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Series GSE1437 Query DataSets for GSE1437
Status Public on Dec 27, 2004
Title F9 cells after exposure to RA or TSA
Organism Mus musculus
Experiment type Expression profiling by array
Summary F9 cells were exposed to two different differentiating agents (retinoic acid or trichostatin A both dissolved in 100% ethonal) for 24 hrs. Control cells were exposed to ethonal for 24hrs
Keywords: repeat sample
 
 
Contributor(s) Sangster NM, Yu L, Eifert C, McCormick PJ
Citation(s) 15467438, 18959802
Submission date May 27, 2004
Last update date Feb 18, 2018
Contact name Niquiche Sangster
E-mail(s) ns0401@albany.edu
Phone (518) 591-8305
Organization name University at Albany
Department Biology
Lab PJ McCormick
Street address
City Albany
State/province NY
ZIP/Postal code 12144
Country USA
 
Platforms (1)
GPL81 [MG_U74Av2] Affymetrix Murine Genome U74A Version 2 Array
Samples (9)
GSM24053 F9 con sample #1
GSM24054 F9 con sample #2
GSM24055 F9 con sample #3
Relations
BioProject PRJNA89977

Table I. Genes positively affected by RA & TSA header descriptions
Probe Set
Title
Symbol
Function(a)
RA(b)
SD
TSA(b)
SD

Data table
Probe Set Title Symbol Function(a) RA(b) SD TSA(b) SD
101194_at stimulated by retinoic acid gene 8 Stra8* spermatogenesis 224 14.9 21.2 5.21
100127_at cellular retinoic acid binding protein II Crabp2* transport 44.8 14.8 18.9 8.65
103477_at caudal type homeo box 1 Cdx-1 regulation of transcription, DNA-dependent;development;pattern specification 13.8 1.69 14.9 4.79
94079_at septin 4 4-Sep* cytokinesis 4.90 1.02 14.9 2.73
93981_at plasminogen activator, tissue Plat/t-PA proteolysis and peptidolysis 5.58 1.13 12.5 6.99
102384_at RIKEN cDNA 2610209L14 gene 2610209L14Rik* regulation of transcription, DNA-dependent 2.92 0.24 12.2 2.37
93750_at gelsolin Gsn* cytoskeleton 2.56 0.25 11.2 2.34
96918_at fructose bisphosphatase 1 Fbp1 carbohydrate metabolism;gluconeogenesis 6.49 4.03 11.0 1.56
95562_at RIKEN cDNA 2410154J16 gene 2410154J16Rik* unknown 27.3 7.39 10.6 4.38
102956_at homeo box, msh-like 2 Msx2 regulation of transcription, DNA-dependent, development 9.77 0.83 10.1 2.36
93714_f_at histocompatibility 2, L region H2-L* defense response 3.81 1.40 9.23 3.04
93664_at ATPase, Na+/K+ transporting, beta 2 polypeptide Atp1b2* sodium transport;potassium transport;cell adhesion 2.93 0.78 8.80 2.65
92502_at zinc finger protein regulator of apoptosis and cell cycle arrest Zac1 regulation of cell cycle;apoptosis 5.42 1.24 7.74 2.11
93028_at H19 fetal liver mRNA H19* development 3.87 1.27 7.56 3.04
92295_at sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E Sema3e development;neurogenesis 12.73 4.94 7.45 3.75
93092_at histocompatibility 2, class II, locus DMa H2-Dma antigen presentation, exogenous antigen;immune response;antigen processing, exogenous antigen via MHC class II;defense response 3.99 1.43 7.21 0.96
93430_at chemokine orphan receptor 1 Cmkor1 G-protein coupled receptor protein signaling pathway, chemotaxis;defense response 10.2 5.23 6.99 2.81
95419_at H1 histone family, member 0 H1f0* chromosome organization and biogenesis;nucleosome assembly 2.42 0.47 6.33 0.57
96337_at septin 5 5-Sep cytokinesis 4.71 0.87 6.24 0.40
160420_r_at tubulin, alpha 3 Tuba3* microtubule-based process;microtubule-based movement 3.03 0.43 6.04 1.00

Total number of rows: 80

Table truncated, full table size 7 Kbytes.




Table II. Genes negatively affected by RA & TSA header descriptions
Probe Set
Title
Symbol
Function(a)
RA(b)
SD
TSA(b)
SD

Data table
Probe Set Title Symbol Function(a) RA(b) SD TSA(b) SD
162076_r_at glutamate receptor, ionotropic, AMPA2 (alpha 2) Gria2* synaptic transmission, transport 0.04 0.02 0.25 0.34
92644_s_at myeloblastosis oncogene Myb* (c-myb) cell growth and/or maintenance;regulation of cell cycle;regulation of transcription, DNA-dependent 0.05 0.02 0.20 0.01
93122_at acidic epididymal glycoprotein 1 Aeg1* sperm maturation 0.07 0.03 0.44 0.21
92813_at cytochrome P450, 2j6 Cyp2j6* electron transport 0.10 0.05 0.37 0.19
94724_at matrix metalloproteinase 10 Mmp10 xenobiotic metabolism;proteolysis and peptidolysis 0.12 0.06 0.20 0.06
93002_r_at teratocarcinoma-derived growth factor Tdgf1* activation of MAPK,positive regulation of cell proliferation,EGF receptor signaling pathway 0.15 0.04 0.31 0.10
162108_f_at salivary protein 1 Spt1 salivary protein 0.17 0.01 0.12 0.06
160828_at inhibin beta-B Inhbb growth factor 0.17 0.13 0.06 0.04
98817_at follistatin Fst TGF Beta Signaling Pathway 0.22 0.01 0.28 0.09
99402_at ADP-ribosyltransferase 2b Art2b peptidyl-arginine ADP-ribosylation 0.23 0.07 0.19 0.11
92889_r_at forkhead box D3 Foxd3* transcription;regulation of transcription, DNA-dependent 0.24 0.16 0.04 0.02
98388_at RIKEN cDNA 9130004K12 gene 9130004K12Rik unknown 0.24 0.05 0.28 0.16
102220_at undifferentiated embryonic cell transcription factor 1 UTF1 regulation of transcription, DNA-dependent 0.27 0.10 0.37 0.10
102370_at hydroxysteroid (17-beta) dehydrogenase 11 Hsd17b11 oxidoreductase 0.31 0.09 0.46 0.08
96518_at expressed sequence AU017197 AU017197 unknown 0.33 0.13 0.46 0.12
98079_at carbonic anhydrase 14 Car14 one-carbon compound metabolism 0.33 0.06 0.32 0.03
103697_at expressed sequence AW061234 AW061234 unknown 0.35 0.08 0.29 0.06
100920_at ectodermal-neural cortex 1 Enc1 cytoskeleton, development 0.35 0.10 0.41 0.13
100023_at myeloblastosis oncogene-like 2 Mybl2 (b-myb) cell growth and/or maintenance;regulation of cell cycle;regulation of transcription, DNA-dependent 0.37 0.04 0.35 0.07
103065_at solute carrier family 20, member 1 Slc20a1 transport 0.38 0.02 0.49 0.07

Total number of rows: 46

Table truncated, full table size 4 Kbytes.




Table III. Genes affected only by RA (no effect TSA) header descriptions
A) Positive

Data table
A) Positive
Probe Set Title Symbol Function(a) RA(b) SD TSA(b) SD
96586_at crystallin, gamma C Crygc sensory organ development 18.01 8.59 0.96 0.23
97386_at expressed sequence AI430822 AI430822 unknown 16.60 0.68 0.96 0.44
103086_at homeo box A5 Hoxa5 pattern specification;organogenesis;development;regulation of transcription, DNA-dependent 8.63 0.40 0.81 0.09
97745_at homeo box A4 Hoxa4 pattern specification;organogenesis;development;regulation of transcription, DNA-dependent 6.48 2.21 0.89 0.17
99034_at Iroquois related homeobox 3 (Drosophila) Irx3 regulation of transcription, DNA-dependent 4.50 1.51 0.93 0.18
97579_f_at Mus musculus CrygF gene, exons 2 and 3, intron B and partial CDS Crygf structural constituent of eye lens, sensory organ development 3.91 0.65 0.93 0.24
103445_at homeo box B6 Hoxb6 pattern specification;organogenesis;development;regulation of transcription, DNA-dependent 3.58 0.23 0.81 0.13
94813_at growth arrest specific 1 Gas1 cell cycle arrest 3.27 0.44 1.04 0.52
94432_at sialyltransferase 1 (beta-galactoside alpha-2,6-sialyltransferase) Siat1 protein amino acid glycosylation 3.03 0.84 0.82 0.08
97811_at ADP-ribosylation factor GTPase activating protein 3 Arfgap3 intracellular protein transport;protein transport 2.88 0.60 1.16 0.15
100491_at solute carrier family 16 (monocarboxylic acid transporters), member 2 Slc16a2 transport 2.77 0.27 1.01 0.12
102389_s_at brain abundant, membrane attached signal protein 2 Basp2/Gap43 regulation of cell growth 2.73 0.86 1.01 0.19
101093_at procollagen, type IV, alpha 1 Col4a1 cell adhesion 2.69 0.65 0.85 0.08
161691_at RIKEN cDNA 2600017A12 gene 2600017A12Rik unknown 2.65 0.35 0.89 0.11
95152_g_at CK2 interacting protein 1 Ckip1-pending unknown 2.45 0.23 0.89 0.17
94817_at serine (or cysteine) proteinase inhibitor, clade H, member 1 Serpinh1/Hsp47 heat shock protein activity 2.33 0.20 0.87 0.13
97509_f_at fibroblast growth factor receptor 1 Fgfr1 signal transduction;salivary gland morphogenesis;inner ear morphogenesis;protein amino acid phosphorylation 2.31 0.26 1.18 0.18
94309_g_at fibulin 1 Fbln1 extracellular matrix 2.11 0.08 0.92 0.14
92914_at homeo box B7 Hoxb7 organogenesis; pattern specification; regulation of transcription, DNA-dependent; development 2.00 0.08 0.99 0.01

Total number of rows: 38

Table truncated, full table size 3 Kbytes.




Table IV. Genes affected only by TSA (no effect RA) header descriptions
A)Positive

Data table
A)Positive
Probe Set Title Symbol Function(a) RA(b) SD TSA(b) SD
94738_s_at defensin related cryptdin, related sequence 2 Defcr-rs2 defense/immunity protein activity 0.94 0.14 41.20 21.38
100959_at S100 calcium binding protein A13 S100a13 calcium ion binding 0.96 0.14 3.54 1.14
102061_at myeloid leukemia factor 1 Mlf1 cell differentiation 0.99 0.56 11.66 2.31
102130_f_at EST 0.94 0.11 2.62 0.59
102742_g_at microtubule-associated protein tau Mapt microtubule-based process 0.94 0.16 2.92 0.90
103094_at small EDRK-rich factor 1 Serf1 spinal muscular atrophy candidate 1.04 0.20 2.26 0.16
103394_at FXYD domain-containing ion transport regulator 5 Fxyd5 ion transport 1.01 0.31 6.02 1.29
103443_at absent in melanoma 1 Aim1 Candidate tumor supressor in melonoma 1.09 0.15 4.08 0.33
161046_at cytokine receptor-like factor 1 Crlf1 immune response, development 0.99 0.34 11.49 1.86
162475_f_at peptidoglycan recognition protein Pglyrp immune response;apoptosis 1.03 0.35 9.10 1.50
92614_at inhibitor of DNA binding 3 Idb3 protein binding 1.02 0.29 4.35 0.84
92770_at S100 calcium binding protein A6 (calcyclin) S100a6 cell proliferation;cell cycle 1.03 0.12 18.17 6.08
93085_at proteosome (prosome, macropain) subunit, beta type 9 (large multifunctional protease 2) Psmb9/LMP2 immune response;ubiquitin-dependent protein catabolism 1.00 0.11 12.69 2.51
94350_f_at NAD(P)H dehydrogenase, quinone 1 Nqo1 electron transport 0.92 0.10 2.91 0.56
94393_r_at elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 2 Elovl2 very-long-chain fatty acid metabolism;fatty acid biosynthesis 1.02 0.21 3.06 0.68
97825_at p53 apoptosis effector related to Pmp22 Perp-pending induction of apoptosis 0.96 0.16 2.62 0.56
99654_s_at ESTs 0.91 0.12 4.45 1.78
99669_at lectin, galactose binding, soluble 1 Lgals1 galactose binding lectin 0.99 0.20 2.58 0.41
99931_at laminin, alpha 5 Lama5 cell adhesion 0.96 0.07 2.22 0.10

Total number of rows: 46

Table truncated, full table size 4 Kbytes.




Table V. Genes inversely affected by RA & TSA header descriptions
A) Increase RA vs. Decrease TSA

Data table
A) Increase RA vs. Decrease TSA
Probe Set Title Symbol Function(a) RA(b) SD TSA(b) SD
102345_at endometrial bleeding associated factor Ebaf/stra3 development, growth factor, cytokine 4.19 1.10 0.23 0.03
102788_s_at paired-like homeodomain transcription factor 2 Pitx2 transcription factor, regulation of transcription, DNA-dependent, development 10.04 1.84 0.07 0.01
161211_r_at SRY-box containing gene 6 Sox6 transcription factor, regulation of transcription, DNA-dependent 2.63 0.71 0.22 0.09
162302_f_at folate receptor 1 (adult) Folr1 post-translational membrane targeting 4.63 1.24 0.46 0.10
93574_at serine (or cysteine) proteinase inhibitor, clade F), member 1 Serpinf1/Pedf serpin 8.97 1.31 0.27 0.13
B) Decrease RA vs Increase TSA
Probe Set Title Symbol Function(a) RA(b) SD TSA(b) SD
101918_at transforming growth factor, beta 1 Tgfb1 necrosis;skeletal development;lymph gland development;myogenesis;organogenesis;negative regulation of cell proliferation;cell growth;defense response;regulation of myogenesis,cell proliferation;inflammatory response 0.30 0.11 8.35 1.87
101952_at C21orf18 homolog LOC224440 unknown 0.38 0.09 2.28 0.22
103317_at coagulation factor C homolog (Limulus polyphemus) Coch blood coagulation factor 0.43 0.33 6.98 1.45
104550_at RIKEN cDNA 1200011C15 gene 1200011C15Rik oxidoreductase, monooxygenase 0.26 0.10 2.90 0.32
160893_at guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 2 Gngt2 G-protein coupled receptor protein signaling pathway;signal transduction 0.49 0.07 8.40 2.89
93573_at metallothionein 1 Mt1; MT-I; Mt-1 heavy metal binding 0.30 0.05 3.12 0.29
93640_s_at testis expressed gene 21 Tex21-pending unknown 0.35 0.20 3.49 1.34
95036_at calbindin 2 Calb2 calcium ion binding 0.35 0.09 3.07 0.38
95655_at RIKEN cDNA 4930434H03 gene 4930434H03Rik unknown 0.47 0.05 3.08 0.87
96273_at neurogranin (protein kinase C substrate, RC3) Nrgn protein kinase cascade 0.38 0.30 4.04 0.20
96599_at ESTs unknown 0.22 0.16 3.04 0.81
97317_at ectonucleotide pyrophosphatase/phosphodiesterase 2 Enpp2 hydrolase, phosphodiesterase I, nucleotide pyrophosphatase 0.42 0.10 3.33 0.12

Total number of rows: 26

Table truncated, full table size 2 Kbytes.




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