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Series GSE620 Query DataSets for GSE620
Status Public on Oct 29, 2003
Title Gene expression profile analysis of 4-phenylbutyrate treatment of IB3-1 bronchial epithelial cell line
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Most individuals with cystic fibrosis (CF) carry one or two mutations that result in a maturation defect of the full-length CFTR protein. The deltaF508 mutation results in a mutant protein that is degraded by the proteasome instead of progressing to the apical membrane where it functions as a cyclic AMP-regulated chloride channel. 4 phenylbutyrate modulates heat shock protein expression and promotes trafficking of deltaF508 thus permitting maturation and membrane insertion. The goal of this study was to gain insight into the genetic mechanism of PBA action through a large-scale analysis of gene expression. The Affymetrix genome spanning U133 microarray set was used to compare mRNA expression in untreated IB3-1 cell line cultures with cultures treated with 1mM 4-phenylbuyterate for 12 and 24 hr. IB3-1 deltaF508/W1282X) bronchial epithelial cells were cultured in T75 flasks with gentamicin-free LHC-8 medium. Cells were fed with 10 ml of media every 2 to 3 days. After reaching 80% confluence cells were treated with 1 mM PBA. A T75 flask of confluent IB3-1 cells was rinsed twice with ice cold Hank’s buffer then scraped into 3ml of ice cold TRIzol (Gibco BRL) then rinsed with 3 ml ice cold TRIzol and the mRNA was isolated according to the TRIzol protocol. A total of 5 control cultures, 3 cultures with 12 hr BPA application and 3 cultures with 24 hr PBA application were processed
Keywords: time-course
 
 
Contributor(s) Wright JM, Zeitlin PL, Cebotaru L, Guggino SE, Guggino WB
Citation(s) 14583596
Submission date Sep 03, 2003
Last update date Aug 10, 2018
Contact name Jerry M. Wright
E-mail(s) jwright@jhmi.edu
Phone 410-614-5010
Organization name Johns Hopkins Medical Institutions
Department Physiology
Street address 725 N. Wolfe St
City Baltimore
State/province MD
ZIP/Postal code 21205
Country USA
 
Platforms (2)
GPL96 [HG-U133A] Affymetrix Human Genome U133A Array
GPL97 [HG-U133B] Affymetrix Human Genome U133B Array
Samples (22)
GSM9514 0 hr Ctl A-chip 3-13-03
GSM9515 0 hr Ctl A-chip 1-21-03
GSM9516 0 hr Ctl A-chip 6-11-02
Relations
BioProject PRJNA87521

Cluster 1: Probe sets significantly changed by PBA treatment header descriptions
Affy ID
0 hr (Normalized intensity)
12 hr (Normalized intensity)
24 hr (Normalized intensity)
Common
GenBank
Description

Data table
Affy ID 0 hr (Normalized intensity) 12 hr (Normalized intensity) 24 hr (Normalized intensity) Common GenBank Description
Signaling
223452_s_at 1.7090658 1.0146277 0.76830274 AL117600 XM_043151; Both Celera and NCBI find same domain, otherwise uncharacterized; ortholog of mouse adp-ribosylation-like factor 6 interacting protein 2 (2-blast 85% identity); Guanylate-binding protein, N-terminal domain. Transcription of the anti-viral guanylate-binding protein (GBP) is induced by interferon-gamma during macrophage induction. This family contains GBP1 and GPB2, both GTPases capable of binding GTP, GDP and GMP
244030_at 1.4802725 0.9826246 0.8801376 STYX NM_145251 NM_145251; serine/threonine/tyrosine interacting protein;STYX domain adds to the repertoire of modular domains that can mediate intracellular signaling in response to protein phosphorylation
RNA
231843_at 1.4336354 1.0347776 0.84700286 KIAA1595 XM_045520 pfam- DEAD-like helicase superfamily. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.
227110_at 1.4029067 1.0758003 0.6353888 HNRPC NM_031314 heterogeneous nuclear ribonucleoprotein C (C1/C2); Ariadne-2 protein homolog (ARI-2) (Triad1 protein).These proteins are associated with pre-mRNAs in the nucleus and appear to influence pre-mRNA processing and other aspects of mRNA metabolism and transport. 2 isoforms NM_004500, NM_031314
224714_at 1.5301582 1.0806509 0.6697256 MKI67IP NM_032390 Interacts with nucleolar phosphoprotein through Forkhead associated domain on pKi-67. Pfam- RNA binding protein. PMID: 11342549
224523_s_at 1.4159906 1.0787356 0.6358406 MGC4308 NM_032359 pfam - DEAD/DEAH box helicase- involved in unwinding nucleic acids and various aspects of RNA metabolism
222398_s_at 1.4112586 1.1386119 0.6309118 U5-116KD NM_004247 U5 snRNP-specific protein. pfam03144 Elongation factor Tu domain 2. Elongation factor Tu consists of three structural domains. This, the second domain, is involved in binding to charged tRNA. This domain is also found in other proteins such as elongation factor G and translation initiation factor IF-2
204658_at 1.4334122 1.1078998 0.65938324 HSU53209 NM_013293 pre-mRNA processing factor; Homo sapiens transformer-2 alpha (htra-2 alpha). RNA binding protein domains
222430_s_at 1.4146345 1.0326276 0.6482412 HGRG8 NM_016258 Homo sapiens, high-glucose-regulated protein 8. Pfam- putative splicing factor, tyrosine-phosphoylated nuclear protein
218156_s_at 1.6291847 0.88601065 0.43491048 FLJ10534 NM_018128 CDD:COG5192, BMS1, GTP-binding protein required for 40S ribosome biogenesis [Translation, ribosomal structure and biogenesis]. NCBI annotates protein as a serine racemase
225348_at 1.3855543 1.0138597 0.6366804 FUSIP1 AK001479 NM_006625; FUS interacting protein (serine-arginine rich) 1 isoform 1 NM_021993; NM_054016; FUS interacting protein (serine-arginine rich) 1 isoform 2; NM_021993 replaced by NM_054016; Member of the serine-arginine (SR) family of proteins, which is involved in constitutive and regulated RNA splicing. Members of this family are characterized by N-terminal RNP1 and RNP2 motifs, which are required for binding to RNA, and multiple C-terminal SR/RS repeats, which are important in mediating association with other cellular proteins.
231718_at 1.4222896 0.8014412 0.66037893 SLU7 NM_006425 step II splicing factor SLU7. functions in restructuring the spliceosome between the catalytic steps of splicing
222443_s_at 1.5378356 1.2278483 0.7533718 RBM8A NM_005105 RNA binding motif protein 8A
223035_s_at 1.3986365 1.2125903 0.8051443 FRSB NM_005687 phenylalanyl-tRNA synthetase beta-subunit.
223416_at 1.3777913 1.2366493 0.8330658 CGI-110 NM_016047 CGI-110 protein, RNA binding domain
244811_at 1.6487906 1.3381889 0.8538915 EEF1E1 AI561173 NM_004280; eukaryotic translation elongation factor 1 epsilon 1; COG - Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones] transferase function not demonstrated in EEF1E1 but domain is also found in HSP26 family of stress response proteins
225107_at 1.4774824 1.0087813 1.1148438 HNRPA2B1 AI963008 heterogeneous nuclear ribonucleoprotein A2/B1, transcript variants 1 NM_031243 & 2 NM_002137
228059_x_at 1.3855706 1.0147347 0.7101465 MRPS22 NM_020191 Mitochondrial ribosomal protein S22

Total number of rows: 133

Table truncated, full table size 22 Kbytes.




Cluster 2: Probe sets significantly changed by PBA treatment header descriptions
Affy ID
0 hr (Normalized intensity)
12 hr (Normalized intensity)
24 hr (Normalized intensity)
Common
Update
Description

Data table
Affy ID 0 hr (Normalized intensity) 12 hr (Normalized intensity) 24 hr (Normalized intensity) Common Update Description
Transporter
202850_at 0.867246 1.6087546 0.8007604 ABCD3 NM_002858 PMP70; PXMP1; ABC43; Peroxisomal membrane protein-1 (70kD); ATP-binding cassette, sub-family D (ALD), member 3 (ABCD3). Pfam-ABC transporter. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, White). This protein is a member of the ALD subfamily, which is involved in peroxisomal import of fatty acids and/or fatty acyl-CoAs in the organelle. All known peroxisomal ABC transporters are half transporters which require a partner half transporter molecule to form a functional homodimeric or heterodimeric transporter. This peroxisomal membrane protein likely plays an important role in peroxisome biogenesis.
Signaling
204115_at 0.87040347 1.8637396 0.7688593 GNG11 NM_004126 Homo sapiens guanine nucleotide binding protein 11. Pfam - domain found in gamma subunit of heteromeric G protein complex and in regulators of g protein signaling.
225171_at 1.0462258 1.5612801 0.6427184 MacGAP NM_033515 pfam-GTPase-activator protein for Rho-like GTPases
Cell fate
201324_at 0.881943 1.9566708 0.4844489 EMP1 NM_001423 TMP; CL-20; Epithelial membrane protein 1. CDD: PMP22_Claudin common to small integral membrane glycoproteins which contain 4 transmembrane segments and appear involved in cell proliferation
201421_s_at 1.2474958 1.6677381 0.8320047 MEP50 NM_024102 MGC2722; Homo sapiens MEP50 protein (MEP50). Pfam - WD40 found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly
207030_s_at 0.734624 1.7776583 1.1605697 CSRP2 NM_001321 CRP2; LMO5; SmLIM; LIM domain only 5, smooth muscle; Homo sapiens cysteine and glycine-rich protein 2. Pfam - LIM domain, binds 2 zinc ions but appears to act as interface for protein-protein interactions rather than DNA binding. Possibly involved in cell growth and differentiation. PMID: 11672422 potential new factor in the JAK/STAT-signalling pathway
214051_at 0.96047467 1.7146008 0.9357601 TMSNB NM_021992 thymosin beta, which is highly conserved acidic polypeptide, originally isolated from calf thymus. Changes in the expression of beta-thymosins appear to be related to the differentiation of cells. Among the effects are induction of metallo-proteinases, chemotaxis, angiogenesis and inhibition of inflammation as well as the inhibition of bone marrow stem cell proliferation
Enzymes
230333_at 0.9743934 2.081771 0.86801493 SAT Z14136 spermidine/spermine N1-acetyltransferase. NM_002970 is supposed to be same gene but no target sequence match.
221750_at 0.9834293 1.8827162 0.8663183 HMGCS1 NM_002130 3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1; expression promoted by butyrate
Transcription
201417_at 0.84249127 1.9114044 1.2865078 SOX4 NM_003107 Homo sapiens SRY (sex determining region Y)-box 4. CDD: HMG - high mobility group - binds single-stranded DNA and unnwinds double stranded DNA. Low molecular weight non-histone components in chromatin. Occurs in SOX family of transcription factors.
202133_at 0.80852044 1.5695218 0.7611693 TAZ NM_015472 Transcriptional co-activator with PDZ-binding motif. Pfam WW domain binds to proline-rich peptide motifs
208937_s_at 0.6953585 1.7443362 0.91894764 ID1 NM_002165 inhibitor of DNA binding 1, dominant negative helix-loop-helix protein. Pfam - HLH binding domain
Protein processing
202194_at 1.0226113 1.6430582 0.7526694 CGI-100 NM_016040 emp24/gp25L/p24 family. Members of this Pfam are implicated in bringing cargo forward from the ER and binding to coat proteins by their cytoplasmic domains
Stress response

Total number of rows: 55

Table truncated, full table size 8 Kbytes.




Cluster 3: Probe sets significantly changed by PBA treatment header descriptions
Affy ID
0 hr (Normalized intensity)
12 hr (Normalized intensity)
24 hr (Normalized intensity)
Common Name
GenBank
Description

Data table
Affy ID 0 hr (Normalized intensity) 12 hr (Normalized intensity) 24 hr (Normalized intensity) Common Name GenBank Description
RNA
201000_at 1.0712643 0.8845977 1.7413116 AARS NM_001605 Homo sapiens alanyl-tRNA synthetase. CDD: t-rna synthethase; DHHA1 associated with DHH domain - probably RNA binding function
202725_at 1.307531 0.8682454 2.4323015 POLR2A NM_000937 RPB1; RPO2; POLR2; POLRA; RPBh1; RPOL2; RpIILS; hsRPB1; hRPB220; polymerase (RNA) II (DNA directed) polypeptide A (220kD); DNA-directed RNA polymerase II largest subunit, RNA polymerase II 220 kd subunit; Homo sapiens polymerase (RNA) II (DNA directed) polypeptide A, 220kDa (POLR2A), mRNA.
212971_at 1.1256014 0.78184724 1.7553929 CARS NM_139273 cysteinyl-tRNA synthetase, transcript variant 1. Pfam - tRNA synthetase class I and (I,L,M and V)
Enzymes
204151_x_at 0.8578472 1.117119 1.690151 AKR1C1 NM_001353 DD1; DDH; DDH1; H-37; HBAB; MBAB; HAKRC; 2-ALPHA-HSD; 20-ALPHA-HSD; dihydrodiol dehydrogenase 1 (trans-1,2-dihydrobenzene-1,2-diol dehydrogenase, high affinity bile acid binding); type II 3-alpha-HSD; Pfam - family includes some K+ ion channel beta chain regulatory domains predicted to have oxidreductase activity; metabolizes neurosteroids derived from progesterone.
Control of gene expression
225263_at 0.95783925 0.9463855 1.5714557 HS6ST BC001196 NM_004807; heparan sulfate 6-O-sulfotransferase; type II integral membrane protein; Heparan sulfate, an abundant component of the cell surface and the extracellular matrix, is involved in a variety of biological processes such as growth factor signaling, cell adhesion, and enzymatic catalysis; possible an evolutionally conserved role for 6-O-sulfated heparan sulfate in FGF signaling.
39966_at 0.65044695 1.2297151 1.8618413 CSPG5 NM_006574 chondroitin sulfate proteoglycan 5 (neuroglycan C). Supposed to be neural tissue specific
Signalling
215735_s_at 1.6807154 0.6690282 1.6052006 TSC2 AC005600 NM_000548; tuberous sclerosis 2 isoform 1 NM_021055; tuberous sclerosis 2 isoform 2 NM_021056; functions as a Rab5 GTPase activating protein (GAP) in vivo to negatively regulate Rab5-GTP activity in endocytosis
210999_s_at 1.1890529 0.7820127 1.6137617 GRB10 NM_005311 growth factor receptor-bound protein 10. Pfam PH - eukaryotic signaling protein, bind to inositol phosphates and other proteins. Pfam SH2 related to smart00252 - bind phosphotyrosine-containing polypeptides
225768_at 1.0700499 0.95432526 2.0508904 NR1D2 AI761621 NM_005126; nuclear (hormone) receptor subfamily 1, group D, member 2
219429_at 0.8812924 1.2887502 1.7910409 FAAH NM_024306 fatty acid hydroxylase; appears to play a major role in regulating the amplitude and duration of FAA class of signaling lipids in vivo (neurobehavioral response)
Transporter
224609_at 0.7983619 0.7132844 1.6059637 CTL2 NM_020428 choline transporter-like protein. At 8 or 9 potential transmembrane regions
204981_at 1.146335 0.9852024 1.6053233 SLC22A1L NM_002555 HET; ITM; BWR1A; IMPT1; TSSC5; ORCTL2; BWSCR1A; p45-BWR1A; p45 Beckwith-Wiedemann region 1A; Beckwith-Wiedemann syndrome chromosome region 1, candidate A; efflux transporter-like protein; organic cation transporter-like 2; tumor-suppressing STF cDNA 5; imprinted multi-membrane spanning polyspecific transporter-related protein; Homo sapiens solute carrier family 22 (organic cation transporter), member 1-like (SLC22A1L), mRNA.
Glutathione
201348_at 0.7842046 1.0969342 1.5792764 GPX3 NM_002084 glutathione peroxidase 3 (plasma) (GPX3), mRNA.
202967_at 1.0946716 1.2513615 1.8354115 GSTA4 NM_001512 GTA4; GSTA4-4; Belongs to the alpha gene class GST family; glutathione S-alkyltransferase A4; glutathione S-aryltransferase A4; S-(hydroxyalkyl)glutathione lyase A4; glutathione S-aralkyltransferase A4; glutathione transferase A4-4; GST class-alpha; glutathione S-transferase, alpha 4; Homo sapiens glutathione S-transferase A4 (GSTA4), mRNA.

Total number of rows: 39

Table truncated, full table size 7 Kbytes.




Genes involved in ER unfolded protein response header descriptions
All data per gene

Data table
All data per gene
Time (hours) 0 12 24
Affy ID Normalized Normalized Normalized Common Genbank Description
239996_x_at 0.96938837 1.074118 1.5431569 ATP2A2 AI671237 wb14h10.x1 NCI_CGAP_GC6 Homo sapiens cDNA clone IMAGE:2305699 3' similar to contains TAR1.t2 MER22 MER22 repetitive element ;, mRNA sequence.
201216_at 0.88684005 0.9190469 1.033773 C12orf8 NM_006817 ERP28; ERP29; PDI-DB; endoplasmic reticulum lumenal protein ERp28; Homo sapiens chromosome 12 open reading frame 8 (C12orf8), mRNA.
205625_s_at 1.0642792 1.1601409 0.48469606 CALB1 AW014927 UI-H-BI0-aaf-f-06-0-UI.s1 NCI_CGAP_Sub1 Homo sapiens cDNA clone IMAGE:2709251 3', mRNA sequence.
205626_s_at 1.0682355 0.7919203 1.007295 CALB1 NM_004929 CALB; calbindin 1, (28kD); Homo sapiens calbindin 1, 28kDa (CALB1), mRNA.
205428_s_at 1.1722579 1.0365603 0.80656564 CALB2 NM_001740 CAL2; full length protein isoform encoded by full length transcript variant CALB2; calbindin 2, (29kD, calretinin); calbindin D29K; Homo sapiens calbindin 2, 29kDa (calretinin) (CALB2), transcript variant CALB2, mRNA.
207885_at 0.57060045 0.5429662 0.47757834 CALB3 NM_004057 CABP1; CABP9K; calbindin 3, (vitamin D-dependent calcium-binding protein); calbindin D9K; Homo sapiens calbindin 3, (vitamin D-dependent calcium binding protein) (CALB3), mRNA.
214315_x_at 0.94037133 0.9238173 1.1148492 CALR AI348935 tb60a01.x1 NCI_CGAP_Br15 Homo sapiens cDNA clone IMAGE:2058696 3' similar to gb:M84739 CALRETICULIN PRECURSOR (HUMAN);, mRNA sequence.
200935_at 0.9486014 1.005216 1.0650926 CALR NM_004343 SSA; RO; This protein was initially named autoantigen Ro but this property was later disputed; Sicca syndrome antigen A (autoantigen Ro; calreticulin); Homo sapiens calreticulin (CALR), mRNA.
212952_at 1.0267859 1.2833138 1.057845 CALR BE251303 601107814F1 NIH_MGC_16 Homo sapiens cDNA clone IMAGE:3344018 5', mRNA sequence.
228091_at 0.9631158 0.85651624 1.1750785 CALR AI800609 wg12e06.x1 Soares_NSF_F8_9W_OT_PA_P_S1 Homo sapiens cDNA clone IMAGE:2364898 3', mRNA sequence.
214316_x_at 0.6254221 1.1562779 0.9962828 CALR AI348935 tb60a01.x1 NCI_CGAP_Br15 Homo sapiens cDNA clone IMAGE:2058696 3' similar to gb:M84739 CALRETICULIN PRECURSOR (HUMAN);, mRNA sequence.
212953_x_at 1.0379649 1.050335 1.1154665 CALR BE251303 601107814F1 NIH_MGC_16 Homo sapiens cDNA clone IMAGE:3344018 5', mRNA sequence.
238034_at 1.0392767 0.8721512 0.9684489 CANX AI890021 wm80f04.x1 NCI_CGAP_Ut2 Homo sapiens cDNA clone IMAGE:2442271 3', mRNA sequence.
208852_s_at 1.0916346 0.90162367 0.8187067 CANX AI761759 wg67h12.x1 Soares_NSF_F8_9W_OT_PA_P_S1 Homo sapiens cDNA clone IMAGE:2370215 3' similar to gb:L10284 CALNEXIN PRECURSOR (HUMAN);, mRNA sequence.
200068_s_at 1.3080641 1.222996 0.9946158 CANX M94859 Human calnexin mRNA, complete cds.
208853_s_at 0.99536645 1.0841155 0.81595665 CANX L18887 Human calnexin mRNA, complete cds.
209476_at 1.2032287 1.2263522 0.8189533 DKFZp564E1962 AL080080 similarity to protein disulphide isomerases; Homo sapiens mRNA; cDNA DKFZp564E1962 (from clone DKFZp564E1962); partial cds.
208370_s_at 1.0720677 1.0199797 0.91292125 DSCR1 NM_004414 MCIP1; ADAPT78; Down syndrome candidate region 1; near DSCR proline-rich protein; human Down syndrome candidate region protein, proline-rich protein; Homo sapiens Down syndrome critical region gene 1 (DSCR1), mRNA.

Total number of rows: 50

Table truncated, full table size 9 Kbytes.




Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE620_RAW.tar 73.3 Mb (http)(custom) TAR (of CEL)

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