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Displaying 100 of 1,039 results for "TGFBRAP1"
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  1. TGFA1_BOVIN UniProt:Swiss-Prot

    ID: A7MB11

    Description: Transforming growth factor-beta receptor-

  2. TGFA1_DANRE UniProt:Swiss-Prot

    ID: A4IG72

    Description: Transforming growth factor-beta receptor-

  3. Transcription profiling by array of HCT-116 cell lines transiently silenced with TRAP1 compared with scrumble ArrayExpress

    ID: E-MTAB-2500

    Description: Trascription profiling analysis was performed on HCT-116 cell lines transiently silenced with TRAP1 compared with scrumble

  4. Crystal structure of human Trap1 with AMPPNP PDB

    ID: PDB:4Z1I

    Description: Trap1

  5. Structure of mitochondrial Hsp90 (TRAP1) with ADP-ALF4- PDB

    ID: PDB:4IYN

    Description: TNF receptor-associated protein 1

  6. Crystal structure of human Trap1 with SMTIN-P01 PDB

    ID: PDB:4Z1H

    Description: Trap1

  7. Crystal structure of human Trap1 with PU-H71 PDB

    ID: PDB:4Z1F

    Description: Trap1

  8. Crystal structure of human Trap1 with BIIB-021 PDB

    ID: PDB:4Z1G

    Description: Trap1

  9. Structure of mitochondrial Hsp90 (TRAP1) with ADP-BeF3 PDB

    ID: PDB:4J0B

    Description: TNF receptor-associated protein 1

  10. Crystal structure of mitochondrial Hsp90 (TRAP1) with AMPPNP PDB

    ID: PDB:4IPE

    Description: TNF receptor-associated protein 1

  11. Transgenic Expression Of Mitochondrial Chaperone Trap1 Accelerates Prostate Cancer Development BioProject

    ID: PRJNA321266

    Access Type: download

  12. Crystal structure of mitochondrial Hsp90 (TRAP1) NTD-Middle domain dimer with AMPPNP PDB

    ID: PDB:4IVG

    Description: TNF receptor-associated protein 1

  13. C-peptide and/or transforming growth factor beta 1 effect on human proximal tubular cell line BioProject

    ID: PRJNA124211

    Keywords: Transcriptome or Gene expression

    Access Type: download

  14. Expression profiling of desmoid tumors and nodular fasciitis BioProject

    ID: PRJNA93023

    Keywords: Transcriptome or Gene expression

    Access Type: download

    dataset.description: T) are rare forms of fibroblastic/myofibroblastic growth that arise in deep soft tissues, display propensity for local infiltration and recurrence but fail to metastasize. Given that both entities are primarily fibroblastic/myofibroblastic lesions with overlapping histological features, we compared their gene expression profile to identify differentially expressed genes that may provide not only...
  15. A Human Model of Cerebral Amyloid Angiopathy Using Neural Crest-Derived Vascular Smooth Muscle Cells BioProject

    ID: PRJNA238730

    Keywords: Transcriptome or Gene expression

    Access Type: download

    dataset.description: myloid angiopathy (CAA), characterised by amyloid-beta (Aβ) deposits in the walls of intracerebral and leptomeningeal arteries, is evident in a majority of Alzheimer’s disease patients and aged people. Here, we leverage on human pluripotent stem cells to generate vascular smooth mu...
  16. 5/6 nephrectomy (5/6Nx) effect on the liver BioProject

    ID: PRJNA155993

    Keywords: Transcriptome or Gene expression

    Access Type: download

    dataset.description: Chronic renal failure (CRF) is associated with a decrease in drug metabolism. The present study investigated the repercussions of CRF on liver cytochrome P450 (CY...
  17. Gene expression profiling of pancreatic cancer cell line BxPC-3 induced by PAR-2 AP BioProject

    ID: PRJNA192255

    Keywords: Transcriptome or Gene expression

    Access Type: download

    dataset.description: Protease-activated receptor-2 (PAR-2), a G protein-coupled receptor activated by trypsin and coagulant factors, ...
  18. CCN5, a novel transcriptional repressor ArrayExpress

    ID: E-GEOD-25431

    Description: CCN5 is a member of the CCN (Connective Tissue Growth Factor/Cysteine-rich 61/Nephroblastoma overexpressed) family and was identified as an estrogen-inducible ...

  19. 5/6 nephrectomy (5/6Nx) effect on the liver ArrayExpress

    ID: E-GEOD-35135

    Description: Chronic renal failure (CRF) is associated with a decrease in drug metabolism. The present study investigated the repercussions of CRF on liver cytochrome P450 (CY...

  20. A gene expression signature of emphysema-related lung destruction and its reversal by the tripeptide GHK. BioProject

    ID: PRJNA138289

    Keywords: Transcriptome or Gene expression

    Access Type: download

    dataset.description: genes whose expression levels were significantly associated with regional emphysema severity while controlling for gene expression differences between individuals. Genes increasing in expression with increasing emphysematous destruction included those involved in inflammation, such as the B-cell receptor signaling pathway, while genes decreasing in expression were enriched in tissue repair processes, including the transforming growth factor beta (TGF beta) pathway, actin organization, and integrin signaling. We found concordant differential expression of these emphysema severity-associated genes in four cross-sectional studies of COPD. Using the Connectivity Map, we identified GHK as a compound that can reverse the gene-expression signature associated with emphysematous destruction and...
  21. Epigenomic Evolution of Diffuse Large B-cell Relapse ArrayExpress

    ID: E-GEOD-66329

    Description: ted regulatory elements and determine a relapse–associated methylation signature converging on key pathways such as transforming growth factor beta (TGF-beta) receptor activity. We also observe decreased intra-tumor methylation heterogeneity from diagnosis to relapsed tumor samples. Relapse-free patients display lower intra-tumor methylation heterogeneity at diagnosis compared to relapsed patients in an independent validation cohort....

  22. Gene expression profiling of pancreatic cancer cell line BxPC-3 induced by PAR-2 AP ArrayExpress

    ID: E-GEOD-44827

    Description: Protease-activated receptor-2 (PAR-2), a G protein-coupled receptor activated by trypsin and coagulant factors, ...

  23. A gene expression signature of emphysema-related lung destruction and its reversal by the tripeptide GHK ArrayExpress

    ID: E-GEOD-27597

    Description: genes whose expression levels were significantly associated with regional emphysema severity while controlling for gene expression differences between individuals. Genes increasing in expression with increasing emphysematous destruction included those involved in inflammation, such as the B-cell receptor signaling pathway, while genes decreasing in expression were enriched in tissue repair processes, including the transforming growth factor beta (TGF beta) pathway, actin organization, and integrin signaling. We found concordant differential expression of these emphysema severity-associated genes in four cross-sectional studies of COPD. Using the Connectivity Map, we identified GHK as a compound that can reverse the gene-expression signature associated with emphysematous destruction and...

  24. Array-comparative genomic hybridization by using DualChip® human cancer 1.1 arrays BioProject

    ID: PRJNA106835

    Keywords: Variation

    Access Type: download

    dataset.description: ridization. Cancer Genetics and Cytogenetics. 177(1): 20-29) and all 294 genes contained in DualChip® human cancer 1.1 arrays were present also in Agilent arrays, it has been possible to compare results obtained by the two different platforms. We assumed aCGH performed by Agilent slides as reference method to assess gene gains and losses in neuroblastoma samples. This approach allowed us to select 120 genes printed on DualChip® arrays as invariant genes (ABI2, ADAM9, ANGPT1, AREG, BAK1, BIK, BARD1, BCL2A1, BCL2L2, BMP1, CASP3, CASP8, CDH12, CFLAR, CTNNA1, CD34, CLK1, CGRRF1, COL6A1, CSF1R, CSPG2, CTGF, CXCL9, CCNA2, CCNB1, CCNG1, CCNH, CDKN1A, CDKN1C, CDKN2A, CDKN2B, CDKL1, DSP, E2F3, E2F5, EFNA1, EGF, EGR1, FASTK, FGF1, FGF2, FGFR1, FGR, FN1, GAS1, HGFAC, HMMR, IGF1R, IGFBP2, IK, IFNAR1, IFNGR1, ILK, IRF1, ITGA1, ITGA4, IL10, IL13, IL15, IL1A, IL2, IL3, IL4, IL5, IL6R, IL8, KDR, KISS1, LIF, MIF, MMP11, MMP14, MDH1, MAP2K1, MAP2K5, MAPK10, MAPK14, MCL1, NF2, NID1, NINJ1, NRG1, NTRK1, PGF, PDGFB, PDGFRA, PLAT, PLG, PDCD2, PPBP, PRODH, PTGES, PCDH1, PTK2, PURA, QSCN6, RIPK1, RRM1, ARHGDIA, SFRP2, SOD1, STAT1, TEK, TERT, THBS1, TIAM1, TNC, TANK, TGFA, TGFB2, XRCC6, TGFB3, TGFBR1, TMED10, TPBG, TYRO3, ERBB4, FLT4, FOS, VIL2)....
  25. Clustering of CpG islands constitutes an important determinant of the interphase chromosome 3D organization [4C-Seq] ArrayExpress

    ID: E-GEOD-51937

    Description: raction with the NPRL3 anchor (anchors near TSR3, TRAP1, PPL genes). In the forth experiment (anchor GENE-Des) the anchor was placed in a gene-poor area that did not interact with the NPRL3 promoter. The libraries for all anchors were pooled and sequenced in paired-end mode with a total depth of 75 million reads. Anchor NPRL3: two replicates for HD3 and two replicates for DT40 cell lines. Other anchors (TSR3, GENE-Des, TRAP1, PPL): two replicates, pooled library...

  26. Epigenetic events in early breast cancer ArrayExpress

    ID: E-GEOD-8007

    Description: EC) have the unique ability to escape a period of growth arrest and continue to proliferate. These cells, called post-selection or variant cells (vHMEC), share features with premalignant breast cancer lesions, including p16INK4A promoter hy...

  27. A Human Model of Cerebral Amyloid Angiopathy Using Neural Crest-Derived Vascular Smooth Muscle Cells ArrayExpress

    ID: E-GEOD-55173

    Description: myloid angiopathy (CAA), characterised by amyloid-beta (Aβ) deposits in the walls of intracerebral and leptomeningeal arteries, is evident in a majority of Alzheimer’s disease patients and aged people. Here, we leverage on human pluripotent stem cells to generate vascular smooth mu...

  28. To study the genomic changes in senescent porcine coronary arterial endothelial cells by multiple passaging in vitro BioProject

    ID: PRJNA102429

    Keywords: Transcriptome or Gene expression

    Access Type: download

    dataset.description: rterial endothelial cells until passage four. The protein presence of endothelial nitric oxide synthase, cyclic GMP levels [basal and during stimulation (bradykinin and A23187)], were reduced. The mRNA expression level was measured by microarray assays. Genes related to oxidative stress [superoxide dismutase (MnSOD), glutathione peroxidase 3, glutathione S-transferase M1] were downregulated, extracellular matrix components (type III collagen, thrombospondin 1 and 3, transforming
  29. Exercise-induced modification of skeletal muscle transcriptome in Arabian horses BioProject

    ID: PRJNA349176

    Keywords: Transcriptome or Gene expression

    Access Type: download

    dataset.description: es expressed in muscle tissue and are potentially associated with exercise adaptation in Arabian horses. Methods: Whole transcriptomes between three time points of muscle tissue collection were compared: T0 (untrained horses), ...
  30. Mitochondrial unfolded protein response controls matrix pre-RNA processing and translation BioProject

    ID: PRJNA304150

    Keywords: Other

    Access Type: download

  31. Mitochondrial unfolded protein response controls matrix pre-RNA processing and translation ArrayExpress

    ID: E-GEOD-75247

    Description: enomes. In C. elegans, the mitochondrial unfolded protein response (UPRmt) senses matrix protein misfolding and induces a program of nuclear gene expression, including mitochondrial chaperonins, to promote mitochondrial proteostasis. While misfolded mitochondrial matrix-localized ornithine trans...

  32. Integrative Transcriptome Analysis Reveals Common Molecular Subtypes of Human Hepatocellular Carcinoma (HT-HG_U133A) BioProject

    ID: PRJNA108143

    Keywords: Transcriptome or Gene expression

    Access Type: download

    dataset.description: ion as well as MYC and AKT activation, and S3 was associated with hepatocyte differentiation. Functional studies indicated that the WNT pathway activation signature characteristic of S1 tumors was not simply the result of beta-catenin mutation but rather was the result of transforming growth factor-beta activation, thus representing a new mechanism of WNT pathway activation in HCC. These experiments establish the first consensus classification framework for HCC based on gene expression profiles and highlight the power of integrating multiple data sets to define a robust molecular taxonomy of the disease. Overall design: Four hepatocellular carcinoma (HCC) cell line samples treated or untreated by TGF-beta...
  33. Antenatal maternal long-term hypoxia: acclimatization responses with altered gene expression in ovine fetal carotid arteries ArrayExpress

    ID: E-GEOD-49920

    Description: a (LTH) during pregnancy can lead to intrauterine growth restriction with reduced body/brain weight, dysregulation of cerebral blood flow (CBF), and other problems in humans and rodents. In contrast, sheep appear to undergo relati...

  34. Crystal structure of human TAK1/TAB1 fusion protein in complex with ligand 11c PDB

    ID: PDB:5JGA

    Description: Mitogen-activated protein kinase kinase kinase 7,TGF-beta-activated kinase 1 and MAP3K7-binding

  35. Crystal structure of human TAK1/TAB1 fusion protein in complex with ligand 10 PDB

    ID: PDB:5JGB

    Description: Mitogen-activated protein kinase kinase kinase 7,TGF-beta-activated kinase 1 and MAP3K7-binding

  36. Structure of TRAP1 fragment PDB

    ID: PDB:5HPH

    Description: Heat shock protein 75 kDa, mitochondrial

  37. Crystal structure of human TAK1/TAB1 fusion protein in complex with ligand 12 PDB

    ID: PDB:5JGD

    Description: Mitogen-activated protein kinase kinase kinase 7,TGF-beta-activated kinase 1 and MAP3K7-binding

  38. Mitochondrial unfolded protein response controls matrix pre-RNA processing and translation ArrayExpress

    ID: E-GEOD-75410

    Description: enomes. In C. elegans, the mitochondrial unfolded protein response (UPRmt) senses matrix protein misfolding and induces a program of nuclear gene expression, including mitochondrial chaperonins, to promote mitochondrial proteostasis. While misfolded mitochondrial matrix-localized ornithine trans...

  39. Gene Expression of ApoE Null and ApoE Null/RAGE Diabetic and Non-diabetic Mice ArrayExpress

    ID: E-GEOD-15729

    Description: The multi-ligand Receptor for AGE (RAGE) contributes to atherosclerosis in apolipoprotein (ApoE) null mice in both the non-diabetic and diabetic sta...

  40. Gene expression profiling in true interval breast cancer reveals overactivation of mTOR signalling pathway ArrayExpress

    ID: E-GEOD-47108

    Description: aimed to identify biological markers that may be associated with the emergence of symptomatic breast cancer in the screening interval. Material and Methods: An unsupervised exploratory gene expression profile analysis was performed among 10 samples (discovery set, TIBC=5 and SDBC=5) using Affymetrix Human Gene 1.0 ST arrays and interpreted by Ingenuity Pathway Analysis. Differential expression of selected genes was confirmed in validation series of 91 patients (TIBC=12 and SDBC=79) by immunohistochemistry and 24 patients (TIBC=8 and SDBC=16) by RT-qPCR, expanding the analysis to other genes in same pathway (mTOR, 4E-BP1, eIF-4G and S6). Results: Exploratory gene expression analysis identified 1...

  41. Clustering of CpG islands constitutes an important determinant of the interphase chromosome 3D organization [4C-Seq] BioProject

    ID: PRJNA225863

    Keywords: Other

    Access Type: download

    dataset.description: raction with the NPRL3 anchor (anchors near TSR3, TRAP1, PPL genes). In the forth experiment (anchor GENE-Des) the anchor was placed in a gene-poor area that did not interact with the NPRL3 promoter. The libraries for all anchors were pooled and sequenced in paired-end mode with a total depth of 75 million reads. Anchor NPRL3: two replicates for HD3 and two replicates for DT40 cell lines. Other anchors (TSR3, GENE-Des, TRAP1, PPL): two replicates, pooled library...
  42. Comparison of gene expression in Wild type and T cell-specific conditional Trim28 KO in TCR stimulated and un-stimulated naive CD4 positive and T regu... ArrayExpress

    ID: E-GEOD-32224

    Description: efective IL-2 production and T cell proliferation associated with defective upregulation of cell-cycle associated proteins. Accordingly, young CKO showed T-lymphopenia. Surprisingly, Trim28 CKO mice eventually accumulated auto-reactive memory-phenotype T cells that produced inflammatory IL-17. CKO mice are also susceptible to induced auto-inflammatory disease with TH-17 dominant immune response. Loss of Trim28 showed aberrant accumulation of TH-17 and FoxP3+ T cells, two key T cells in inflammation vs. tolerance. We found CKO T cells showed a cell-extrinsic promotion of TH-17 and FoxP3+ T cell development by a mechanism involving overproduction of TGF-beta. Our study revealed unexpected roles of Trim28, a global chromatin regulator in both T cell activation and tolerance. Trim28 conditional KO mice and age-matched control mice were sacrificed, and neive CD4+ T cells (CD4+CD62+CD25-) and Treg (CD4+CD62+CD25+) were sorted. Stimulation of naive T cells was done with anti-CD3 and anti-CD28 for 13 hours. We collected quadru...

  43. T-cell intracellular antigen (TIA) proteins deficiency in murine embryonic fibroblasts alters cell cycle progression and induces autophagy ArrayExpress

    ID: E-GEOD-43077

    Description: Mice lacking either T-cell intracellular antigen 1 (TIA1) or TIA1-related/like protein (TIAR/TIAL1) show high rates of embryonic lethality, suggesting a relevant role for t...

  44. Gene expression data from MDA-MB231 cells stably transduced with lentiviral vectors encoding a control shRNA (shscramble) or two shRNAs targeting Coco... ArrayExpress

    ID: E-GEOD-28049

    Description: we found that Coco, a secreted antagonist of TGF-beta ligands, induces solitary mammary carcinoma cells that have extravasated in the lung stroma to exit from dormancy. Mechanistic studies demonstrate that Coco awakens dormant metastasis-initiating cells by blocking stroma-derived Bone Morphogenetic Proteins. Inhibition of canonical BMP signaling reverses the commitment to differentiation of these cells and enhances their self-renewal and tumor-initiation capacity. Expression of Coco induces a discrete gene...

  45. Microarray analysis of T-cell death-associated gene 8 (TDAG8)-mediated gene expression in mouse Lewis lung carcinoma (LLC) cells ArrayExpress

    ID: E-GEOD-31776

    Description: eviously identified an extracellular pH-sensing G protein-coupled receptor T cell death associated gene 8 (TDAG8) as an extracellular pH sensor of t...

  46. Obesity study in transgenic and knockout animals OmicsDI

    ID: E-GEOD-12000

    Date Released: 05-01-2014

    Description: -enriched metabolic network module that is highly associated with metabolic traits in mice and humans. Integration of gene expression in the design and analysis of traditional F2 intercross studies allows high confidence prediction of causal genes, and identification of involved pathways and networks. This SuperSeries is composed of the following subset Series: GSE11991: Liver gene expression profiling of lipoprotein lipase heterozygous knockout mice GSE11992: Liver gene expression profiling of cytosolic malic enzyme knockout mice GSE11993: Liver gene expression profiling of zinc finger binding protein 90 (Zfp90) transgenic mice GSE11994: Liver gene expression profiling of transforming growth factor beta receptor 2 heterozygous knockout (Tgfbr2+/-) mice GSE11995: Liver gene expression profiling of comple...

  47. TRAP_STAEP UniProt:Swiss-Prot

    ID: Q8GQQ1

    Description: Signal transduction protein TRAP ABM Phosphohistidine Phosphohistidine Phosphohistidine

  48. Transcription profiling by array of HCT-116 cell lines transiently silenced with TRAP1 compared with scrumble OmicsDI

    ID: E-MTAB-2500

    Date Released: 09-19-2014

    Description: Trascription profiling analysis was performed on HCT-116 cell lines transiently silenced with TRAP1 compared with scrumble

  49. T-cell intracellular antigen (TIA) proteins deficiency in murine embryonic fibroblasts alters cell cycle progression and induces autophagy BioProject

    ID: PRJNA184349

    Keywords: Transcriptome or Gene expression

    Access Type: download

    dataset.description: Mice lacking either T-cell intracellular antigen 1 (TIA1) or TIA1-related/like protein (TIAR/TIAL1) show high rates of embryonic lethality, suggesting a relevant role for t...
  50. DKK2 Mediates Osteolysis, Invasiveness, and Metastatic Spread in Ewing Sarcoma BioProject

    ID: PRJNA152971

    Keywords: Transcriptome or Gene expression

    Access Type: download

    dataset.description: ated by the DKK effector matrix metalloproteinase 1 (MMP1). Furthermore, gene expression analyses established the ability of DKK2 to differentially regulate genes such as CXCR4, PTHrP, RUNX2, and TGFb1 that are associated with homing, invasion, and growth of cancer cells in bone tissue as well as genes important for osteolysis, including HIF1a, JAG1, IL6, and VEGF. DKK2 promoted bone infiltration and osteolysis in vivo and further analyses defined DKK2 as a key factor in osteotropic malignancy. Interestingly, in Ewing sarcoma cells, DKK2 suppression simultaneously increased the potential for neuronal differentiation while decreasing chondrogenic and osteogenic differentiation. Our results provide ...
  51. Transcriptional Profiling of Cultured, Embryonic Epicardial Cells Identifies Novel Genes and Signaling Pathways Regulated by TGFβR3 in vitro BioProject

    ID: PRJNA302322

    Keywords: Transcriptome or Gene expression

    Access Type: download

    dataset.description: - mice exhibit failed coronary vessel development associated with decreased epicardial cell invasion. Immortalized Tgfbr3-/- epicardial cells display the same defects. Tgfbr3+/+ and Tgfbr3-/- cells incubated for 72 hours with VEH or ligands known to promote inv...
  52. SIAT_HAEI8 UniProt:Swiss-Prot

    ID: Q4QP40

    Description: Sialic acid TRAP transporter permease protein SiaT Helical Helical Helical Helical Helical Helical Helical Helical Helical H...

  53. Obesity study in transgenic and knockout animals ArrayExpress

    ID: E-GEOD-12000

    Description: -enriched metabolic network module that is highly associated with metabolic traits in mice and humans. Integration of gene expression in the design and analysis of traditional F2 intercross studies allows high confidence prediction of causal genes, and identification of involved pathways and networks. This SuperSeries is composed of the following subset Series: GSE11991: Liver gene expression profiling of lipoprotein lipase heterozygous knockout mice GSE11992: Liver gene expression profiling of cytosolic malic enzyme knockout mice GSE11993: Liver gene expression profiling of zinc finger binding protein 90 (Zfp90) transgenic mice GSE11994: Liver gene expression profiling of transforming growth factor beta receptor 2 heterozygous knockout (Tgfbr2+/-) mice GSE11995: Liver gene expression profiling of comple...

  54. Sample 1 - Injection 1 Orbitrap-Ion Trap Dryad

    DateIssued: 08-01-2016

    Description: Sample 1 - Injection 2

  55. TRAP_STAES UniProt:Swiss-Prot

    ID: Q8CNR9

    Description: Signal transduction protein TRAP ABM Phosphohistidine Phosphohistidine Phosphohistidine

  56. TRAP_STAEQ UniProt:Swiss-Prot

    ID: Q5HNA3

    Description: Signal transduction protein TRAP ABM Phosphohistidine Phosphohistidine Phosphohistidine

  57. TRAP_STAAN UniProt:Swiss-Prot

    ID: Q7A4W3

    Description: Signal transduction protein TRAP ABM Phosphohistidine Phosphohistidine Phosphohistidine

  58. TRAP_ECOLI UniProt:Swiss-Prot

    ID: P41068

    Description: Protein TraP

  59. Gene expression profiling in erythroid progenitors through ontogeny BioProject

    ID: PRJNA166911

    Keywords: Transcriptome or Gene expression

    Access Type: download

    dataset.description: ked to hematological system development, cellular growth and proliferation. The KITLG, EPO, GATA1, PIM1 and STAT3 genes represent the major connection points in the hematological system development linked genes. Some JAK-STAT signaling pathway-linked genes were steadily upregulated throughout ontogeny (PIM1, SOCS, MYC, PTPN11), while others were downregulated (PTPN6, PIAS, SPRED2). In addition, some JAK-STAT pathway related genes have specific expression just at certain stages of ontogeny (STATs, GRB2, CREBB). Beside continuously upregulated (AKT1, PPP2CA, CHUK, NFKB1) and downregulated (FOXO1, PDPK1, PIK3CG) genes in the PI3K-AKT signaling pathway, we also observed intermittently regulated gene expression (NFKBIA, YWHAH). Conclusions: This broad overview of gene expression in erythropoiesis revealed transcription factors with a prevalence at certain stages of ontogenesis. Finally, our results show that EPO-mediated proliferation and survival of erythroid progenitors occurs mainly through modulation of JAK-STAT pathway associated STATs, GRB2 and PIK3 genes, as well as AKT pathway- coupled NFKBIA and YWHAH genes. Overall design: Adult peripheral blood mononuclear cells were isolated from buffy coats of 3 healthy donors using Lymphocyte Separation Medium (BioWhittaker, Walkersville, MD). We washed mononuclear cells twice with Dulbecco's phosphate-buffered saline (PBS, Invitrogen Corporation, Carlsbad, CA), and CD34+ c...
  60. Trap-80-dependence of TNF-alpha-induced genes BioProject

    ID: PRJNA112709

    Keywords: Transcriptome or Gene expression

    Access Type: download

  61. Sample 2 - Injection 1 Orbitrap-Ion Trap Dryad

    DateIssued: 08-01-2016

    Description: Sample 2 - Injection 1

  62. Sample 1 - Injection 2 Orbitrap-Ion Trap Dryad

    DateIssued: 08-01-2016

    Description: Sample 1 - Injection 2

  63. Buffer control 1 - Injection 1 Orbitrap Ion Trap Dryad

    DateIssued: 08-01-2016

    Description: Buffer control 1 - Injection 1

  64. Mitochondrial unfolded protein response controls matrix pre-RNA processing and translation BioProject

    ID: PRJNA302895

    Keywords: Transcriptome or Gene expression

    Access Type: download

  65. Gene expression arrays of cardiomyocyte ribosome-associated RNAs during zebrafish heart regeneration BioProject

    ID: PRJNA212301

    Keywords: Transcriptome or Gene expression

    Access Type: download

  66. Age-dependent aorta transcriptomes in wild-type and apoE-deficient C57BL/6J mice GEMMA

    ID: 1621

    Keywords: functional genomics

    Description: clerosis cluster and cytokine activity, chemokine receptor activity, and antigen binding in the ATLO cluster suggested candidate genes in relation to inflammation triggered by macrophages or adventitia infiltration, respectively. Among other prototype atherosclerosis genes such as Itgax (complement receptor 4), Cd68, Lysz (lysozyme), Vcam1, and Icam1, the atherosclerosis cluster showed markedly overrepresented prototype macrophage/foam cell genes regulating inflammation in cytokine activity (GO: 0005125): Spp1 (osteopontin) and Il6; in cytokine binding (GO: 0019955) Cd74, Il10rb, Ccr2, and Ccr5; and in immunoglobulin binding (GO: 00119865) the proinflammatory galactose-binding lectin Lgals3, as well as genes in scavenger receptor activity and lipid transporter activity. By contrast, the adventitia cluster showed overrepresented genes regulating B cell recruitment, B cell maturation, germinal center formation, and autoimmunity in cytokine activity including Cxcl13, Ccl21, and Ltb, in CXC chemokine receptor activity the secondary lymphoid organ counterreceptor of CXCL13 Blr1 (also known as Cxcr5), Cxcr3, and Cxcr6; and in antigen binding several histocompatibility-2 loci and various markedly expressed immunoglobulin genes. As embryonic lymph node development and tertiary lymphoid organ neogenesis share common features signal intensities of genes specifying the GO molecular function term lymph node development (GO: 0048535) were examined in arrays prepared from wild-type and apoE-/- aortae. These results showed that Id2, Nfkb1, and Ltbr were constitutively expressed at significant levels in aortae of both mouse genotypes whereas other genes including Lta, Ltb, Glycam1, and the two lymphorganogenic genes Cxcl13 and Ccl21 were induced at 78 w in apoE-deficient aortae only. Thus, genes expressed by macrophage-foam cells and genes regulating ATLO neogenesis, embryonic lymph node development, or B cell maturation were constitutively expressed in the arterial wall in both genotypes or emerged in a stepwise fashion at 32 w and 78 w. To verify microarray signal intensity data, separate aortae extracts were examined by quantitative RT-PCR (QRT-PCR) analyses of wild-type and apoE-deficient mice at 32 and 78 w. These data showed that array signal values accurately reflected gene transcripts. Cell lineage analyses of the adventitial infiltrate a...

  67. Integrative Transcriptome Analysis Reveals Common Molecular Subtypes of Human Hepatocellular Carcinoma ArrayExpress

    ID: E-GEOD-10186

    Description: ion as well as MYC and AKT activation, and S3 was associated with hepatocyte differentiation. Functional studies indicated that the WNT pathway activation signature characteristic of S1 tumors was not simply the result of beta-catenin mutation but rather was the result of transforming growth factor-beta activation, thus representing a new mechanism of WNT pathway activation in HCC. These experiments establish the first consensus classification framework for HCC based on gene expression profiles and highlight the power of integrating multiple data sets to define a robust molecular taxonomy of the disease. Surgically resected 118 tumor tissues from patients with hepatocellular carcinoma (HCC)...

  68. Buffer control 2 - Injection 1 Orbitrap Ion Trap Dryad

    DateIssued: 08-01-2016

    Description: Buffer control 2 - Injection 1

  69. Buffer control 1 - Injection 2 Orbitrap Ion Trap Dryad

    DateIssued: 12-24-2016

    Description: Buffer control 1 - Injection 2

  70. UEHC_RUEPO UniProt:Swiss-Prot

    ID: Q5LUA9

    Description: Ectoine/5-hydroxyectoine TRAP transporter large permease protein UehC Helical Helical Helical Helical Helical Helical Helical Helical Hel...

  71. DCTQ_PSEAE UniProt:Swiss-Prot

    ID: Q9HU17

    Description: C4-dicarboxylate TRAP transporter small permease protein DctQ Helical Helical Helical Helical

  72. DCTQ_RHOCA UniProt:Swiss-Prot

    ID: O07837

    Description: C4-dicarboxylate TRAP transporter small permease protein DctQ Cytoplasmic Helical Periplasmic Helical Cytoplasmic Helical Peripla...

  73. DCTM_RHOCA UniProt:Swiss-Prot

    ID: O07838

    Description: C4-dicarboxylate TRAP transporter large permease protein DctM Helical Helical Helical Helical Helical Helical Helical Helical Hel...

  74. DCTM_PSEAE UniProt:Swiss-Prot

    ID: Q9HU16

    Description: C4-dicarboxylate TRAP transporter large permease protein DctM Helical Helical Helical Helical Helical Helical Helical Helical Hel...

  75. DCTQ_VIBCH UniProt:Swiss-Prot

    ID: Q9KQS0

    Description: C4-dicarboxylate TRAP transporter small permease protein DctQ Helical Helical Helical Helical

  76. TRAP_STAAB UniProt:Swiss-Prot

    ID: Q2YU04

    Description: Signal transduction protein TRAP ABM Phosphohistidine Phosphohistidine Phosphohistidine

  77. SIAM_VIBCH UniProt:Swiss-Prot

    ID: Q9KR66

    Description: Sialic acid TRAP transporter large permease protein SiaM Helical Helical Helical Helical Helical Helical Helical Helical Hel...

  78. Gene expression profiling in erythroid progenitors through ontogeny ArrayExpress

    ID: E-GEOD-37869

    Description: ked to hematological system development, cellular growth and proliferation. The KITLG, EPO, GATA1, PIM1 and STAT3 genes represent the major connection points in the hematological system development linked genes. Some JAK-STAT signaling pathway-linked genes were steadily upregulated throughout ontogeny (PIM1, SOCS, MYC, PTPN11), while others were downregulated (PTPN6, PIAS, SPRED2). In addition, some JAK-STAT pathway related genes have specific expression just at certain stages of ontogeny (STATs, GRB2, CREBB). Beside continuously upregulated (AKT1, PPP2CA, CHUK, NFKB1) and downregulated (FOXO1, PDPK1, PIK3CG) genes in the PI3K-AKT signaling pathway, we also observed intermittently regulated gene expression (NFKBIA, YWHAH). Conclusions: This broad overview of gene expression in erythropoiesis revealed transcription factors with a prevalence at certain stages of ontogenesis. Finally, our results show that EPO-mediated proliferation and survival of erythroid progenitors occurs mainly through modulation of JAK-STAT pathway associated STATs, GRB2 and PIK3 genes, as well as AKT pathway- coupled NFKBIA and YWHAH genes. Adult peripheral blood mononuclear cells were isolated from buffy coats of 3 healthy donors using Lymphocyte Separation Medium (BioWhittaker, Walkersville, MD). We washed mononuclear cells twice with Dulbecco's phosphate-buffered saline (PBS, Invitrogen Corporation, Carlsbad, CA), and CD34+ cells were purifi...

  79. UEHB_RUEPO UniProt:Swiss-Prot

    ID: Q5LUA8

    Description: Ectoine/5-hydroxyectoine TRAP transporter small permease protein UehB Helical Helical Helical Helical

  80. SIAQ_VIBCH UniProt:Swiss-Prot

    ID: Q9KR65

    Description: Sialic acid TRAP transporter small permease protein SiaQ Helical Helical Helical Helical

  81. DCTM_VIBCH UniProt:Swiss-Prot

    ID: Q9KQS1

    Description: C4-dicarboxylate TRAP transporter large permease protein DctM Helical Helical Helical Helical Helical Helical Helical Helical Hel...

  82. Integrative Transcriptome Analysis Reveals Common Molecular Subtypes of Human Hepatocellular Carcinoma BioProject

    ID: PRJNA108343

    Keywords: Transcriptome or Gene expression

    Access Type: download

    dataset.description: ion as well as MYC and AKT activation, and S3 was associated with hepatocyte differentiation. Functional studies indicated that the WNT pathway activation signature characteristic of S1 tumors was not simply the result of beta-catenin mutation but rather was the result of transforming growth factor-beta activation, thus representing a new mechanism of WNT pathway activation in HCC. These experiments establish the first consensus classification framework for HCC based on gene expression profiles and highlight the power of integrating multiple data sets to define a robust molecular taxonomy of the disease. Overall design: Surgically resected 118 tumor tissues from patients with hepatocellular carcinoma (HCC)...
  83. Gene expression arrays of cardiomyocyte ribosome-associated RNAs during zebrafish heart regeneration OmicsDI

    ID: E-GEOD-48914

    Date Released: 08-12-2013

    Description: A transgenic line cmlc2:TRAP was made to express EGFP-fused ribosomal protein L10a (EGFP-L10a) in zebrafish cardiomyocytes. Then ribosom...

  84. Age-dependent aorta transcriptomes in wild-type and apoE-deficient C57BL/6J mice BioProject

    ID: PRJNA104025

    Keywords: Transcriptome or Gene expression

    Access Type: download

    dataset.description: clerosis cluster and cytokine activity, chemokine receptor activity, and antigen binding in the ATLO cluster suggested candidate genes in relation to inflammation triggered by macrophages or adventitia infiltration, respectively. Among other prototype atherosclerosis genes such as Itgax (complement receptor 4), Cd68, Lysz (lysozyme), Vcam1, and Icam1, the atherosclerosis cluster showed markedly overrepresented prototype macrophage/foam cell genes regulating inflammation in cytokine activity (GO: 0005125): Spp1 (osteopontin) and Il6; in cytokine binding (GO: 0019955) Cd74, Il10rb, Ccr2, and Ccr5; and in immunoglobulin binding (GO: 00119865) the proinflammatory galactose-binding lectin Lgals3, as well as genes in scavenger receptor activity and lipid transporter activity. By contrast, the adventitia cluster showed overrepresented genes regulating B cell recruitment, B cell maturation, germinal center formation, and autoimmunity in cytokine activity including Cxcl13, Ccl21, and Ltb, in CXC chemokine receptor activity the secondary lymphoid organ counterreceptor of CXCL13 Blr1 (also known as Cxcr5), Cxcr3, and Cxcr6; and in antigen binding several histocompatibility-2 loci and various markedly expressed immunoglobulin genes. As embryonic lymph node development and tertiary lymphoid organ neogenesis share common features signal intensities of genes specifying the GO molecular function term lymph node development (GO: 0048535) were examined in arrays prepared from wild-type and apoE-/- aortae. These results showed that Id2, Nfkb1, and Ltbr were constitutively expressed at significant levels in aortae of both mouse genotypes whereas other genes including Lta, Ltb, Glycam1, and the two lymphorganogenic genes Cxcl13 and Ccl21 were induced at 78 w in apoE-deficient aortae only. Thus, genes expressed by macrophage-foam cells and genes regulating ATLO neogenesis, embryonic lymph node development, or B cell maturation were constitutively expressed in the arterial wall in both genotypes or emerged in a stepwise fashion at 32 w and 78 w. To verify microarray signal intensity data, separate aortae extracts were examined by quantitative RT-PCR (QRT-PCR) analyses of wild-type and apoE-deficient mice at 32 and 78 w. These data showed that array signal values accurately reflected gene transcripts. Cell lineage analyses of the adventitial infiltrate a...
  85. The Proteasome Stress Regulon is Controlled by a Pair of NAC Transcription Factors in Arabidopsis BioProject

    ID: PRJNA322265

    Keywords: Transcriptome or Gene expression

    Access Type: download

    dataset.description: differences between 5DAG Arabidopsis Col-0, rpn10-1, and rpn12a-1 seedlings treated with 100 uM MG132 for 0, 3, or 24 hours. Overall design: Examination of 3 different Arabidopsis seedlin...
  86. Effect of telmisartan on prostate carcinogenesis in TRAP rats BioProject

    ID: PRJNA141557

    Keywords: Transcriptome or Gene expression

    Access Type: download

  87. Trap-80-dependence of TNF-alpha-induced genes OmicsDI

    ID: E-GEOD-12697

    Date Released: 05-01-2014

    Description: can be sub-divided, depending on whether they are Trap-80-dependent or -independent. To examine the generality of this grouping, we performed a microarray analysis of wild-type and Trap-80 knock-do...

  88. Gene trapping in the Asian malaria vector, Anopheles stephensi ArrayExpress

    ID: E-GEOD-78771

    Description: A piggyBac transposon-based gene trap element was transformed into the Asian malaria vector, Anopheles stephensi, and remobilized using the jumpstarter approach usi...

  89. colour data for artificial traps placed on natural backgrounds Dryad

    DateIssued: 04-30-2014

    Description: related to measurement of the colour of a single trap and its background. Data were measured electronically using image analysis of digital photographs. ‘Trap’: trap i.d. (these relate directly to ‘trap’ in ‘Artificial_On_Natural’. Colour: Trap colou...

  90. Microarray analysis of wildtype, Klf3 H275R homozygous and heterozygous, Klf3 CH gene trap homozygous and heterozygous E12.5 embryos ArrayExpress

    ID: E-GEOD-43908

    Description: pression in whole E12.5 embryos containing a gene trap (CH) or point mutation (H275R) within the Klf3 gene Affymetrix microarrays were performed on RNA from wildtype, Klf3 H275R/H275R, Klf3 H275R/+, Klf3 CH homozygous and Klf3 CH heterozygous E12.5 embryo...

  91. Trap-80-dependence of TNF-alpha-induced genes ArrayExpress

    ID: E-GEOD-12697

    Description: can be sub-divided, depending on whether they are Trap-80-dependent or -independent. To examine the generality of this grouping, we performed a microarray analysis of wild-type and Trap-80 knock-do...

  92. Gene expression arrays of cardiomyocyte ribosome-associated RNAs during zebrafish heart regeneration ArrayExpress

    ID: E-GEOD-48914

    Description: A transgenic line cmlc2:TRAP was made to express EGFP-fused ribosomal protein L10a (EGFP-L10a) in zebrafish cardiomyocytes. Then ribosom...

  93. Video 1 - May 29 2015 - Bottlenose dolphin using the one-step process to manipulate a fish trap Dryad

    DateIssued: 11-23-2016

  94. Crystal structure of B.licheniformis Anti-TRAP protein, an antagonist of TRAP-RNA interactions PDB

    ID: PDB:3LD0

    Description: Inhibitor of TRAP, regulated by T-BOX (Trp) sequence RtpA

  95. Colour data for artificial traps placed on artificial backgrounds Dryad

    DateIssued: 04-30-2014

    Description: related to measurement of the colour of a single trap and its background. These traps are a sample created with used in the study, though these traps were not used in the study itself. Data were collected electronically using image analysis of digital photographs. ‘Trap’: Trap i.d. ‘TrpClr’: trap colou...

  96. Crystal structure of a TRAP periplasmic solute binding protein from Chromohalobacter salexigens DSM 3043 (Csal_0678), Target EFI-501078... PDB

    ID: PDB:4XF5

    Description: TRAP PERIPLASMIC SOLUTE BINDING PROTEIN

  97. X-Ray Crystallographic Structure of hTrap1 N-terminal Domain-apo PDB

    ID: PDB:5F3K

    Description: Heat shock protein 75 kDa, mitochondrial

  98. CRYSTAL STRUCTURE OF B.SUBTILIS ANTI-TRAP PROTEIN, AN ANTAGONIST OF TRAP-RNA INTERACTIONS PDB

    ID: PDB:2BX9

    Description: TRYPTOPHAN RNA-BINDING ATTENUATOR PROTEIN-INHIBITORY PROTEIN

  99. Rovero et al_EAM cam trap database.csv Figshare

    ID: doi:10.6084/M9.FIGSHARE.3444005

    Release Date: 12-28-2016

    Description: Camera trap records of medium to large mammals detected in selected mountain blocks and forests within the the Eastern Arc Mountains of Ta...

  100. DawrinCode records - Diptera Dryad

    DateIssued: 09-26-2016

    Description: Specimens were collected at a site in Steel Creek, in Northwest Arkansas, using Malaise pitfall, colored pan, Lindgren funnel, and canopy traps.

    identifiers.ID: doi:10.5061/dryad.bk225/1

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