Table 4

Gene sets negatively correlated with time, as analyzed by GSEA for total SGZ NSCs from E16.5 to P132 (related to Fig. 6)

Pathway namesAdj. p value
(FDR)
Norm.
Enr. Score
nMore-
Extreme
SizeCategory
CYTOPLASMIC RIBOSOMAL PROTEINS%WIKIPATHWAYS_20191210%WP163%MUS MUSCULUS2.29E-03−2.73080RNA translation + ribosomes
FORMATION OF A POOL OF FREE 40S SUBUNITS%REACTOME DATABASE ID RELEASE 71%726892.29E-03−2.59051RNA translation + ribosomes
VIRAL MRNA TRANSLATION%REACTOME DATABASE ID RELEASE 71%1928232.29E-03−2.57039IR
L13A-MEDIATED TRANSLATIONAL SILENCING OF CERULOPLASMIN EXPRESSION%REACTOME DATABASE ID RELEASE 71%1568272.29E-03−2.57061Miscellaneous
EUKARYOTIC TRANSLATION ELONGATION%REACTOME%R-HSA-156842.22.29E-03−2.57042RNA translation + ribosomes
NONSENSE MEDIATED DECAY (NMD) INDEPENDENT OF THE EXON JUNCTION COMPLEX (EJC)%REACTOME%R-HSA-975956.12.29E-03−2.56045DNA + cell cycle
SELENOCYSTEINE SYNTHESIS%REACTOME DATABASE ID RELEASE 71%24085572.29E-03−2.55043Miscellaneous
REGULATION OF EXPRESSION OF SLITS AND ROBOS%REACTOME DATABASE ID RELEASE 71%90105532.29E-03−2.540111Signaling
EUKARYOTIC TRANSLATION TERMINATION%REACTOME%R-HSA-72764.42.29E-03−2.53043RNA translation + ribosomes
RESPONSE OF EIF2AK4 (GCN2) TO AMINO ACID DEFICIENCY%REACTOME DATABASE ID RELEASE 71%96330122.29E-03−2.51050RNA translation + ribosomes
SRP-DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE%REACTOME%R-HSA-1799339.22.29E-03−2.48061Protein processing
ACTIVATION OF THE MRNA UPON BINDING OF THE CAP-BINDING COMPLEX AND EIFS, AND SUBSEQUENT BINDING TO 43S%REACTOME%R-HSA-72662.32.29E-03−2.42043RNA translation + ribosomes
HALLMARK_MYC_TARGETS_V1%MSIGDB_C2%HALLMARK_MYC_TARGETS_V12.29E-03−2.400184DNA + cell cycle
SELENOAMINO ACID METABOLISM%REACTOME DATABASE ID RELEASE 71%24085222.29E-03−2.39062Metabolism
AUF1 (HNRNP D0) BINDS AND DESTABILIZES MRNA%REACTOME DATABASE ID RELEASE 71%4504082.29E-03−2.39049RNA translation + ribosomes
REGULATION OF ORNITHINE DECARBOXYLASE (ODC)%REACTOME%R-HSA-350562.22.29E-03−2.37048Miscellaneous
PROTEASOME DEGRADATION%WIKIPATHWAYS_20191210%WP519%MUS MUSCULUS2.29E-03−2.35050Protein processing
THE ROLE OF GTSE1 IN G2 M PROGRESSION AFTER G2 CHECKPOINT%REACTOME DATABASE ID RELEASE 71%88522762.29E-03−2.35053DNA + cell cycle
APC C:CDC20 MEDIATED DEGRADATION OF SECURIN%REACTOME%R-HSA-174154.22.29E-03−2.34061IR
CYTOPLASMIC TRANSLATION%GOBP%GO:00021812.29E-03−2.33061RNA translation + ribosomes
ER-PHAGOSOME PATHWAY%REACTOME DATABASE ID RELEASE 71%12369742.29E-03−2.31069Protein processing
SCF(SKP2)-MEDIATED DEGRADATION OF P27 P21%REACTOME%R-HSA-187577.32.29E-03−2.29056DNA + cell cycle
INFLUENZA VIRAL RNA TRANSCRIPTION AND REPLICATION%REACTOME DATABASE ID RELEASE 71%1682732.29E-03−2.27080IR
INFLUENZA INFECTION%REACTOME%R-HSA-168254.22.29E-03−2.22096IR
ASSEMBLY OF THE PRE-REPLICATIVE COMPLEX%REACTOME%R-HSA-68867.42.29E-03−2.20063DNA + cell cycle
REGULATION OF MITOTIC CELL CYCLE%REACTOME%R-HSA-453276.22.29E-03−2.20078DNA + cell cycle
REGULATION OF MRNA STABILITY BY PROTEINS THAT BIND AU-RICH ELEMENTS%REACTOME%R-HSA-450531.42.29E-03−2.19077RNA translation + ribosomes
MAJOR PATHWAY OF RRNA PROCESSING IN THE NUCLEOLUS AND CYTOSOL%REACTOME%R-HSA-6791226.32.29E-03−2.190124RNA translation + ribosomes
SWITCHING OF ORIGINS TO A POST-REPLICATIVE STATE%REACTOME DATABASE ID RELEASE 71%690522.29E-03−2.15084DNA + cell cycle
RUNX1 REGULATES TRANSCRIPTION OF GENES INVOLVED IN DIFFERENTIATION OF HSCS%REACTOME%R-HSA-8939236.12.29E-03−2.14072IR
MITOCHONDRIAL TRANSLATION ELONGATION%REACTOME%R-HSA-5389840.12.29E-03−2.13083RNA translation + ribosomes
HOST INTERACTIONS OF HIV FACTORS%REACTOME%R-HSA-162909.12.29E-03−2.130110IR
RIBOSOMAL LARGE SUBUNIT BIOGENESIS%GOBP%GO:00422732.29E-03−2.12066RNA translation + ribosomes
NEGATIVE REGULATION OF RNA SPLICING%GOBP%GO:00331192.29E-03−2.10028RNA translation + ribosomes
MRNA SPLICING%REACTOME%R-HSA-72172.32.29E-03−2.090176RNA translation + ribosomes
RIBOSOME ASSEMBLY%GOBP%GO:00422552.29E-03−2.09057RNA translation + ribosomes
RRNA PROCESSING%GOBP%GO:00063642.29E-03−2.090148RNA translation + ribosomes
SYNTHESIS OF DNA%REACTOME DATABASE ID RELEASE 71%692392.29E-03−2.070113DNA + cell cycle
COOPERATION OF PREFOLDIN AND TRIC CCT IN ACTIN AND TUBULIN FOLDING%REACTOME%R-HSA-389958.22.29E-03−2.05024Miscellaneous
UBIQUITIN PROTEASOME PATHWAY%PANTHER PATHWAY%P000602.29E-03−2.05039Protein processing
TRANSLATION FACTORS%WIKIPATHWAYS_20191210%WP307%MUS MUSCULUS2.29E-03−2.00047RNA translation + ribosomes
RIBOSOMAL SMALL SUBUNIT BIOGENESIS%GOBP%GO:00422742.29E-03−2.00063RNA translation + ribosomes
RNA SPLICING%GOBP%GO:00083802.29E-03−1.990198RNA processing + translation
HALLMARK_OXIDATIVE_PHOSPHORYLATION%MSIGDB_C2%HALLMARK_OXIDATIVE_PHOSPHORYLATION2.29E-03−1.970178Metabolism: Ox-Phos
RIBONUCLEOPROTEIN COMPLEX ASSEMBLY%GOBP%GO:00226182.29E-03−1.940187RNA processing + translation
PID_MYC_ACTIV_PATHWAY%MSIGDB_C2%PID_MYC_ACTIV_PATHWAY2.29E-03−1.93066DNA + cell cycle
PROGRAMMED CELL DEATH%REACTOME%R-HSA-5357801.22.29E-03−1.930139Miscellaneous
PROTEIN REFOLDING%GOBP%GO:00420262.29E-03−1.92023Protein processing
G2 M CHECKPOINTS%REACTOME%R-HSA-69481.32.29E-03−1.920122DNA + cell cycle
TOXIN TRANSPORT%GOBP%GO:19019982.29E-03−1.92034Miscellaneous
PROTEIN FOLDING%GOBP%GO:00064572.29E-03−1.910101Protein processing
HALLMARK_E2F_TARGETS%MSIGDB_C2%HALLMARK_E2F_TARGETS2.29E-03−1.910193DNA + cell cycle
MITOTIC ANAPHASE%REACTOME DATABASE ID RELEASE 71%688822.29E-03−1.900161DNA + cell cycle
PROTEIN LOCALIZATION TO MITOCHONDRION%GOBP%GO:00705852.29E-03−1.90067Protein processing
G1 S TRANSITION%REACTOME DATABASE ID RELEASE 71%692062.29E-03−1.890123DNA + cell cycle
TRANSCRIPTIONAL REGULATION BY RUNX1%REACTOME%R-HSA-8878171.32.29E-03−1.880156Transcriptional regulation
NEGATIVE REGULATION OF MRNA METABOLIC PROCESS%GOBP%GO:19033122.29E-03−1.88072RNA processing + translation
RNA POLYMERASE II TRANSCRIPTION TERMINATION%REACTOME%R-HSA-73856.42.29E-03−1.87055Transcriptional regulation
G2 M TRANSITION%REACTOME%R-HSA-69275.52.29E-03−1.860164DNA + cell cycle
NUCLEOSIDE TRIPHOSPHATE BIOSYNTHETIC PROCESS%GOBP%GO:00091422.29E-03−1.86062DNA + cell cycle
GENE AND PROTEIN EXPRESSION BY JAK-STAT SIGNALING AFTER INTERLEUKIN-12 STIMULATION%REACTOME%R-HSA-8950505.32.29E-03−1.84027Signaling
EUKARYOTIC TRANSCRIPTION INITIATION%WIKIPATHWAYS_20191210%WP567%MUS MUSCULUS2.29E-03−1.83041Transcriptional regulation
NADH DEHYDROGENASE COMPLEX ASSEMBLY%GOBP%GO:00102572.29E-03−1.82045Metabolism: Ox-Phos
RIBONUCLEOPROTEIN COMPLEX LOCALIZATION%GOBP%GO:00711662.29E-03−1.82054RNA processing + translation
RNA LOCALIZATION%GOBP%GO:00064032.29E-03−1.810104RNA processing + translation
PROTEIN TRANSMEMBRANE TRANSPORT%GOBP%GO:00718062.29E-03−1.81051Protein processing
TAT-MEDIATED ELONGATION OF THE HIV-1 TRANSCRIPT%REACTOME DATABASE ID RELEASE 71%1672462.29E-03−1.80040IR
HALLMARK_MTORC1_SIGNALING%MSIGDB_C2%HALLMARK_MTORC1_SIGNALING2.29E-03−1.800188Signaling
ELECTRON TRANSPORT CHAIN%WIKIPATHWAYS_20191210%WP295%MUS MUSCULUS2.29E-03−1.79094Metabolism: Ox-Phos
NUCLEOTIDE EXCISION REPAIR%REACTOME DATABASE ID RELEASE 71%56963982.29E-03−1.780101DNA + cell cycle
MITOCHONDRIAL RESPIRATORY CHAIN COMPLEX ASSEMBLY%GOBP%GO:00331082.29E-03−1.77075Metabolism: Ox-Phos
REGULATION OF MRNA SPLICING, VIA SPLICEOSOME%GOBP%GO:00480242.29E-03−1.76092RNA processing + translation
POSITIVE REGULATION OF VIRAL GENOME REPLICATION%GOBP%GO:00450702.29E-03−1.76030IR
TNF-ALPHA NF-KB SIGNALING PATHWAY%WIKIPATHWAYS_20191210%WP246%MUS MUSCULUS2.29E-03−1.750165Signaling
OXIDATIVE PHOSPHORYLATION%WIKIPATHWAYS_20191210%WP1248%MUS MUSCULUS2.29E-03−1.75057Metabolism: Ox-Phos
REGULATION OF UBIQUITIN-PROTEIN TRANSFERASE ACTIVITY%GOBP%GO:00514382.29E-03−1.73045Protein processing
MITOCHONDRIAL GENE EXPRESSION%GOBP%GO:01400532.29E-03−1.73075Transcriptional regulation
HALLMARK_DNA_REPAIR%MSIGDB_C2%HALLMARK_DNA_REPAIR2.29E-03−1.710143DNA + cell cycle
HALLMARK_UNFOLDED_PROTEIN_RESPONSE%MSIGDB_C2%HALLMARK_UNFOLDED_PROTEIN_RESPONSE2.29E-03−1.700108Protein processing
HIV LIFE CYCLE%REACTOME%R-HSA-162587.22.29E-03−1.690132IR
CELLULAR RESPONSE TO HEAT STRESS%REACTOME%R-HSA-3371556.12.29E-03−1.69079Miscellaneous
THE CITRIC ACID (TCA) CYCLE AND RESPIRATORY ELECTRON TRANSPORT%REACTOME%R-HSA-1428517.12.29E-03−1.680149Metabolism: Ox-Phos
ATP METABOLIC PROCESS%GOBP%GO:00460342.29E-03−1.670121Metabolism
NUCLEOSIDE TRIPHOSPHATE METABOLIC PROCESS%GOBP%GO:00091412.29E-03−1.670161DNA + cell cycle
HALLMARK_G2M_CHECKPOINT%MSIGDB_C2%HALLMARK_G2M_CHECKPOINT2.29E-03−1.660180DNA + cell cycle
PROTEIN-DNA COMPLEX SUBUNIT ORGANIZATION%GOBP%GO:00718242.29E-03−1.620127Transcriptional regulation
NUCLEOSIDE MONOPHOSPHATE METABOLIC PROCESS%GOBP%GO:00091232.29E-03−1.620150DNA + cell cycle
PROTEIN STABILIZATION%GOBP%GO:00508212.29E-03−1.590156Protein processing
CILIUM ASSEMBLY%REACTOME DATABASE ID RELEASE 71%56178332.29E-03−1.580169Miscellaneous
PROTEIN TARGETING%GOBP%GO:00066052.29E-03−1.580183Protein processing
METHYLATION%GOBP%GO:00322592.29E-03−1.510191Miscellaneous
HALLMARK_GLYCOLYSIS%MSIGDB_C2%HALLMARK_GLYCOLYSIS2.29E-03−1.490172Metabolism
PROTEASOMAL UBIQUITIN-INDEPENDENT PROTEIN CATABOLIC PROCESS%GOBP%GO:00104992.30E-03−2.27021Protein processing
ATP SYNTHESIS COUPLED PROTON TRANSPORT%GOBP%GO:00159862.30E-03−2.08016Metabolism: Ox-Phos
CELLULAR RESPONSE TO INTERLEUKIN-7%GOBP%GO:00987612.30E-03−2.07016Signaling
FORMATION OF TUBULIN FOLDING INTERMEDIATES BY CCT TRIC%REACTOME%R-HSA-389960.22.30E-03−2.03017Miscellaneous
CELLULAR RESPONSE TO INTERLEUKIN-4%GOBP%GO:00713532.30E-03−1.94018Signaling
SPERM-EGG RECOGNITION%GOBP%GO:00350362.30E-03−1.97015IR
ER TO GOLGI VESICLE-MEDIATED TRANSPORT%GOBP%GO:00068883.91E-03−1.61193Protein processing
HALLMARK_MYC_TARGETS_V2%MSIGDB_C2%HALLMARK_MYC_TARGETS_V23.95E-03−1.75156DNA + cell cycle
REGULATION OF SIGNAL TRANSDUCTION BY P53 CLASS MEDIATOR%GOBP%GO:19017963.95E-03−1.72158Signaling
CELLULAR RESPONSE TO HEAT%GOBP%GO:00346053.98E-03−1.69146Miscellaneous
CRISTAE FORMATION%REACTOME DATABASE ID RELEASE 71%89496134.17E-03−1.83124Miscellaneous
RIBOSOMAL SMALL SUBUNIT ASSEMBLY%GOBP%GO:00000284.18E-03−1.89118RNA processing + translation
PROTEIN PEPTIDYL-PROLYL ISOMERIZATION%GOBP%GO:00004134.18E-03−1.83118Protein processing
POSITIVE REGULATION OF TRANSCRIPTION INITIATION FROM RNA POLYMERASE II PROMOTER%GOBP%GO:00602614.18E-03−1.81120Transcriptional regulation
VIRAL GENE EXPRESSION%GOBP%GO:00190804.18E-03−1.81120IR
BBSOME-MEDIATED CARGO-TARGETING TO CILIUM%REACTOME DATABASE ID RELEASE 71%56209224.18E-03−1.79121Miscellaneous
MITOTIC PROMETAPHASE%REACTOME%R-HSA-68877.55.40E-03−1.482167DNA + cell cycle
POSITIVE REGULATION OF TRANSLATION%GOBP%GO:00457275.40E-03−1.622104RNA processing + translation
DNA REPLICATION%GOBP%GO:00062605.40E-03−1.572117DNA + cell cycle
RNA CATABOLIC PROCESS%GOBP%GO:00064015.40E-03−1.542112RNA processing + translation
MITOCHONDRIAL PROTEIN IMPORT%REACTOME DATABASE ID RELEASE 71%12680205.50E-03−1.69257Miscellaneous
DEADENYLATION-DEPENDENT MRNA DECAY%REACTOME DATABASE ID RELEASE 71%4299145.50E-03−1.69255RNA processing + translation
NEGATIVE REGULATION OF PROTEIN POLYMERIZATION%GOBP%GO:00322725.52E-03−1.67252Protein processing
RNA MODIFICATION%GOBP%GO:00094516.86E-03−1.553114RNA processing + translation
DNA RECOMBINATION%GOBP%GO:00063106.86E-03−1.533142DNA + cell cycle
REGULATION OF NUCLEAR DIVISION%GOBP%GO:00517836.86E-03−1.533144DNA + cell cycle
INTERSPECIES INTERACTION BETWEEN ORGANISMS%GOBP%GO:00444196.86E-03−1.463173IR
CHROMOSOME MAINTENANCE%REACTOME%R-HSA-73886.26.97E-03−1.65372DNA + cell cycle
SIG_REGULATION_OF_THE_ACTIN_CYTOSKELETON_BY_RHO_GTPASES%MSIGDB_C2%SIG_REGULATION_OF_THE_ACTIN_CYTOSKELETON_BY_RHO_GTPASES7.29E-03−1.73328Signaling
NEGATIVE REGULATION OF UBIQUITIN-PROTEIN TRANSFERASE ACTIVITY%GOBP%GO:00514447.60E-03−1.76316Protein processing
TRNA METABOLIC PROCESS%GOBP%GO:00063998.03E-03−1.514137RNA processing + translation
REGULATION OF TP53 ACTIVITY%REACTOME%R-HSA-5633007.39.43E-03−1.505138Miscellaneous
AUTOPHAGY%REACTOME%R-HSA-9612973.19.46E-03−1.525107Miscellaneous
NEGATIVE REGULATION OF PROTEOLYSIS INVOLVED IN CELLULAR PROTEIN CATABOLIC PROCESS%GOBP%GO:19030519.65E-03−1.62567Protein processing
  • Shown are gene sets that are negatively correlated with time (decreasing in the transition from embryonic RPs to adult NSCs) where FDR < 0.01, analyzed from the combined SGZ RP/NSC dataset (a total of 885 cells, highlighted in blue in Fig. 3C). Also shown are the adjusted p values (adj. p value; FDR), enrichment scores (Norm. Enr. score), the size of the gene set and the number of times a random gene set had a more extreme enrichment score than the gene set (nMoreExtreme). Gene sets are ordered from most to least significant from top to bottom. These gene sets were also categorized with regard to a number of broad categories, including DNA replication, DNA repair, chromosome stability and segregation and the cell cycle (DNA + cell cycle), transcription, epigenetics and chromatin regulation (transcriptional regulation), RNA homeostasis, translation and tRNA and ribosome biogenesis (RNA processing + translation), general protein processing and trafficking including ubiquitination and sumoylation (protein processing), signaling pathways (signaling), and metabolism, oxidative phosphorylation and mitochondrial activity (metabolism). Other categories are termed as miscellaneous (misc.) and irrelevant gene sets are termed as IR.