Summary of the datasets

Gene Expression

Num Datasets TFEB Gene Perturbation Experimental Data Species GEO Accession Code Summary Experimental Details References PubMed ID
1TFEB Time Seriesover-expressionRNA-seqHomo Sapiens GSE98247 Transcriptome profile of a stable clone over-expressing TFEB in HEK293 cells by TET-OFF system (HEK293-PFL-TFEB) Total RNA was extracted at time 0 in presence of tetracycline to evaluate the basal expression level of TFEB and at each time point (from 6 to 90h) from the removal of tetracyclineto evaluate the effect of TFEB over-expression.Gambardella G, Staiano L, Moretti MN, De Cegli R et al. GADD34 is a modulator of autophagy during starvation. Sci Adv 2020 Sep;6(39). PMID: 32978159 32978159
2TFEB HeLaover-expressionmicroarraysHomo Sapiens GSE16267 The first TFEB transcriptome study performed in HeLa cells following TFEB transient transfectionTotal RNA samples from three biological replicates in which TFEB was transiently over-expressed in HeLa cells by transfection using a pcDNA3 vector and total RNA samples from HeLa cells transfected with an empty pcDNA3 vector were used as controlSardiello, M., et al., A gene network regulating lysosomal biogenesis and function. Science, 2009. 325(5939): p. 473-7. PMID:  19556463 19556463
3TFEB-GFP HeLa over-expressionmicroarraysHomo Sapiens GSE73055 Transcriptome analysis of HeLa cells stable clones over-expressing TFEB-GFPTotal RNA was extracted from the cells of three TFEB-GFP biological replicates; RNA extracted from HeLa WT cells was used as control.Nnah, I.C., et al., TFEB-driven endocytosis coordinates MTORC1 signaling and autophagy. Autophagy, 2019. 15(1): p. 151-164. PMID:  30145926 30145926
4TFEB-3xFLAG HeLaover-expressionmicroarraysHomo Sapiens GSE73054 Transcriptome analysis of HeLa cells stable clones over-expressing TFEB-3xFLAGTotal RNA was extracted from the cells of three TFEB-3xFLAG biological replicates; RNA extracted from HeLa WT cells was used as control.generated for this study
5TFEB LIVER - OEover-expressionmicroarraysMus Musculus GSE41139 Transcriptome analysis of the injected mice overexpressing TFEB specifically in liver in order to identify the effects of TFEB overexpression on the liver transcriptomeTotal RNA was extracted from mice injected with an adenoviral vector that expresses human TFEB (HDAd-TFEB) under control of the liver-specific promoter PEPCK. Mice injected with a transgene-less vector were used as control. Settembre, C., et al., TFEB controls cellular lipid metabolism through a starvation-induced autoregulatory loop. Nat Cell Biol, 2013. 15(6): p. 647-58. PMID:  23604321 23604321
6TFEB LIVER - OE/ PPARA-KOover-expression of TFEB and KO of PPARαmicroarraysMus Musculus GSE41140 Transcriptome analysis of PPARα (peroxisome proliferator activated receptor alpha) knockout (KO) mice injected with TFEB specifically in liver For the analysis on the injected PPARα-KO mice overexpressing TFEB, total RNA was extracted from the liver of three mice; RNA extracted from the liver of not-injected mice was used as control.Settembre, C., et al., TFEB controls cellular lipid metabolism through a starvation-induced autoregulatory loop. Nat Cell Biol, 2013. 15(6): p. 647-58. PMID:  23604321 23604321
7TFEB MUSCLE - OEover-expressionmicroarraysMus Musculus GSE62975 Transcriptome analysis of the injected mice overexpressing Tcfeb specifically in skeletal muscle For the analysis on the injected mice with an AAV vector expressing Tcfeb, total RNA was extracted from the muscle of three mice; RNA extracted from the muscle of mice injected with an AAV vector expressing GFP was used as control.Mansueto, G., et al., Transcription Factor EB Controls Metabolic Flexibility during Exercise. Cell Metab, 2017. 25(1): p. 182-196. PMID:  28011087 28011087
8TFEB MUSCLE - KOKOmicroarraysMus Musculus GSE62976 Transcriptome analysis of the Muscle-specific conditional TFEB KO mice Muscle-specific conditional TFEB KO mice were generated by crossing Tcfeb floxed with MLC1f-Cre transgenic mice: total RNA was extracted from the muscle of three mice; RNA extracted from the muscle of three wt muscles was used as control.Mansueto, G., et al., Transcription Factor EB Controls Metabolic Flexibility during Exercise. Cell Metab, 2017. 25(1): p. 182-196. PMID:  28011087 28011087
9TFEB KIDNEY P0 - OEover-expressionmicroarraysMus Musculus GSE62977 Transcriptome analysis of mice overexpressing Tcfeb specifically in kidney: the age of the mice was P0Transcriptome analysis of Tcfeb overexpression on the kidney transcriptome, was performed for the double heterozygous KSP_CRE/KSP_Tcfeb mice as compared to control KSP_CRE mice: total RNA was extracted from the kidney of three mice at P0; RNA extracted from the kidney of two mice at P0 was used as control.Calcagni, A., et al., Modelling TFE renal cell carcinoma in mice reveals a critical role of WNT signaling. Elife, 2016. 5. PMID:  27668431 27668431
10TFEB KIDNEY P14 - OEover-expressionmicroarraysMus Musculus GSE63376 Transcriptome analysis of on 14 days old mice overexpressing Tcfeb specifically in kidney.Transcriptome analysis of Tcfeb overexpression on the kidney transcriptome, was performed for the double heterozygous KSP_CRE/KSP_Tcfeb mice as compared to control KSP_CRE mice: total RNA was extracted from the kidney of three mice at P14; RNA extracted from the kidney of three mice at P14 was used as control.Calcagni, A., et al., Modelling TFE renal cell carcinoma in mice reveals a critical role of WNT signaling. Elife, 2016. 5. PMID:  27668431 27668431

ChIP-seq

Num Datasets TFEB Gene Perturbation Experimental Data Species GEO Accession Code Summary Experimental Details References PubMed ID
1TFEB HEK-293over-expressionChIP-seqHomo Sapiens GSE98246 Genome-wide chromatin immunoprecipitation sequencing (ChIP-seq) in a monoclonal population of HEK-293 cells stably expressing a Tet-OFF regulatory system (i.e. HEK293-PFL-TFEB).In order to identify the direct target of TFEB, a ChIP-seq in HEK293-PFL-TFEB cells was performed after removal of tetracycline: samples were collected at 18, 36 and 90 hours. Two ChIP samples for each timepoint and one immunoglobulin G (IgG) control samples were subjected to Illumina high-throughput sequencing and mapped to the reference human genome hg19Gambardella, G., et al., GADD34 is a modulator of autophagy during starvation. Sci Adv, 2020. 6(39). PMID:  32978159 32978159
2TFEB HeLaover-expressionChIP-seqHomo Sapiens Smiley face The first comprehensive map of the TFEB targetome performed by ChIP-seq in Hela stable clones, in a steady-state condition.In our database we named the TFEB direct targets identified in this study as “YES” if the binding was found in the promoter region at -1kb from the transcription start site (TSS), otherwise the absence of binding is shown as “NO”. For each peak we reported genomic coordinates on hg19 (i.e. start and end); distance from the Transcriptional Start Site (TSS) of the closest gene; official gene symbol. TFEB ChIP-seq binding sites within -1 Kb and 0 from their transcription start site (705 gene symbols in total)Palmieri, M., et al., Characterization of the CLEAR network reveals an integrated control of cellular clearance pathways. Hum Mol Genet, 2011. 20(19): p. 3852-66. PMID:  21752829 21752829

Bioinformatics predictions

Num Species Assembly Bioinformatics predictions (TFEB Position Weight Matrix)
1Homo Sapienshg19 Genome-wide prediction of TFEB binding sites
2Mus Musculusmm10 Genome-wide prediction of TFEB binding sites
3Rattus Norvegicusrn6 Genome-wide prediction of TFEB binding sites




Copyright © 2020 Tigem. Designed by Diego Carrella in collaboration with Rossella De Cegli
Data produced by Ballabio’s and di Bernardo’s lab

Please cite De Cegli R., Carrella D., et al., TFEBdb: An integrated database of genes regulated by the stress-responsive Transcription Factor EB.

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