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| Open reading frame (ORF) annotation in the exon skipping event |
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| 3'-UTR located exon skipping events lost miRNA binding sites |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
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Gene summary for TGFB1 |
 Gene summary |
| Gene information | Gene symbol | TGFB1 | Gene ID | 7040 |
| Gene name | transforming growth factor beta 1 | |
| Synonyms | CED|DPD1|IBDIMDE|LAP|TGF-beta1|TGFB|TGFbeta | |
| Cytomap | 19q13.2 | |
| Type of gene | protein-coding | |
| Description | transforming growth factor beta-1 proproteinTGF-beta-1latency-associated peptideprepro-transforming growth factor beta-1transforming growth factor beta1 | |
| Modification date | 20200329 | |
| UniProtAcc | A0A024R0P8, A0A078BBI5, A0A078BC11, | |
| Context | - 16082716(Association Studies of Transforming Growth Factor-Beta 1 and Alzheimer's Disease) |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
| TGFB1 | GO:0001837 | epithelial to mesenchymal transition | 25893292|29529050 |
| TGFB1 | GO:0001933 | negative regulation of protein phosphorylation | 8053900 |
| TGFB1 | GO:0001934 | positive regulation of protein phosphorylation | 18625725 |
| TGFB1 | GO:0002062 | chondrocyte differentiation | 15040835 |
| TGFB1 | GO:0002244 | hematopoietic progenitor cell differentiation | 15451575 |
| TGFB1 | GO:0006611 | protein export from nucleus | 9770491|17438144|18588859 |
| TGFB1 | GO:0006754 | ATP biosynthetic process | 10513816 |
| TGFB1 | GO:0006796 | phosphate-containing compound metabolic process | 10513816 |
| TGFB1 | GO:0006954 | inflammatory response | 21147091 |
| TGFB1 | GO:0007050 | cell cycle arrest | 14555988 |
| TGFB1 | GO:0007093 | mitotic cell cycle checkpoint | 15334054 |
| TGFB1 | GO:0007173 | epidermal growth factor receptor signaling pathway | 18625725 |
| TGFB1 | GO:0007179 | transforming growth factor beta receptor signaling pathway | 9389648|11157754 |
| TGFB1 | GO:0007182 | common-partner SMAD protein phosphorylation | 20573232 |
| TGFB1 | GO:0007183 | SMAD protein complex assembly | 17438144 |
| TGFB1 | GO:0008284 | positive regulation of cell proliferation | 10513816|14633705 |
| TGFB1 | GO:0008285 | negative regulation of cell proliferation | 15334054 |
| TGFB1 | GO:0010628 | positive regulation of gene expression | 18625725|18832382|18941241|19913496|25322725|26634652|26687115|27162619|29167509 |
| TGFB1 | GO:0010629 | negative regulation of gene expression | 19913496|20067797|22269326|25163461|26634652|29167509|29529050 |
| TGFB1 | GO:0010718 | positive regulation of epithelial to mesenchymal transition | 17999987|18505915 |
| TGFB1 | GO:0010763 | positive regulation of fibroblast migration | 18555217 |
| TGFB1 | GO:0010800 | positive regulation of peptidyl-threonine phosphorylation | 18625725|19736306 |
| TGFB1 | GO:0010862 | positive regulation of pathway-restricted SMAD protein phosphorylation | 9389648|19736306|26634652 |
| TGFB1 | GO:0010936 | negative regulation of macrophage cytokine production | 20875417 |
| TGFB1 | GO:0016477 | cell migration | 25893292 |
| TGFB1 | GO:0017015 | regulation of transforming growth factor beta receptor signaling pathway | 15334054 |
| TGFB1 | GO:0022408 | negative regulation of cell-cell adhesion | 18593713 |
| TGFB1 | GO:0030214 | hyaluronan catabolic process | 17324121 |
| TGFB1 | GO:0030308 | negative regulation of cell growth | 15334054 |
| TGFB1 | GO:0030335 | positive regulation of cell migration | 19736306 |
| TGFB1 | GO:0031293 | membrane protein intracellular domain proteolysis | 25310401 |
| TGFB1 | GO:0031334 | positive regulation of protein complex assembly | 19366691 |
| TGFB1 | GO:0031663 | lipopolysaccharide-mediated signaling pathway | 21147091 |
| TGFB1 | GO:0032270 | positive regulation of cellular protein metabolic process | 15219857 |
| TGFB1 | GO:0032355 | response to estradiol | 18039789 |
| TGFB1 | GO:0032570 | response to progesterone | 18039789 |
| TGFB1 | GO:0032740 | positive regulation of interleukin-17 production | 18453574 |
| TGFB1 | GO:0032801 | receptor catabolic process | 17878231 |
| TGFB1 | GO:0032930 | positive regulation of superoxide anion generation | 22073128 |
| TGFB1 | GO:0032967 | positive regulation of collagen biosynthetic process | 19734317|22269326|25310401 |
| TGFB1 | GO:0033138 | positive regulation of peptidyl-serine phosphorylation | 18625725|19736306 |
| TGFB1 | GO:0035307 | positive regulation of protein dephosphorylation | 14555988 |
| TGFB1 | GO:0042307 | positive regulation of protein import into nucleus | 19366691 |
| TGFB1 | GO:0043117 | positive regulation of vascular permeability | 21168935 |
| TGFB1 | GO:0043406 | positive regulation of MAP kinase activity | 18625725 |
| TGFB1 | GO:0043536 | positive regulation of blood vessel endothelial cell migration | 18555217 |
| TGFB1 | GO:0043537 | negative regulation of blood vessel endothelial cell migration | 18555217 |
| TGFB1 | GO:0043552 | positive regulation of phosphatidylinositol 3-kinase activity | 18625725 |
| TGFB1 | GO:0045216 | cell-cell junction organization | 18505915 |
| TGFB1 | GO:0045599 | negative regulation of fat cell differentiation | 15040835 |
| TGFB1 | GO:0045662 | negative regulation of myoblast differentiation | 9770491 |
| TGFB1 | GO:0045786 | negative regulation of cell cycle | 11502704 |
| TGFB1 | GO:0045892 | negative regulation of transcription, DNA-templated | 15702480|18832382 |
| TGFB1 | GO:0045893 | positive regulation of transcription, DNA-templated | 9389648|14517293|15334054|16816361 |
| TGFB1 | GO:0045918 | negative regulation of cytolysis | 24586048 |
| TGFB1 | GO:0045930 | negative regulation of mitotic cell cycle | 14555988 |
| TGFB1 | GO:0045944 | positive regulation of transcription by RNA polymerase II | 18832382 |
| TGFB1 | GO:0048298 | positive regulation of isotype switching to IgA isotypes | 14988498 |
| TGFB1 | GO:0048642 | negative regulation of skeletal muscle tissue development | 9770491 |
| TGFB1 | GO:0050680 | negative regulation of epithelial cell proliferation | 9950587 |
| TGFB1 | GO:0050714 | positive regulation of protein secretion | 18505915 |
| TGFB1 | GO:0050731 | positive regulation of peptidyl-tyrosine phosphorylation | 21168935 |
| TGFB1 | GO:0050921 | positive regulation of chemotaxis | 18555217 |
| TGFB1 | GO:0051897 | positive regulation of protein kinase B signaling | 18625725 |
| TGFB1 | GO:0060389 | pathway-restricted SMAD protein phosphorylation | 11157754|17999987|18453574|25893292 |
| TGFB1 | GO:0060390 | regulation of SMAD protein signal transduction | 25893292 |
| TGFB1 | GO:0060391 | positive regulation of SMAD protein signal transduction | 9389648|19366691|29167509 |
| TGFB1 | GO:0070168 | negative regulation of biomineral tissue development | 26634652 |
| TGFB1 | GO:0070374 | positive regulation of ERK1 and ERK2 cascade | 25310401 |
| TGFB1 | GO:0070723 | response to cholesterol | 17878231 |
| TGFB1 | GO:0071407 | cellular response to organic cyclic compound | 21147091 |
| TGFB1 | GO:0071560 | cellular response to transforming growth factor beta stimulus | 19736306|22269326 |
| TGFB1 | GO:0085029 | extracellular matrix assembly | 19734317 |
| TGFB1 | GO:0090263 | positive regulation of canonical Wnt signaling pathway | 12893825|15040835 |
| TGFB1 | GO:0097191 | extrinsic apoptotic signaling pathway | 15334054 |
| TGFB1 | GO:1900126 | negative regulation of hyaluronan biosynthetic process | 17324121 |
| TGFB1 | GO:1900182 | positive regulation of protein localization to nucleus | 26634652 |
| TGFB1 | GO:1901666 | positive regulation of NAD+ ADP-ribosyltransferase activity | 22073128 |
| TGFB1 | GO:1902895 | positive regulation of pri-miRNA transcription by RNA polymerase II | 26311719|26493107 |
| TGFB1 | GO:1903077 | negative regulation of protein localization to plasma membrane | 21168935|24586048 |
| TGFB1 | GO:1903800 | positive regulation of production of miRNAs involved in gene silencing by miRNA | 18548003 |
| TGFB1 | GO:2000679 | positive regulation of transcription regulatory region DNA binding | 22073128 |
| TGFB1 | GO:2000727 | positive regulation of cardiac muscle cell differentiation | 25163461 |
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Gene structures and expression levels for TGFB1 |
| Skipped exons in the ROSMAP, MSBB, and Mayo based on Ensembl gene isoform structure. * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
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ENSG00000105329
| Differentially expressed gene analysis across multiple brain tissues between AD and control. |
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| Tissue type | DEG direction | Base mean exp. | log2FC(AD/control) | P-value | Adj. p-value |
| PG | UP | 8.823237e+01 | 8.514204e-01 | 2.045050e-08 | 1.044669e-06 |
| Differentially expressed isoform analysis across multiple brain tissues between AD and control. |
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| Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
| PG | UP | ENST00000221930.6 | TGFB1-201:protein_coding:TGFB1 | 8.646997e+01 | 8.815112e-01 | 2.951018e-06 | 2.025504e-04 |
| PG | UP | ENST00000597453.1 | TGFB1-202:retained_intron:TGFB1 | 3.505387e+00 | 1.112781e+00 | 4.847053e-05 | 1.603242e-03 |
| Landscape of isoform expressions across multiple brain tissues between AD and control. |
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Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for TGFB1 |
| Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap). |
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| All exon skipping events in AD cohorts. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon |
| exon_skip_177248 | chr19 | 41344747:41344864:41348295:41348455:41352690:41353922 | 41348295:41348455 |
| exon_skip_286934 | chr19 | 41332055:41332281:41341883:41342030:41342170:41342247 | 41341883:41342030 |
| exon_skip_76788 | chr19 | 41332128:41332281:41341883:41342030:41342170:41342247 | 41341883:41342030 |
| Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control. |
| Exon skipping information | Tissue type | Avg(PSIs) in AD | Avg(PSIs) in control | Difference (PSI) | Adj. p-value |
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Open reading frame (ORF) annotation in the exon skipping event for TGFB1 |
| Open reading frame (ORF) of individual exon skipping events in ROSMAP based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000221930 | 41341883 | 41342030 | Frame-shift |
| ENST00000221930 | 41348295 | 41348455 | Frame-shift |
| Open reading frame (ORF) of individual exon skipping events in MSBB based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| Open reading frame (ORF) of individual exon skipping events in Mayo based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000221930 | 41341883 | 41342030 | Frame-shift |
| ENST00000221930 | 41348295 | 41348455 | Frame-shift |
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Infer the effects of exon skipping event on protein functional features for TGFB1 |
| Loci of skipped exons in ROSMAP across genomic, transcript, and protein sequence levels of In-frame cases. |
| ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
| Loci of skipped exons in MSBB across genomic, transcript, and protein sequence levels of In-frame cases. |
| ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
| Loci of skipped exons in Mayo across genomic, transcript, and protein sequence levels of In-frame cases. |
| ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
| Lost protein functional features of individual exon skipping events in ROSMAP. |
| UniProt acc. | Start of exon skipping (AA) | End of exon skipping (AA) | Protein feature start (AA) | Protein feature end (AA) | Category of protein feature | Description of feature |
| Lost protein functional features of individual exon skipping events in MSBB. |
| UniProt acc. | Start of exon skipping (AA) | End of exon skipping (AA) | Protein feature start (AA) | Protein feature end (AA) | Category of protein feature | Description of feature |
| Lost protein functional features of individual exon skipping events in Mayo. |
| UniProt acc. | Start of exon skipping (AA) | End of exon skipping (AA) | Protein feature start (AA) | Protein feature end (AA) | Category of protein feature | Description of feature |
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3'-UTR located exon skipping events that lost miRNA binding sites in TGFB1 |
| 3'-UTR exon skipping evnets lost miRNA binding. |
| Tissue type | ENST | Exon skip start | Exon skip end | microRNA | Binding site by TargetScan | Binding type by TargetScan | Bdinding site by miRanda | Score of miRanda | Energy by miRanda |
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SNVs in the skipped exons for TGFB1 |
| - Differential PSIs between mutated versus non-mutated samples. |
| - Depth of Coverage in the skipped exon of the mutated samples. |
| - Sashimi plot in the skipped exon of the mutated samples. |
| - Non-synonymous mutations located in the skipped exons. |
| Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
| - Non-synonymous mutations located in the skipped exons in CCLE. |
| Sample | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
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AD stage-associated exon skippint events for TGFB1 |
| Associated exon skipping events with Braak staging or Clinical Dementia Rating (CDR). |
| AD stage info | Cohort | Tissue | SE id | Coefficient | P-value | Chromosome | Strand | E1 start | E1 end | Skipped start | Skipped end | E2 start | E2 end |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for TGFB1 |
| sQTL information located at the skipped exons. |
| Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
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Correlation with RNA binding proteins (RBPs) for TGFB1 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for TGFB1 |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for TGFB1 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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