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Platform GPL16221 Query DataSets for GPL16221
Status Public on Oct 27, 2012
Title Illumina HumanRef-8 v3.0 expression beadchip (Search Key version)
Technology type oligonucleotide beads
Distribution custom-commercial
Organism Homo sapiens
Manufacturer Illumina, Inc.
Manufacture protocol See manufacturer's website.
 
Description The HumanRef-8 v3.0 Expression BeadChip features up-to-date content derived from the National Center for Biotechnology Information Reference Sequence (NCBI RefSeq) database (Build 36.2, Release 22).

Please use the GEO Data Submission Report Plug-in v1.0 for Gene Expression which may be downloaded from https://icom.illumina.com/icom/software.ilmn?id=234 to format the normalized and raw data. These should be submitted as part of a GEOarchive. Instructions for assembling a GEOarchive may be found at http://www.ncbi.nlm.nih.gov/projects/geo/info/spreadsheet.html
 
Submission date Oct 26, 2012
Last update date Jan 18, 2013
Contact name ROOPA THAPAR
E-mail(s) rthapar@hwi.buffalo.edu, rthapar@rice.edu
Phone 713-201-7875
URL http://www.hwi.buffalo.edu/faculty_research/Thapar/thapar.html
Organization name Hauptman Woodward Medical Research Institute
Department Structural Biology
Lab Roopa Thapar
Street address 700 Ellicott Street
City Buffalo
State/province NY
ZIP/Postal code 14203
Country USA
 
Samples (55) GSM1026822, GSM1026823, GSM1169960, GSM1169961, GSM1169962, GSM1169963 
Series (3)
GSE41868 Genome-wide analysis of mRNA levels in response to a Pin1 knock-down
GSE48149 Lung tissues in systemic sclerosis have gene expression patterns unique to pulmonary fibrosis and pulmonary hypertension
GSE76809 Multi-tissue functional genomic study of systemic sclerosis
Relations
Alternative to GPL6883

Data table header descriptions
ID Internal id useful for custom design array
Transcript Internal transcript ID
GB_ACC RefSeq nucleotide accession.version
ILMN_Gene Internal gene symbol
Entrez_Gene_ID NCBI Entrez Gene ID
GI RefSeq GI
Symbol Gene symbol from the source database
Protein_Product RefSeq protein accession.version
Chromosome Chromosome
Probe_Chr_Orientation Orientation on the NCBI genome build
Cytoband Cytoband
Definition Gene description from the source
Ontology_Component Cellular component annotations from Gene Ontology project
Ontology_Process Biological process annotations from Gene Ontology project
Ontology_Function Molecular function annotations from Gene Ontology project
Synonyms Gene symbol synonyms from RefSeq

Data table
ID Transcript GB_ACC ILMN_Gene Entrez_Gene_ID GI Symbol Protein_Product Chromosome Probe_Chr_Orientation Cytoband Definition Ontology_Component Ontology_Process Ontology_Function Synonyms
ACTB ILMN_2565 NM_001101.2 ACTB 60 5016088 ACTB NP_001092.1 7 - 7p22.1c Homo sapiens actin, beta (ACTB), mRNA. cytoskeleton [goid 5856] [evidence IEA]; actin filament [goid 5884] [evidence IEA]; TIP60 histone acetyltransferase complex [goid 35267] [pmid 10966108] [evidence IDA]; cytoskeleton [goid 5856] [evidence IEA]; actin filament [goid 5884] [evidence IEA]; TIP60 histone acetyltransferase complex [goid 35267] [pmid 10966108] [evidence IDA] ATP binding [goid 5524] [evidence IEA]; nucleotide binding [goid 166] [evidence IEA]; protein binding [goid 5515] [pmid 15527767] [evidence IPI]; structural constituent of cytoskeleton [goid 5200] [evidence IEA]; ATP binding [goid 5524] [evidence IEA]; nucleotide binding [goid 166] [evidence IEA]; protein binding [goid 5515] [pmid 15527767] [evidence IPI]; structural constituent of cytoskeleton [goid 5200] [evidence IEA] PS1TP5BP1; beta-actin
ILMN_10000 ILMN_10000 NM_007112.3 THBS3 7059 40317629 THBS3 NP_009043.1 1 - 1q22a Homo sapiens thrombospondin 3 (THBS3), mRNA. extracellular region [goid 5576] [evidence IEA]; extracellular matrix (sensu Metazoa) [goid 5578] [evidence NR ] cell motility [goid 6928] [evidence NR ]; cell adhesion [goid 7155] [evidence IEA]; cell-matrix adhesion [goid 7160] [pmid 8468055] [evidence TAS] structural molecule activity [goid 5198] [evidence IEA]; heparin binding [goid 8201] [evidence NR ]; calcium ion binding [goid 5509] [pmid 8288588] [evidence TAS]; protein binding [goid 5515] [evidence IEA] MGC119564; TSP3; MGC119565
ILMN_10001 ILMN_10001 NM_018976.3 SLC38A2 54407 31543637 SLC38A2 NP_061849.2 12 - 12q13.11a Homo sapiens solute carrier family 38, member 2 (SLC38A2), mRNA. SAT2; KIAA1382; PRO1068; ATA2; SNAT2
ILMN_10002 ILMN_10002 NM_175569.1 XG 7499 28212219 XG NP_780778.1 X + Xp22.33c Homo sapiens Xg blood group (XG), mRNA. membrane [goid 16020] [evidence NAS]; integral to membrane [goid 16021] [evidence IEA] biological process unknown [goid 4] [evidence ND ] molecular function unknown [goid 5554] [pmid 8054981] [evidence ND ] MGC118760; MGC118759; MGC118758; PBDX; MGC118761
ILMN_10003 ILMN_10003 NM_001002000.1 GMPR2 51292 50541951 GMPR2 NP_001002000.1 14 + 14q12a Homo sapiens guanosine monophosphate reductase 2 (GMPR2), transcript variant 2, mRNA. metabolism [goid 8152] [evidence IEA]; nucleotide metabolism [goid 9117] [evidence IEA] metal ion binding [goid 46872] [evidence IEA]; oxidoreductase activity [goid 16491] [evidence IEA]; potassium ion binding [goid 30955] [evidence IEA]; catalytic activity [goid 3824] [evidence IEA]; GMP reductase activity [goid 3920] [evidence IEA] MGC15084; MGC830
ILMN_10004 ILMN_10004 NM_001954.3 DDR1 780 38327631 DDR1 NP_001945.3 6 + 6p21.33a Homo sapiens discoidin domain receptor family, member 1 (DDR1), transcript variant 2, mRNA. integral to plasma membrane [goid 5887] [pmid 8390675] [evidence TAS]; membrane [goid 16020] [evidence IEA]; membrane [goid 16020] [evidence IEA]; integral to plasma membrane [goid 5887] [pmid 8390675] [evidence TAS] cell adhesion [goid 7155] [pmid 8302582] [evidence TAS]; transmembrane receptor protein tyrosine kinase signaling pathway [goid 7169] [evidence IEA]; protein amino acid phosphorylation [goid 6468] [evidence IEA]; cell adhesion [goid 7155] [pmid 8302582] [evidence TAS]; transmembrane receptor protein tyrosine kinase signaling pathway [goid 7169] [evidence IEA]; protein amino acid phosphorylation [goid 6468] [evidence IEA] transferase activity [goid 16740] [evidence IEA]; protein-tyrosine kinase activity [goid 4713] [evidence IEA]; nucleotide binding [goid 166] [evidence IEA]; transmembrane receptor protein tyrosine kinase activity [goid 4714] [pmid 9659899] [evidence TAS]; ATP binding [goid 5524] [evidence IEA]; receptor activity [goid 4872] [evidence IEA]; nucleotide binding [goid 166] [evidence IEA]; transmembrane receptor protein tyrosine kinase activity [goid 4714] [pmid 9659899] [evidence TAS]; receptor activity [goid 4872] [evidence IEA]; transferase activity [goid 16740] [evidence IEA]; ATP binding [goid 5524] [evidence IEA]; protein-tyrosine kinase activity [goid 4713] [evidence IEA] CAK; EDDR1; CD167; TRKE; NEP; PTK3A; PTK3; NTRK4; MCK10; RTK6; DDR
ILMN_10005 ILMN_10005 NM_031966.2 CCNB1 891 34304372 CCNB1 NP_114172.1 5 + 5q13.2a Homo sapiens cyclin B1 (CCNB1), mRNA. nucleus [goid 5634] [evidence IEA] cell division [goid 51301] [evidence IEA]; mitosis [goid 7067] [evidence IEA]; G2/M transition of mitotic cell cycle [goid 86] [evidence NAS]; cell cycle [goid 7049] [evidence IEA] protein binding [goid 5515] [pmid 10373560] [evidence IPI] CCNB
ILMN_10006 ILMN_10006 NM_032752.1 ZNF496 84838 14249385 ZNF496 NP_116141.1 1 - 1q44e Homo sapiens zinc finger protein 496 (ZNF496), mRNA. nucleus [goid 5634] [evidence IEA]; intracellular [goid 5622] [evidence IEA] transcription [goid 6350] [evidence IEA]; regulation of transcription, DNA-dependent [goid 6355] [evidence IEA] transcription factor activity [goid 3700] [evidence IEA]; zinc ion binding [goid 8270] [evidence IEA]; metal ion binding [goid 46872] [evidence IEA]; nucleic acid binding [goid 3676] [evidence IEA]; protein binding [goid 5515] [pmid 16189514] [evidence IPI] ZKSCAN17; MGC15548; NIZP1
ILMN_10009 ILMN_10009 NM_001014444.1 CRYM 1428 62241007 CRYM NP_001014444.1 16 - 16p12.2b Homo sapiens crystallin, mu (CRYM), transcript variant 2, mRNA. visual perception [goid 7601] [pmid 1384048] [evidence TAS] ornithine cyclodeaminase activity [goid 8473] [pmid 1384048] [evidence TAS] THBP; DFNA40
ILMN_1001 ILMN_1001 NM_033128.1 SCIN 85477 14916472 SCIN NP_149119.1 7 + 7p21.3a Homo sapiens scinderin (SCIN), mRNA. cytoskeleton [goid 5856] [evidence IEA]; cell cortex [goid 5938] [evidence ISS]; cytoplasm [goid 5737] [evidence ISS] calcium ion-dependent exocytosis [goid 17156] [evidence ISS]; positive regulation of apoptosis [goid 43065] [pmid 11568009] [evidence IMP]; barbed-end actin filament capping [goid 51016] [evidence IEA]; positive regulation of secretion [goid 51047] [evidence ISS]; negative regulation of cell proliferation [goid 8285] [pmid 11568009] [evidence IMP]; actin nucleation [goid 45010] [evidence ISS]; actin filament severing [goid 51014] [pmid 11568009] [evidence IMP]; positive regulation of megakaryocyte differentiation [goid 45654] [pmid 11568009] [evidence IMP] actin filament binding [goid 51015] [evidence ISS]; phosphatidylserine binding [goid 1786] [evidence ISS]; phosphatidylinositol binding [goid 5545] [pmid 11568009] [evidence TAS]; phosphatidylinositol-4,5-bisphosphate binding [goid 5546] [evidence ISS]; calcium ion binding [goid 5509] [pmid 11568009] [evidence TAS] KIAA1905
ILMN_10010 ILMN_10010 NM_000042.1 APOH 350 4557326 APOH NP_000033.1 17 - 17q24.2a Homo sapiens apolipoprotein H (beta-2-glycoprotein I) (APOH), mRNA. extracellular region [goid 5576] [pmid 14718574] [evidence NAS] defense response [goid 6952] [evidence NR ] heparin binding [goid 8201] [evidence IEA]; lipid transporter activity [goid 5319] [evidence NR ] BG; B2G1
ILMN_10011 ILMN_10011 NM_005904.2 SMAD7 4092 52856403 SMAD7 NP_005895.1 18 - 18q21.1e Homo sapiens SMAD family member 7 (SMAD7), mRNA. nucleus [goid 5634] [evidence IEA]; intracellular [goid 5622] [evidence IEA] transcription [goid 6350] [evidence IEA]; regulation of transcription, DNA-dependent [goid 6355] [evidence IEA]; response to stress [goid 6950] [pmid 9256479] [evidence TAS]; transforming growth factor beta receptor signaling pathway [goid 7179] [pmid 10823886] [evidence TAS] transforming growth factor beta receptor, inhibitory cytoplasmic mediator activity [goid 30617] [pmid 9215638] [evidence TAS]; receptor signaling protein serine/threonine kinase signaling protein activity [goid 5076] [evidence NR ]; protein binding [goid 5515] [pmid 9256479] [evidence TAS] MADH8; MADH7; FLJ16482
ILMN_10012 ILMN_10012 NM_001008539.1 SLC7A2 6542 56549678 SLC7A2 NP_001008539.1 8 + 8p22b Homo sapiens solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 (SLC7A2), transcript variant 2, mRNA. membrane [goid 16020] [evidence IEA]; integral to plasma membrane [goid 5887] [pmid 8954799] [evidence TAS]; membrane fraction [goid 5624] [pmid 8954799] [evidence TAS]; integral to membrane [goid 16021] [evidence IEA] amino acid metabolism [goid 6520] [pmid 8954799] [evidence TAS]; amino acid transport [goid 6865] [evidence IEA]; transport [goid 6810] [pmid 8954799] [evidence TAS] amino acid permease activity [goid 15359] [evidence IEA]; basic amino acid transporter activity [goid 15174] [pmid 8954799] [evidence TAS] CAT-2; HCAT2; ATRC2
ILMN_10013 ILMN_10013 NM_002289.2 LALBA 3906 62739152 LALBA NP_002280.1 12 - 12q13.11c Homo sapiens lactalbumin, alpha- (LALBA), mRNA. extracellular space [goid 5615] [pmid 7644538] [evidence TAS] lactose biosynthesis [goid 5989] [pmid 7708733] [evidence TAS]; cell-cell signaling [goid 7267] [pmid 7644538] [evidence TAS]; induction of apoptosis [goid 6917] [pmid 7644538] [evidence TAS]; signal transduction [goid 7165] [pmid 7644538] [evidence TAS] lactose synthase activity [goid 4461] [evidence IEA]; calcium ion binding [goid 5509] [evidence IEA]
ILMN_10014 ILMN_10014 NM_020535.3 KIR2DL5A 57292 65508540 KIR2DL5A NP_065396.1 19 + Homo sapiens killer cell immunoglobulin-like receptor, two domains, long cytoplasmic tail, 5A (KIR2DL5A), mRNA. receptor activity [goid 4872] [evidence IEA]; receptor activity [goid 4872] [evidence IEA]; receptor activity [goid 4872] [evidence IEA] KIR2DL5; CD158F; KIR2DL5.1; KIR2DL5.3
ILMN_10016 ILMN_10016 NM_001362.2 DIO3 1735 55750010 DIO3 NP_001353.3 14 + 14q32.31b Homo sapiens deiodinase, iodothyronine, type III (DIO3), mRNA. integral to membrane [goid 16021] [evidence IEA]; membrane [goid 16020] [evidence IEA] hormone biosynthesis [goid 42446] [evidence IEA] thyroxine 5'-deiodinase activity [goid 4800] [pmid 7593630] [evidence NAS]; selenium binding [goid 8430] [evidence IEA] D3; DIOIII; 5DIII; TXDI3
ILMN_10019 ILMN_10019 NM_001024808.1 BCL7A 605 67190735 BCL7A NP_001019979.1 12 + 12q24.31c Homo sapiens B-cell CLL/lymphoma 7A (BCL7A), transcript variant 2, mRNA. BCL7
ILMN_1002 ILMN_1002 NM_175053.2 K6IRS4 121391 31341312 K6IRS4 NP_778223.1 12 - 12q13.13d Homo sapiens keratin 74 (KRT74), mRNA. intermediate filament [goid 5882] [evidence IEA] structural molecule activity [goid 5198] [evidence IEA] K6IRS4; KRT5C; KRT6IRS4
ILMN_10020 ILMN_10020 NM_003304.3 TRPC1 7220 27545448 TRPC1 NP_003295.1 3 + 3q23d Homo sapiens transient receptor potential cation channel, subfamily C, member 1 (TRPC1), mRNA. integral to plasma membrane [goid 5887] [pmid 7568191] [evidence TAS]; plasma membrane [goid 5886] [pmid 8663995] [evidence NAS] cation transport [goid 6812] [evidence IEA]; calcium ion transport [goid 6816] [pmid 8646775] [evidence TAS] store-operated calcium channel activity [goid 15279] [pmid 8663995] [evidence TAS]; calcium ion binding [goid 5509] [evidence IEA] HTRP-1; TRP1
ILMN_10021 ILMN_10021 NM_013975.2 LIG3 3980 73747828 LIG3 NP_039269.2 17 + 17q12a Homo sapiens ligase III, DNA, ATP-dependent (LIG3), nuclear gene encoding mitochondrial protein, transcript variant alpha, mRNA. nucleus [goid 5634] [pmid 7565692] [evidence TAS] cell cycle [goid 7049] [evidence IEA]; cell division [goid 51301] [evidence IEA]; meiotic recombination [goid 7131] [pmid 7565692] [evidence TAS]; spermatogenesis [goid 7283] [pmid 7565692] [evidence TAS]; DNA replication [goid 6260] [evidence IEA]; DNA repair [goid 6281] [pmid 7565692] [evidence TAS] metal ion binding [goid 46872] [evidence IEA]; nucleotide binding [goid 166] [evidence IEA]; DNA ligase (ATP) activity [goid 3910] [evidence IEA]; DNA binding [goid 3677] [pmid 7565692] [evidence TAS]; ATP binding [goid 5524] [evidence IEA]; ligase activity [goid 16874] [evidence IEA]

Total number of rows: 22304

Table truncated, full table size 10748 Kbytes.




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