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Studies
Differential expression results all studies
GSEA results
DE results
Boxplot selected gene(s)
DepMap correlation selected Cell Line
Volcano plot
Selected points
Preranked GSEA plot
Running score plot
Preranked GSEA table
GSEA plot
GSEA table
MES/ADRN rank percentile score
Venn Diagram
GSEA table of venn selection
DE table of venn selection
DE results
Boxplot selected phospho-site(s)
DepMap correlation selected Cell Line
Volcano plot
Selected points
Preranked GSEA plot
Running score plot
Preranked GSEA table
GSEA plot
GSEA table
Venn Diagram
GSEA table of venn selection
DE table of venn selection
2024-08-19
Notes
In this update, we added: instructional videos, accessible through the 'Videos'-button in the upper, right corner; MES/ADRN percentile rank scoring plot for RNA-Seq data; kinase-tyrosine substrate specificities from Johnson et al. 2024, now allowing users to perform kinase enrichment for Y-kinases in addition to S/T-kinases in the phosphoproteomics tab; fixed data upload issue.New Studies(14)
AbuZaid_2024
- Title: 'Histone lysine demethylase 4 family proteins maintain the transcriptional program and adrenergic cellular state of MYCN-amplified neuroblastoma'
- Data Type: RNA
- Conditions: QC6352(KDM4Ci)[200nM], KDM4A(KD), KDM4C(KD)
Chang_2024
- Title: 'Therapeutic SHPRH-146aa encoded by circ-SHPRH dynamically upregulates P21 to inhibit CDKs in neuroblastoma'
- Data Type: RNA
- Conditions: circ-SHPRH(OE)
Chen_2024
- Title: 'Super-enhancer-driven IRF2BP2 enhances ALK activity and promotes neuroblastoma cell proliferation'
- Data Type: RNA
- Conditions: IRF2BP2(KD)
Chennakesavalu_2024
- Title: '5-Hydroxymethylcytosine Profiling of Cell-Free DNA Identifies Bivalent Genes That Are Prognostic of Survival in High-Risk Neuroblastoma'
- Data Type: RNA
- Conditions: Tazemetostat(EZH2i)[600nM]
Ekstrom_2024
- Title: 'USP44 overexpression drives a MYC-like gene expression program in neuroblastoma through epigenetic reprogramming'
- Data Type: RNA
- Conditions: USP44(OE)
Forbes_2024
- Title: 'L-Glyceraldehyde Inhibits Neuroblastoma Cell Growth via a Multi-Modal Mechanism on Metabolism and Signaling'
- Data Type: PP
- Conditions: L-glyceraldehyde[1mM], L-glyceraldehyde[1mM] + N-acetyl-cysteine[5mM]
Fredlund_2024
- Title: 'MOXD1 is a gate-keeper of organ homeostasis and functions as a tumor-suppressor in neuroblastoma'
- Data Type: RNA
- Conditions: MOXD1(OE)
Huang_2024
- Title: 'ALK upregulates POSTN and WNT signaling to drive neuroblastoma'
- Data Type: RNA
- Conditions: MYCN/ALK vs MYCN
Malone_2024
- Title: 'The KAT module of the SAGA complex maintains the oncogenic gene expression program in MYCN- amplified neuroblastoma'
- Data Type: RNA
- Conditions: TADA2B(deg), TADA2B(KO), KAT2A/B(KO)
Murray_2024
- Title: 'The transcriptional co-repressor Runx1t1 is essential for MYCN-driven neuroblastoma tumorigenesis'
- Data Type: RNA
- Conditions: RUNX1T1(KO)(sh1), RUNX1T1(KO)(sh2)
Salib_2024
- Title: 'MYCN and SNRPD3 cooperate to maintain a balance of alternative splicing events that drives neuroblastoma progression'
- Data Type: RNA
- Conditions: MYCN(KD), SNRPD3(KD)(si1), SNRPD3(KD)(si2), MYCN(KD)+SNRPD3(KD)(si1), MYCN(KD)+SNRPD3(KD)(si2)
VanGerven_2023
- Title: 'Two opposing gene expression patterns within ATRX aberrant neuroblastoma'
- Data Type: RNA
- Conditions: ATRX(KO), ATRX(MED)[e2-13], ATRX(MED)[e2-10]
Wang_2024
- Title: 'METTL14 promotes neuroblastoma formation by inhibiting YWHAH via an m6A-YTHDF1-dependent mechanism'
- Data Type: RNA
- Conditions: METTL14(KD)
Zhuo_2024
- Title: 'CDK5RAP3 is a novel super-enhancer-driven gene activated by master TFs and regulates ER-Phagy in neuroblastoma'
- Data Type: RNA
- Conditions: CDK5RAP3(KD)
2024-03-25
Notes
We added mesenchymal (MES) and adrenergic (ADRN) signatures from van Groningen et al 2017 as gene sets for enrichment (selectable under 'GSEA Settings' as 'MES & ADRN Signature' in the lefthand sidebar in the RNA-Seq and Phospho-Proteomics tabs, and under 'GSEA' in the Search tab).2024-03-01
New Studies(10)
Chaudhry_2023
- Title: 'Aryl hydrocarbon receptor is a tumor promoter in MYCN-amplified neuroblastoma cells through suppression of differentiation'
- Data Type: RNA
- Conditions: AHR(KD)(1), AHR(KD)(2)
Dharaskar_2023
- Title: 'Analysis and functional relevance of the chaperone TRAP-1 interactome in the metabolic regulation and mitochondrial integrity of cancer cells'
- Data Type: RNA
- Conditions: TRAP1(KD), TRAP1(OE)
Ferguson_2023
- Title: 'Palbociclib releases the latent differentiation capacity of neuroblastoma cells'
- Data Type: RNA
- Conditions: Palbociclib(CDK4/6i)[1uM], AT-Retinoic Acid, Palbociclib(CDK4/6i)[1uM]+AT-Retinoic Acid
Fuchs_2023
- Title: 'Defining the landscape of circular RNAs in neuroblastoma unveils a global suppressive function of MYCN'
- Data Type: RNA
- Conditions: MYCN(OE)
Jablonowski_2023
- Title: 'Metabolic reprogramming of cancer cells by JMJD6-mediated pre-mRNA splicing is associated with therapeutic response to splicing inhibitor'
- Data Type: RNA
- Conditions: JMJD6(KD)
Leung_2024
- Title: 'Temporal Quantitative Proteomic and Phosphoproteomic Profiling of SH-SY5Y and IMR-32 Neuroblastoma Cells during All- Trans-Retinoic Acid-Induced Neuronal Differentiation'
- Data Type: PP
- Conditions: AT-Retinoic Acid(8uM)
Liu_2023
- Title: 'MYCN driven oncogenesis involves cooperation with WDR5 to activate canonical MYC targets and G9a to repress differentiation genes'
- Data Type: RNA
- Conditions: MYCN(KD), WDR5(KD), EHMT2(KD)
Szwarc_2023
- Title: 'FAM193A is a positive regulator of p53 activity'
- Data Type: RNA
- Conditions: Nutlin(MDM2i)[10uM], FAM193A(KO), FAM193A(KO)+Nutlin(MDM2i)[10uM]
Yu_2022
- Title: 'ERK Inhibitor Ulixertinib Inhibits High-Risk Neuroblastoma Growth In Vitro and In Vivo'
- Data Type: RNA
- Conditions: Ulixertinib(ERKi)
Wang_2023_2
- Title: 'ASCL1 characterizes adrenergic neuroblastoma via its pioneer function and cooperation with core regulatory circuit factors'
- Data Type: RNA
- Conditions: ASCL1(OE), MYCN(OE)+PHOX2B(OE)+ISL1(OE)+LMO1(OE), MYCN(OE)+PHOX2B(OE)+ISL1(OE)+LMO1(OE)+ASCL1(OE)
Can I compare counts/intensities between different studies or MS runs?
We normalize each study individually, comparing counts/intensities from different studies is therefor not ideal. The same goes for intensities from different MS runs. For cross-study/run comparisons we also recommend the venn diagram.
Do you save data that I upload via the upload dataset function?
No, the data will be deleted after your session.
My study falls within the criteria to be included in CLEAN, but I don't find the data on your platform, why?
This can be due to one of two reasons. (1) The study was published very recently and we haven't had time to curate it yet. (2) Or the processing of the data failed at some step. This can have many reasons. With manual curation of so many studies, there will be issues we haven't had time to get into yet. If you feel like your study should be in there, but it isn't, please send us an email (by clicking contact us in the upper right corner).
How is data processed?
For RNA-Seq we used HISAT2 for alignment, HTSeq for quantification and DESeq2 for differential expression analysis. For differential phosphorylation analysis we use the DEP package.
Updating tables sometimes takes a lot of time, why?
This is often caused by multiple processes running at the same time. Any box that is open will perform analysis, so if the enrichment (fGSEA/GSEA) boxes are all open, it means they will it will be running whenever changes are made in the left-hand sidebar. It is adviced to close any box that you aren't using at the moment.
Sometimes the venn diagram shows genes/proteins/phosphosites that doesn't fall within my thresholds, why?
This can be due to one of two reasons. (1) We offer to set a hyperbolic threshold, meaning you can chose to be more stringent the closer to the p-value and log2FC thresholds you get. You can disable this by setting the 'curve' value under 'Differential Expression' in the lefthand sidebar to 0. (2) Or it can be a rounding issue; the DE/DP discrimination is performed before the rounding of the values you see in the table, so it may seem they are falling outside the cutoffs.
How to cite CLEAN?
Please cite our manuscript 'Preclinical exploration of the DNA damage response pathway using the interactive neuroblastoma cell line explorer CLEAN': https://doi.org/10.1093%2Fnarcan%2Fzcad062