Table 2 Gene sets overrepresented in LN vs PB and PDLS vs PB comparatives.

From: Patient-derived follicular lymphoma spheroids recapitulate lymph node signaling and immune profile uncovering galectin-9 as a novel immunotherapeutic target

Biological process

# of enriched gene sets

LN vs PB

PDLS vs PB

NES (max)

FDR, q value (min)

NES (max)

FDR, q value (min)

Cellular processes

Apoptosis

6

2.324

0.004

1.996

0.002

Cell Signaling

4

1.860

0.029

1.864

0.002

Cellular response

11

2.407

0.004

2.049

0.002

Enzymatic activity

1

1.819

0.008

1.610

0.002

Proteasome

5

2.221

0.004

1.657

0.003

Protein transport

3

2.231

0.004

2.080

0.002

Senescence

2

2.202

0.004

1.964

0.002

Transcriptional regulation

17

2.374

0.004

1.973

0.002

Epigenetic regulation

DNA methylation

7

2.339

0.004

1.992

0.002

EZH2

2

1.896

0.035

1.864

0.002

DNA damage

DNA damage/repair

11

2.245

0.004

1.882

0.002

p53

3

1.995

0.004

1.654

0.003

Immune pathways

Antigen presentation

1

2.168

0.004

1.688

0.002

Cytokines

35

2.345

0.004

2.056

0.002

Immune response

88

2.402

0.004

2.047

0.002

Complement

1

1.640

0.034

1.554

0.002

Metabolic pathways

Fatty Acid metabolism

4

2.346

0.004

2.038

0.002

Glucose metabolism

2

1.873

0.035

1.687

0.002

Oxidative phosphorylation (OXPHOS)

5

1.772

0.015

1.724

0.002

Protein metabolism

1

1.799

0.021

1.675

0.002

RNA metabolism

1

1.945

0.013

1.679

0.002

Proliferation

Cell cycle regulation

91

2.484

0.004

2.051

0.002

Cyclins

2

2.079

0.007

1.903

0.002

DNA replication

20

2.499

0.004

2.085

0.002

Kinase regulation

3

1.838

0.021

1.702

0.002

MYC regulated genes

15

2.265

0.004

1.971

0.002

RAS pathway

3

2.107

0.004

2.022

0.002

Survival pathways

mTOR

3

2.341

0.004

1.857

0.002

Others

Angiogenesis

1

2.093

0.004

1.753

0.002

Cytoskeleton

2

1.846

0.006

1.878

0.002

Drug response

4

2.241

0.004

2.034

0.002

Extracellular matrix

1

2.126

0.004

1.954

0.002

Hypoxia

3

2.106

0.004

1.699

0.002

Metastasis

4

2.230

0.004

1.861

0.002

Mitochondrial protein import

1

1.965

0.014

1.617

0.007

Protein folding

4

2.439

0.004

1.563

0.002

Redox balance

1

1.681

0.046

1.599

0.003

Stemness

6

1.927

0.004

1.880

0.002

Telomeres

3

2.325

0.004

1.709

0.002

Unfolded protein response

1

2.022

0.004

1.584

0.003

  1. GSEA was used to test for significant enrichment of defined gene signatures. NES normalized enriched score, FDR false discovery rate. Threshold FDR < 0.05 and NES > 1.5. Gene sets were obtained from the MSigDB v2023.1.Hs (Mar 2023).
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