A Gene Expression Barcode for Microarray Data Rafael A Irizarry.

A Gene Expression Barcode A Gene Expression Barcode for Microarray Datafor Microarray Data

Rafael A Irizarry

• Zilliox MJ and Irizarry RA (2007) Nature Methods 4(11):911-913.

• http://www.rafalab.org/barcode

Probe EffectProbe Effect

BarcodeBarcode

Samples Comparison Type PAM (% correct) Bar code (% correct) Human Normal Tissues Different tissues 95 98

Mouse Normal Tissues Different tissues 91 96

Normal versus disease 60 70 Alzheimer's disease

Normal versus severe disease 83 91

Three different conditions 83 83 Adenocarcinoma

Normal versus cancer/precursor 91 91

Three different conditions 73 83 Bladder Cancer

Normal versus cancer 90 96

Renal Cell Carcinoma Normal versus cancer 94 100

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August May

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Human TissuesHuman TissuesMemory T cells 3293 cells (Kidney HEK) 5721 B lymphoblast cell line 2Adrenal Gland 2Atrial myocardium 30Amygdala 2Left ventricular apex samples 6Appendix 2Atrioventricular Node 2Bronchial epithelia 15CD71 Early Erythroid Progenito2Bone marrow CD34+ 8Bone Marrow 2Caudate nucleus 33Stem Cells (Umbilical Cord CD34+

9Na\225ve CD4 cells 3Single positive CD4 cells 3Cerebellum 29Cerebellum peduncles 2Ciliary ganglion 2Colorectal adenocarcinoma 2T cells 6Cultured adipocyte 2Lung 11DRG 2Esophageal Epithelium 8

Fetal Brain 2Fetal Lung 2Fetal Thyroid 2Vastus lateralis 4Myometrium 9Bladder 4Testis 5Skeletal myoblast, embryonic 3Hair follicle bulge 5Hair follicle sub-bulge 5Oral squamous cell epithelium 3Myoblasts 3Hematopoietic stem cells 3Frontal Cortex 28I-6 ES SSEA+ 3I-6 ES SSEA- 3Hematopoeitic stem cell- FB +/+ 3Hematopoeitic stem cell- MB +/+ 3Hematopoeitic stem cell- FB +/- 3Hematopoeitic stem cell- CB +/- 3Hematopoeitic stem cell- CB +/+ 3Hematopoeitic stem cell- BM +/+ 3Hematopoeitic stem cell- BM +/- 3Fibroblast 9HBEC 2

9HBEC 2Heart 2Hippocampus 9HMEC 3HUVEC 3Hypothalamus 25IB3-1 bronchial epithelial cells 4Intervertebral disc 4Islet 2K562 Cell line 24Kidney cells 5Leukemia Chronic Myelogenous (K562) 2Leukemia Lymphoblastic (MOLT4) 2Leukemia Promyelocytic (HL-60) 2Liver 2Lymph Node 2Lymphoma Burkitts Daudi 2Lymphoma Raji 2Medulla Oblongata 2Hep-2 4Colonic mucosal (IBS) 5Skeletal muscle 3Occipital Lobe 2Olfactory Bulb 2Ovary 2

Pancreas 2Parietal Lobe 2CD4 T cell 2CD8 T cell 2Placenta 2Pons 2Prefrontal Cortex 2Prostate 2Quadriceps femoris muscle 3Salivary Gland 2Skin 2Smooth Muscle 2Spinal Cord 2Subthalamic Nucleus 2Superior Cervical Ganglion 2Temporal Lobe 2Testi Germ Cell 2Testi Intersitial 2Testi Seminiferous Tubule 2Thalamus 2Theca cells 4Thymus 2Thyroid 2Tongue 2Tonsil 2Intrathymic T cell progenitors 3Trachea 2Trigeminal Ganglion 2Uterus 2Ventricular myocardium 5