TOP TEN perturbations for 38578_at (Homo sapiens)

Organism: Homo sapiens
Gene: 38578_at
Selected probe(set): 218747_s_at
Platform: Affymetrix Human Genome U133 Plus 2.0 Array

Expression of 38578_at (218747_s_at) across 6674 perturbations tested by GENEVESTIGATOR:

RAF1 overexpr. study 1 (retrovirus) / control virus infected MCF7 cell sample

Relative Expression (log2-ratio):-3.3819609
Number of Samples:2 / 2
Experimental RAF1 overexpr. study 1 (retrovirus)
MCF-7 cell line stably transfected with retrovirus containing cDNA for RAF1. The following retroviral construct was used: pLNCRaf-1 contains human Raf-1 cDNA encoding an amino terminally truncated form of Raf-1 that is constitutively active, which is inserted into retroviral vector pLNCX encoding neomycin resistance gene (NeoR). MCF7 cells were maintained in EMEM supplemented with 10% FBS and 20ug/ml insulin.
Control control virus infected MCF7 cell sample
MCF7 cell line transfected with pZipneo retrovirus, which is an empty retroviral vector encoding neomycine resistance gene (NeoR). MCF7 cells were maintained in EMEM supplemented with 10% FBS and 20ug/ml insulin.

OPM-1 / MM1.S

Relative Expression (log2-ratio):-3.2333012
Number of Samples:4 / 4
Experimental OPM-1
Human primary cancer cell line derived from the peripheral blood of a patient with multiple myeloma. Dexamethasone-resistant. Synonyms:OPM1 Cellosaurus code:
Control MM1.S
Human primary cancer cell line derived from the peripheral blood of a patient with multiple myeloma. Dexamethasone-sensitive. Parental cell line:: MM.1 Synonyms:MM.1S; MM1-S; MM-1S; MM1S Cellosaurus code:

glioma study 16 (LN-18) / normal astrocyte sample

Relative Expression (log2-ratio):2.7736645
Number of Samples:2 / 3
Experimental glioma study 16 (LN-18)
Human glioma cell line LN018 was cultured in DMEM supplemented with 10% FCS (fetal calf serum) and antibiotics at 37C and 5% CO2.
Control normal astrocyte sample
Normal brain astrocytes. Clonetics normal human astrocytes (NHA) from Cambrex (primary-derived cultures) and cultured according to the manufacturer's recommendations.

IFN-g study 9 (24h) / untreated epidermal keratinocyte sample

Relative Expression (log2-ratio):2.6727343
Number of Samples:3 / 6
Experimental IFN-g study 9 (24h)
Primary keratinocytes treated with interferon gamma (IFN-g) for 24 hours. Monolayer normal human keratinocyte (NHK) cultures were established and used in the second or third passage. Cultures were grown to 40 or 80% confluence, or maintained to 4 days postconfluency. Cultures were starved of growth factors in nonsupplemented M154 medium for 24 hours, and afterwards stimulated with recombinant human IFN-g for 24 hours.
Control untreated epidermal keratinocyte sample
Untreated primary epidermal keratinocytes. Monolayer normal human keratinocyte (NHK) cultures were established and used in the second or third passage. Cultures were grown to 40 or 80% confluence, or maintained to 4 days postconfluency.

glioma study 16 (LN-229) / normal astrocyte sample

Relative Expression (log2-ratio):2.619853
Number of Samples:2 / 3
Experimental glioma study 16 (LN-229)
Human glioma cell line LN229 was cultured in DMEM supplemented with 10% FCS (fetal calf serum) and antibiotics at 37°C and 5% CO2.
Control normal astrocyte sample
Normal brain astrocytes. Clonetics normal human astrocytes (NHA) from Cambrex (primary-derived cultures) and cultured according to the manufacturer's recommendations.

wound healing study 2 (ex vivo; DMSO) / normal skin tissue (ex vivo)

Relative Expression (log2-ratio):-2.4525175
Number of Samples:3 / 3
Experimental wound healing study 2 (ex vivo; DMSO)
Ex vivo skin samples obtained from healthy donors following reduction surgery of abdomen, and incubated in culture medium containing DMSO for 4 days. To make sure that mainly epidermis was present in the samples, as much dermal tissue as possible was removed by dissection. Skin was sliced into 1x10 mm slices and incubated in keratinocyte medium for four days with 1:1000 fold dilution of DMSO. The cultivation was performed in serum-free keratinocyte medium supplemented with transferrin, hEGF (0.15 ng/mL), 0.5 mg/mL hydrocortisone, gentamicin, amphotericin B, and epinephrine but without insulin.
Control normal skin tissue (ex vivo)
Normal skin samples obtained from healthy donors following reduction surgery of abdomen. To make sure that mainly epidermis was present in the samples, as much dermal tissue as possible was removed by dissection.

HCC827 / A-549

Relative Expression (log2-ratio):2.4262877
Number of Samples:6 / 6
Experimental HCC827
Human primary cancer cell line derived from the lung of a patient with non-small-cell lung cancer. Synonyms:HCC-827; HCC0827 Cellosaurus code:
Control A-549
Human primary cancer cell line derived from the lung of a patient with carcinoma. Synonyms:A 549; A549; NCI-A549; A549/ATCC; hA549 Cellosaurus code:

glioma study 16 (LN-319) / normal astrocyte sample

Relative Expression (log2-ratio):2.355587
Number of Samples:2 / 3
Experimental glioma study 16 (LN-319)
Human glioma cell line LN319 was cultured in DMEM supplemented with 10% FCS (fetal calf serum) and antibiotics at 37°C and 5% CO2.
Control normal astrocyte sample
Normal brain astrocytes. Clonetics normal human astrocytes (NHA) from Cambrex (primary-derived cultures) and cultured according to the manufacturer's recommendations.

renal cell carcinoma study 4 / normal kidney tissue (fetal)

Relative Expression (log2-ratio):2.2972755
Number of Samples:26 / 2
Experimental renal cell carcinoma study 4
Tumor tissue samples from the kidney of patients with renal cell carcinoma (RCC).
Control normal kidney tissue (fetal)
Normal fetal kidney tissue samples.

renal cell carcinoma study 6 (chromophobe type) / normal kidney tissue (fetal)

Relative Expression (log2-ratio):2.254384
Number of Samples:4 / 2
Experimental renal cell carcinoma study 6 (chromophobe type)
Tumor tissue samples from the kidney of patients with chromophobe renal cell carcinoma (cRCC).
Control normal kidney tissue (fetal)
Normal fetal kidney tissue samples.

Organism: Homo sapiens
Gene: 38578_at
Selected probe(set): 206150_at
Platform: Affymetrix Human Genome U133 Plus 2.0 Array

Expression of 38578_at (206150_at) across 6674 perturbations tested by GENEVESTIGATOR:

CML study 1 / B-CLL study 5

Relative Expression (log2-ratio):-4.2923737
Number of Samples:75 / 441
Experimental CML study 1
Bone marrow samples of patients with chronic myeloid leukemia (CML).
Control B-CLL study 5
Bone marrow samples of patients with B-cell chronic lymphocytic leukemia (B-CLL).

immune cell study 10 (IgM memory B-cell) / immune cell study 10 (naive B-cell)

Relative Expression (log2-ratio):3.957592
Number of Samples:5 / 5
Experimental immune cell study 10 (IgM memory B-cell)
IgM memory B-cells (IgM+IgD+CD27+) isolated from peripheral blood of healthy adult donors (between 25 and 60 years of age). Mononuclear cells were isolated by Ficoll–Paque density centrifugation and CD19+ B-cells were enriched by magnetic cell separation using the MACS system or by negative selection using the EasySep Human B-Cell Enrichment Kit. B-cell suspensions were stained with anti-CD27 APC, anti-IgD PE–Cy7, anti-IgM FITC, and anti-IgG PE or anti-CD21 PE antibodies and sorted with a FACSDiva cell sorter as IgM memory B-cells.
Control immune cell study 10 (naive B-cell)
Naive B-cells (IgM+IgD+CD27-) isolated from peripheral blood of healthy adult donors (between 25 and 60 years of age). Mononuclear cells were isolated by Ficoll–Paque density centrifugation and CD19+ B-cells were enriched by magnetic cell separation using the MACS system or by negative selection using the EasySep Human B-Cell Enrichment Kit. B-cell suspensions were stained with anti-CD27 APC, anti-IgD PE–Cy7, anti-IgM FITC, and anti-IgG PE or anti-CD21 PE antibodies and sorted with a FACSDiva cell sorter as naive B cells.

precursor-B-ALL study 3 (TEL-AML1) / precursor-B-ALL study 3 (MLL-rearranged)

Relative Expression (log2-ratio):3.9152803
Number of Samples:15 / 5
Experimental precursor-B-ALL study 3 (TEL-AML1)
Peripheral blood and bone marrow samples of pediatric patients with precursor B-ALL [t(12;21)(p13,q22)/TEL-AML1]. Patients were part of the Nordic Society Of Pediatric Hematology And Oncology Group (NOPHO).
Control precursor-B-ALL study 3 (MLL-rearranged)
Peripheral blood and bone marrow samples of pediatric patients with precursor B-ALL [t(v;11q23)/MLL rearranged]. Patients were part of the Nordic Society Of Pediatric Hematology And Oncology Group (NOPHO).

kidney transplantation study 11 (1 week) / normal blood sample

Relative Expression (log2-ratio):-3.7568283
Number of Samples:11 / 5
Experimental kidney transplantation study 11 (1 week)
Whole blood samples derived from kidney transplant patients 1 week post-transplantation. Samples were collected 1 week after transplantation and administration of immunosuppressive therapy (day 1-4: methylprednisolone (60 mg); 3 doses: rabbit polyclonal anti-thymocyte globulin (ThymoglobulinH; 6 mg/kg); mycophenolate mofetil (CellCeptH); and tacrolimus (PrografH).
Control normal blood sample
Blood samples derived from healthy control subjects.

immune cell study 10 (IgG memory B-cell) / immune cell study 10 (naive B-cell)

Relative Expression (log2-ratio):3.7032385
Number of Samples:5 / 5
Experimental immune cell study 10 (IgG memory B-cell)
Class switched IgG memory B-cells (IgG+CD27+) isolated from peripheral blood of healthy adult donors (between 25 and 60 years of age). Mononuclear cells were isolated by Ficoll–Paque density centrifugation and CD19+ B-cells were enriched by magnetic cell separation using the MACS system or by negative selection using the EasySep Human B-Cell Enrichment Kit. B-cell suspensions were stained with anti-CD27 APC, anti-IgD PE–Cy7, anti-IgM FITC, and anti-IgG PE or anti-CD21 PE antibodies and sorted with a FACSDiva cell sorter as class switched IgG memory B-cells.
Control immune cell study 10 (naive B-cell)
Naive B-cells (IgM+IgD+CD27-) isolated from peripheral blood of healthy adult donors (between 25 and 60 years of age). Mononuclear cells were isolated by Ficoll–Paque density centrifugation and CD19+ B-cells were enriched by magnetic cell separation using the MACS system or by negative selection using the EasySep Human B-Cell Enrichment Kit. B-cell suspensions were stained with anti-CD27 APC, anti-IgD PE–Cy7, anti-IgM FITC, and anti-IgG PE or anti-CD21 PE antibodies and sorted with a FACSDiva cell sorter as naive B cells.

immune cell study 10 (IgM only memory B-cell) / immune cell study 10 (naive B-cell)

Relative Expression (log2-ratio):3.6632586
Number of Samples:5 / 5
Experimental immune cell study 10 (IgM only memory B-cell)
IgM only memory B-cells (IgM+IgD-/lowCD27+) isolated from peripheral blood of healthy adult donors (between 25 and 60 years of age). Mononuclear cells were isolated by Ficoll–Paque density centrifugation and CD19+ B-cells were enriched by magnetic cell separation using the MACS system or by negative selection using the EasySep Human B-Cell Enrichment Kit. B-cell suspensions were stained with anti-CD27 APC, anti-IgD PE–Cy7, anti-IgM FITC, and anti-IgG PE or anti-CD21 PE antibodies and sorted with a FACSDiva cell sorter as IgM only memory B-cells.
Control immune cell study 10 (naive B-cell)
Naive B-cells (IgM+IgD+CD27-) isolated from peripheral blood of healthy adult donors (between 25 and 60 years of age). Mononuclear cells were isolated by Ficoll–Paque density centrifugation and CD19+ B-cells were enriched by magnetic cell separation using the MACS system or by negative selection using the EasySep Human B-Cell Enrichment Kit. B-cell suspensions were stained with anti-CD27 APC, anti-IgD PE–Cy7, anti-IgM FITC, and anti-IgG PE or anti-CD21 PE antibodies and sorted with a FACSDiva cell sorter as naive B cells.

B-CLL study 11 (rolipram) / rolipram study 4 (normal B-cell; 20uM)

Relative Expression (log2-ratio):3.636858
Number of Samples:4 / 4
Experimental B-CLL study 11 (rolipram)
Peripheral blood mononuclear cells (PBMCs) obtained from chronic lymphocytic leukemia (CLL) patients and in vitro treated with rolipram (20 uM, cyclic nucleotide phosphodiesterase (PDE4) inhibitor) for 4 hours. PBMCs’ samples contained 90% CD19+ CD5+ B lineage CLL cells (B-CLL). Inclusion criteria: untreated CLL patients or at least 1 month after chemotherapy. Exclusion criteria: patients with active infections or other serious medical conditions or with white blood cell (WBC) counts of 15,000/l. ATC code:---
Control rolipram study 4 (normal B-cell; 20uM)
MACS purified resting B-cells from healthy donor peripheral blood treated with rolipram (20 uM, cyclic nucleotide phosphodiesterase (PDE4) inhibitor) for 4 hours. ATC code:---

precursor-B-ALL study 3 (hyperdiploid) / precursor-B-ALL study 3 (TEL-AML1)

Relative Expression (log2-ratio):-3.2729368
Number of Samples:17 / 15
Experimental precursor-B-ALL study 3 (hyperdiploid)
Peripheral blood and bone marrow samples of pediatric patients with precursor B-ALL (hyperdiploidy). Patients were part of the Nordic Society Of Pediatric Hematology And Oncology Group (NOPHO).
Control precursor-B-ALL study 3 (TEL-AML1)
Peripheral blood and bone marrow samples of pediatric patients with precursor B-ALL [t(12;21)(p13,q22)/TEL-AML1]. Patients were part of the Nordic Society Of Pediatric Hematology And Oncology Group (NOPHO).

PMA; ionomycine study 2 / unstimulated CD4 memory T-cell sample

Relative Expression (log2-ratio):-3.2011576
Number of Samples:8 / 8
Experimental PMA; ionomycine study 2
CD4+ memory T cells derived from peripheral blood of healthy subjects were stimulated for 3 hours with phorbol 12-myristate 13-acetate (PMA, 10 ng/ml) and ionomycin (1 µg/ml). ATC code:---
Control unstimulated CD4 memory T-cell sample
Unstimulated CD4+ memory T cells derived from peripheral blood of healthy subjects.

kidney transplantation study 12 (2 week) / normal T-cell (CD4+) sample

Relative Expression (log2-ratio):-3.1727648
Number of Samples:6 / 5
Experimental kidney transplantation study 12 (2 week)
CD4+ T-cell samples derived from kidney transplant patients 2 weeks post-transplantation. Samples were collected 2 week after transplantation and administration of immunosuppressive therapy (day 1-4: methylprednisolone (60 mg); 3 doses: rabbit polyclonal anti-thymocyte globulin (ThymoglobulinH; 6 mg/kg); mycophenolate mofetil (CellCeptH); and tacrolimus (PrografH).
Control normal T-cell (CD4+) sample
CD4+ T-cell samples derived from healthy control subjects.