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature.; Type: float; Scale: linear_scale<br>CORR = The correlation between channel1 (Cy3) & Channel 2 (Cy5) pixels within the spot, and is a useful quality control parameter. Generally, high values imply better fit & good spot quality.; Type: float; Scale: linear_scale<br>DIAMETER = The diameter in um of the feature-indicator.; Type: integer; Scale: linear_scale<br>X_COORD = X-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale<br>Y_COORD = Y-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale<br>TOP = Box top: int(((centerX - radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale<br>BOT = Box bottom: int(((centerX + radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale<br>LEFT = Box left: int(((centerY - radius) - yoffset) / pixelSize).; Type: integer; Scale: linear_scale<br>RIGHT = Box right: int(((centerY + radius) - yoffset) / pixelSize); Type: integer; Scale: linear_scale<br>FLAG = The type of flag associated with a feature: -100 = user-flagged null spot; -50 = software-flagged null spot; 0 = spot valid.; Type: integer; Scale: linear_scale<br>CH2IN_MEAN = Normalized value of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel<br>CH2BN_MEDIAN = Normalized value of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background<br>CH2DN_MEAN = Normalized value of mean Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale; Channel: Cy5 channel<br>RAT2N_MEAN = Type: float; Scale: linear_scale<br>CH2IN_MEDIAN = Normalized value of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale<br>CH2DN_MEDIAN = Normalized value of median Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEDIAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale<br>RAT1N_MEAN = Ratio of the means of Channel 1 (usually 532 nm) intensity to normalized Channel 2 (usually 635 nm) intensity with median background subtracted (CH1D_MEAN/CH2DN_MEAN). Channel 1/Channel 2 ratio normalized or Green/Red ratio normalized.; Type: float; Scale: linear_scale<br>RAT2N_MEDIAN = Channel 2/Channel 1 ratio normalized, RAT2_MEDIAN/Normalization factor or Red/Green median ratio normalized.; Type: float; Scale: linear_scale<br>LOG_RAT2N_MEAN = Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEAN)].; Type: float; Scale: log_base_2<br>VALUE = Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEDIAN)].; Type: float; Scale: log_base_2
Feature Extraction - VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
Image Adquisition - GenePix 4000Bsample_synonymsMyelogenous Leukemias, Myelocytic, Acute Myeloblastic, Ribonucleic, kidney marrow, Nonlymphocytic Leukemia, Myeloid, Blood, Myelocytic Leukemia, A4, 血细胞, Acute Myeloid, BLAST, TYPE, acute myeloid leukemia in remission, 3-dihydro-3, Acute Myelocytic Leukemias, DAGA4, Blasts, method, Electrophoreses, medulla ossea, Marrow, method used in an experiment, Gene Products, Line, Acute Myelocytic, Acute Nonlymphoblastic, 3'-deoxy-5-(((((2, Yellow, 外周血, MAM, SCG3, Non Polyadenylated, Myeloblastic Leukemia, RNA Gene Products, 骨髓(medulla of bone), Normalities, average, Leukemia, head kidney, acute myeloblastic leukemia (disorder), 循环细胞(circulating cell), cell, Acute Myelogenous, N, Acute Myeloblastic Leukemia, Myelogenous Leukemia, labeling, Acute Nonlymphocytic Leukemias, 3-dimethyl-5-sulfo-2-(3, Bone marrow part, Red Marrow, Non-Polyadenylated RNA, Acute Myeloid Leukemia without Maturation, acute non-lymphocytic leukaemia, circulating cells, Acute Nonlymphoblastic Leukemia, Karyotypes, Acute Nonlymphocytic Leukemia, Cy3-dUTP, Myeloid Leukemia, Myelocytic Leukemias, Red, ANLL, Nonlymphoblastic Leukemias, Myelogenous, RNA, M1, M2, whole blood, total RNA extract, ribose nucleic acid, ribonucleic acids, Cell Lines, RNS, Normalcy, 骨髓(medulla ossium), trait, Cell, Leukemias, LGMD2C, AML, Acute Myelocytic Leukemia, Nonlymphoblastic Leukemia, Nonlymphocytic Leukemias, Nonlymphoblastic, extracted material., anterior kidney, Acute Myeloid Leukemias, blood cells, 3-dimethyl-5-sulfo-3H-indolium-2-yl)propylidene)indol-1-yl)-1-oxohexyl)amino)-1-propenyl)uridine 5'-trisphosphate, medulla ossium, yeast nucleic acid, Ribonukleinsaeure, Myeloid Leukemias, pentosenucleic acids, Ribonucleic acids, Acute Nonlymphocytic, Acute Myelogenous Leukemia, Lines, ribonucleic acid, Acid, Yellow Marrow, acute myeloid leukemia without mention of remission, 髓质骨, Peripheral Blood, DMDA1, Normality, Myeloblastic, medullary bone, medulla of bone, Non Polyadenylated RNA, ANLL in Remission, Myeloblastic Leukemias, Non-Polyadenylated, 全血, pooled, acute myeloid leukaemia, reagent, Ribonucleic Acid, circulating cell, Nonlymphocytic, study protocol, Reticuloendothelial System, plan specification, disease, Acute Myeloid Leukemia with Maturation, Ficoll gradient, Health, Acute, DMDA, Acute Nonlymphoblastic Leukemias, Acute Myeloblastic Leukemias, Ficoll WBC Isolation, 循环细胞(circulating cells), SCARMD2, Acute Myelogenous Leukemias, 网状内皮系统，血液, acute myeloid leukemia in remission (disorder), Bone, AML - acute Myeloid Leukemia, acute myeloid leukaemia - categorydescription_synonymsMyelocytic, Extended Families, Networks, Extended, Kinship, Nonlymphocytic Leukemia, determination, Myeloid, adult stage, Myelocytic Leukemia, Mini Exon, Extended Family, Isocitrate:NAD+ oxidoreductase (decarboxylating), Acute Myeloid, Mutations, Transcript Expression Analysis, Risk Factors, Roles, Method, Associations, responsivity, Ayu17-449, Gene Expression Monitorings, Acute Myelocytic, Concepts, Life Cycle, Mutations., Profilings, Analysis, adult, Family Life Cycle, treatment, Kinship Network, Gene Expressions, mKIAA1546, Analyses, Acute Myeloblastic Leukemia, Population at, Myelogenous Leukemia, procedures, RGD1311625, Acute Nonlymphoblastic Leukemia, Methodological Studies, Acute Nonlymphocytic Leukemia, Role Concepts, disease management, ANLL, Family Life Cycles, associated, Display, Myelogenous, NAD Isocitrate, Populations at, Monitorings, Procedure, Isocitrate Dehydrogenase-I, results, Isocitrate Dehydrogenase, Acute Myelocytic Leukemia, Nonlymphoblastic Leukemia, Gene Expression, Nonlymphoblastic, Role Concept, Acute Myeloid Leukemias, count, Role, Acute Nonlymphocytic, Filiation, Adults, Acute Myelogenous Leukemia, acute myeloid leukemia without mention of remission, adults, Factors, Displays, Risk, death rate, Reconstituted Family, Myeloblastic, Transcriptome Profilings, ANLL in Remission, Myeloblastic Leukemias, expanded, mRNA Differential, Methodological, Nonlymphocytic, Methodological Study, Life Cycles, disease, Reconstituted, enlarged, Patient, Acute Nonlymphoblastic Leukemias, Acute Myeloblastic Leukemias, NAD, E430016J11Rik, acute myeloid leukemia in remission (disorder), AML - acute Myeloid Leukemia, Myelogenous Leukemias, big, Acute Myeloblastic, Family Member, Procedures, Dehydrogenase, Isocitrate Dehydrogenase I, number, Gene, Network, presence, acute myeloid leukemia in remission, Acute Myelocytic Leukemias, Gene Expression Profilings, large, mRNA Differential Displays, Gene Expression Pattern Analysis, Isocitrate Dehydrogenase (NAD+), Mini-Exon, Studies, Acute Nonlymphoblastic, Myeloblastic Leukemia, Risk Factor, reactivity, Leukemia, Populations at Risk, pattern, acute myeloblastic leukemia (disorder), Research, distribution, Acute Myelogenous, weak, E130014J05Rik, Acute Nonlymphocytic Leukemias, Transcript Expression, Transcriptome Analysis, Expressions, Monitoring, Population at Risk, Acute Myeloid Leukemia without Maturation, Study, acute non-lymphocytic leukaemia, time of survival, Clients, great, Myeloid Leukemia, Myelocytic Leukemias, Nonlymphoblastic Leukemias, Expression, Kinship Networks, Mcm, MCM, Family, Profiling, M1, data, M2, Transcriptome, Family Research, KIAA1546, Reconstituted Families, Factor, Client, MDS, Leukemias, AML, Concept, Family Members, Nonlymphocytic Leukemias, Differential Display, transcription profiling, count in organism, Transcript Expression Analyses, survival, Stepfamily, Myeloid Leukemias, chemical analysis, techniques, Isocitrate, mRNA Differential Display, gene expression profiling, Gene Expression Monitoring, Transcriptome Profiling, distinct, mRNA, Mini-Exons, D230010K02Rik, Exon, acute myeloid leukaemia, Differential Displays, Transcriptome Analyses, Acute Myeloid Leukemia with Maturation, NAD Isocitrate Dehydrogenase, Acute, Families, Acute Myelogenous Leukemias, 数据, assay, quantitative, response, Relatives, Stepfamilies, acute myeloid leukaemia - category, RWDD5, methodology, presence or absence in organismdata_synonymsscale tissue, C6orf190, Pak3bp, peltate hair, number, A4, IMAGE, EXTR1, Tuberosities, Computer, PAPSS 2, PAPSS 1, TYPE, DAGA4, Adenylyl-sulfate kinase, SPOT, SSAT-1, Sulfate adenylate transferase, THOC4, Software Engineering, PDZK6, spot, MAM, SCG3, Computer Program, Application, ALY|REF, hYAK3-2, proportion, p85SPR, Pip92, Cool, SK 2, Radial, Ch1, bA325O24.3, Software Application, plant peltate hair, SK 1, Computer Programs and Programming, Sulfate adenylyltransferase, C6orf207, number of, study assay, EXTL1L, APS kinase, Cy5, PDZD6, Computer Software Application, 2.7.1.25, BEF, data processing, Quality Controls, Tools, scientific observation, CH1, has or lacks parts of type, RED, REF, scale (sensu Metazoa), associated, REGR, PIX, ratio, Sulfurylase kinase 1, DYRK5, Applications Software, measuring, Sulfurylase kinase 2, betaPix, PAPS synthase 2, PAPS synthase 1, 3'-phosphoadenosine-5'-phosphosulfate synthase, Computer Software, ALY, BOTV, GASP, extra or missing physical or functional parts, trait, radius, feature_extraction, CSA2, LGMD2C, Software Tools, Tool, AI317238, Programs, mereological quality, any method, Program, Computer Applications, Software Tool, Adenosine-5'-phosphosulfate 3'-phosphotransferase, KFSDX, p85Cool1, Computer Applications Software, Computer Applications Softwares, bA325O24.4, median, SSAT, background, Softwares, scales, Software, Regressions (Psychology), IMAGE., Radial Tuberosities, Software Applications, SAT, DMDA1, scale, INT, KFSD, proportionality, TSEPA, Engineering, Control, rate, RPR, arithmetic mean, Quality, SK1, 2.7.7.4, Controls, SK2, REDK, introduction, betaPix-b, betaPix-c, DC21, Computer Programs, data analysis, Applications, DMDA, Applications Softwares, Regression, Rat2, cool-1, SCARMD2, cardinality, quotient, Radial Tuberosity, Adenylylsulfate 3'-phosphotransferase, mKIAA0142, ATP-sulfurylase, Tuberosity, Computer Software Applicationsname_synonymsMyelogenous Leukemias, Myelocytic, Myelogenous, Acute Myeloblastic, M1, M2, Nonlymphocytic Leukemia, determination, Myeloid, KIAA1546, Myelocytic Leukemia, MDS, Leukemias, Acute Myeloid, results, acute myeloid leukemia in remission, Acute Myelocytic Leukemias, AML, Mutations, Acute Myelocytic Leukemia, Nonlymphoblastic Leukemia, Nonlymphocytic Leukemias, Nonlymphoblastic, Acute Myeloid Leukemias, Ayu17-449, Myeloid Leukemias, chemical analysis, Acute Myelocytic, Acute Nonlymphoblastic, Acute Nonlymphocytic, Myeloblastic Leukemia, Acute Myelogenous Leukemia, acute myeloid leukemia without mention of remission, Leukemia, mKIAA1546, acute myeloblastic leukemia (disorder), Myeloblastic, Acute Myelogenous, ANLL in Remission, Acute Myeloblastic Leukemia, Myeloblastic Leukemias, E130014J05Rik, study., acute myeloid leukaemia, Myelogenous Leukemia, Acute Nonlymphocytic Leukemias, Nonlymphocytic, RGD1311625, Acute Myeloid Leukemia without Maturation, acute non-lymphocytic leukaemia, disease, Acute Myeloid Leukemia with Maturation, Acute, Acute Nonlymphoblastic Leukemia, Acute Nonlymphocytic Leukemia, Acute Nonlymphoblastic Leukemias, Acute Myeloblastic Leukemias, Myeloid Leukemia, Acute Myelogenous Leukemias, Myelocytic Leukemias, ANLL, Nonlymphoblastic Leukemias, assay, acute myeloid leukemia in remission (disorder), AML - acute Myeloid Leukemia, acute myeloid leukaemia - categoryview_count139additional_accessionGSE32246is_claimabletruenameTET2 mutations in acute myeloid leukemia: Results from a comprehensive genetic and clinical analysis of the AML Study Group (AMLSG)descriptionPurpose: The tet oncogene family member 2 (TET2) gene was recently identified mutated in myeloid disorders including acute myeloid leukemia (AML). To date, there is increasing evidence for a functional role of TET2 mutations (TET2mut) in AML. Thus, we explored frequency, gene expression pattern, and clinical impact of TET2mut in a large cohort of AML patients, in the context of other AML-associated aberrations. Patients and Methods: Samples from 783 younger adult AML patients were analyzed for the presence of TET2mut (coding exons 3-11), and results were correlated with data from molecular genetic analyses, gene expression profiling, and clinical outcome. Results: In total, 66 TET2mut were found in 60 (60/783; 7.6%) patients, including missense (n=37), frameshift (n=16), and nonsense (n=13) mutations, which with one exception were all heterozygous. TET2mut were not correlated with distinct clinical features or genetic alterations, except for isocitrate dehydrogenase mutations (IDHmut) that were almost mutually exclusive with TET2mut (p<0.001). TET2mut were characterized by only a weak gene expression pattern, which nevertheless reflected TET2mut-associated biology. TET2mut did not impact response to induction therapy and clinical outcome; combining patients exhibiting TET2mut and/or IDHmut revealed shorter overall survival (p=0.03), although this association was not independent from known risk factors. Conclusion: TET2mut were identified in 7.6% of younger adult AML patients and did not impact response to therapy and survival. Mutations were mutually exclusive with IDHmut, thereby supporting recent data on a common mechanism of action, which might obscure the impact of TET2mut if compared against all other AML cases. We performed a supervised class comparison analysis comparing 31 TET-mutated AML cases (TET2 mut) vs. 302 TET2-wildtype AML cases (TET wt) to see if a specific gene expression pattern associated with the presence of the identified TET2 mutations could be determined. No technical replicates were performed.datespublication2011-12-31updated2014-05-02accessionE-GEOD-32246cross_referencesTAXONOMY9606