Pathway names | Adj. p value (FDR) | Norm. Enr. Score | nMore- Extreme | Size | Category |
---|---|---|---|---|---|
CYTOPLASMIC RIBOSOMAL PROTEINS%WIKIPATHWAYS_20191210%WP163%MUS MUSCULUS | 2.29E-03 | −2.73 | 0 | 80 | RNA translation + ribosomes |
FORMATION OF A POOL OF FREE 40S SUBUNITS%REACTOME DATABASE ID RELEASE 71%72689 | 2.29E-03 | −2.59 | 0 | 51 | RNA translation + ribosomes |
VIRAL MRNA TRANSLATION%REACTOME DATABASE ID RELEASE 71%192823 | 2.29E-03 | −2.57 | 0 | 39 | IR |
L13A-MEDIATED TRANSLATIONAL SILENCING OF CERULOPLASMIN EXPRESSION%REACTOME DATABASE ID RELEASE 71%156827 | 2.29E-03 | −2.57 | 0 | 61 | Miscellaneous |
EUKARYOTIC TRANSLATION ELONGATION%REACTOME%R-HSA-156842.2 | 2.29E-03 | −2.57 | 0 | 42 | RNA translation + ribosomes |
NONSENSE MEDIATED DECAY (NMD) INDEPENDENT OF THE EXON JUNCTION COMPLEX (EJC)%REACTOME%R-HSA-975956.1 | 2.29E-03 | −2.56 | 0 | 45 | DNA + cell cycle |
SELENOCYSTEINE SYNTHESIS%REACTOME DATABASE ID RELEASE 71%2408557 | 2.29E-03 | −2.55 | 0 | 43 | Miscellaneous |
REGULATION OF EXPRESSION OF SLITS AND ROBOS%REACTOME DATABASE ID RELEASE 71%9010553 | 2.29E-03 | −2.54 | 0 | 111 | Signaling |
EUKARYOTIC TRANSLATION TERMINATION%REACTOME%R-HSA-72764.4 | 2.29E-03 | −2.53 | 0 | 43 | RNA translation + ribosomes |
RESPONSE OF EIF2AK4 (GCN2) TO AMINO ACID DEFICIENCY%REACTOME DATABASE ID RELEASE 71%9633012 | 2.29E-03 | −2.51 | 0 | 50 | RNA translation + ribosomes |
SRP-DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE%REACTOME%R-HSA-1799339.2 | 2.29E-03 | −2.48 | 0 | 61 | Protein processing |
ACTIVATION OF THE MRNA UPON BINDING OF THE CAP-BINDING COMPLEX AND EIFS, AND SUBSEQUENT BINDING TO 43S%REACTOME%R-HSA-72662.3 | 2.29E-03 | −2.42 | 0 | 43 | RNA translation + ribosomes |
HALLMARK_MYC_TARGETS_V1%MSIGDB_C2%HALLMARK_MYC_TARGETS_V1 | 2.29E-03 | −2.40 | 0 | 184 | DNA + cell cycle |
SELENOAMINO ACID METABOLISM%REACTOME DATABASE ID RELEASE 71%2408522 | 2.29E-03 | −2.39 | 0 | 62 | Metabolism |
AUF1 (HNRNP D0) BINDS AND DESTABILIZES MRNA%REACTOME DATABASE ID RELEASE 71%450408 | 2.29E-03 | −2.39 | 0 | 49 | RNA translation + ribosomes |
REGULATION OF ORNITHINE DECARBOXYLASE (ODC)%REACTOME%R-HSA-350562.2 | 2.29E-03 | −2.37 | 0 | 48 | Miscellaneous |
PROTEASOME DEGRADATION%WIKIPATHWAYS_20191210%WP519%MUS MUSCULUS | 2.29E-03 | −2.35 | 0 | 50 | Protein processing |
THE ROLE OF GTSE1 IN G2 M PROGRESSION AFTER G2 CHECKPOINT%REACTOME DATABASE ID RELEASE 71%8852276 | 2.29E-03 | −2.35 | 0 | 53 | DNA + cell cycle |
APC C:CDC20 MEDIATED DEGRADATION OF SECURIN%REACTOME%R-HSA-174154.2 | 2.29E-03 | −2.34 | 0 | 61 | IR |
CYTOPLASMIC TRANSLATION%GOBP%GO:0002181 | 2.29E-03 | −2.33 | 0 | 61 | RNA translation + ribosomes |
ER-PHAGOSOME PATHWAY%REACTOME DATABASE ID RELEASE 71%1236974 | 2.29E-03 | −2.31 | 0 | 69 | Protein processing |
SCF(SKP2)-MEDIATED DEGRADATION OF P27 P21%REACTOME%R-HSA-187577.3 | 2.29E-03 | −2.29 | 0 | 56 | DNA + cell cycle |
INFLUENZA VIRAL RNA TRANSCRIPTION AND REPLICATION%REACTOME DATABASE ID RELEASE 71%168273 | 2.29E-03 | −2.27 | 0 | 80 | IR |
INFLUENZA INFECTION%REACTOME%R-HSA-168254.2 | 2.29E-03 | −2.22 | 0 | 96 | IR |
ASSEMBLY OF THE PRE-REPLICATIVE COMPLEX%REACTOME%R-HSA-68867.4 | 2.29E-03 | −2.20 | 0 | 63 | DNA + cell cycle |
REGULATION OF MITOTIC CELL CYCLE%REACTOME%R-HSA-453276.2 | 2.29E-03 | −2.20 | 0 | 78 | DNA + cell cycle |
REGULATION OF MRNA STABILITY BY PROTEINS THAT BIND AU-RICH ELEMENTS%REACTOME%R-HSA-450531.4 | 2.29E-03 | −2.19 | 0 | 77 | RNA translation + ribosomes |
MAJOR PATHWAY OF RRNA PROCESSING IN THE NUCLEOLUS AND CYTOSOL%REACTOME%R-HSA-6791226.3 | 2.29E-03 | −2.19 | 0 | 124 | RNA translation + ribosomes |
SWITCHING OF ORIGINS TO A POST-REPLICATIVE STATE%REACTOME DATABASE ID RELEASE 71%69052 | 2.29E-03 | −2.15 | 0 | 84 | DNA + cell cycle |
RUNX1 REGULATES TRANSCRIPTION OF GENES INVOLVED IN DIFFERENTIATION OF HSCS%REACTOME%R-HSA-8939236.1 | 2.29E-03 | −2.14 | 0 | 72 | IR |
MITOCHONDRIAL TRANSLATION ELONGATION%REACTOME%R-HSA-5389840.1 | 2.29E-03 | −2.13 | 0 | 83 | RNA translation + ribosomes |
HOST INTERACTIONS OF HIV FACTORS%REACTOME%R-HSA-162909.1 | 2.29E-03 | −2.13 | 0 | 110 | IR |
RIBOSOMAL LARGE SUBUNIT BIOGENESIS%GOBP%GO:0042273 | 2.29E-03 | −2.12 | 0 | 66 | RNA translation + ribosomes |
NEGATIVE REGULATION OF RNA SPLICING%GOBP%GO:0033119 | 2.29E-03 | −2.10 | 0 | 28 | RNA translation + ribosomes |
MRNA SPLICING%REACTOME%R-HSA-72172.3 | 2.29E-03 | −2.09 | 0 | 176 | RNA translation + ribosomes |
RIBOSOME ASSEMBLY%GOBP%GO:0042255 | 2.29E-03 | −2.09 | 0 | 57 | RNA translation + ribosomes |
RRNA PROCESSING%GOBP%GO:0006364 | 2.29E-03 | −2.09 | 0 | 148 | RNA translation + ribosomes |
SYNTHESIS OF DNA%REACTOME DATABASE ID RELEASE 71%69239 | 2.29E-03 | −2.07 | 0 | 113 | DNA + cell cycle |
COOPERATION OF PREFOLDIN AND TRIC CCT IN ACTIN AND TUBULIN FOLDING%REACTOME%R-HSA-389958.2 | 2.29E-03 | −2.05 | 0 | 24 | Miscellaneous |
UBIQUITIN PROTEASOME PATHWAY%PANTHER PATHWAY%P00060 | 2.29E-03 | −2.05 | 0 | 39 | Protein processing |
TRANSLATION FACTORS%WIKIPATHWAYS_20191210%WP307%MUS MUSCULUS | 2.29E-03 | −2.00 | 0 | 47 | RNA translation + ribosomes |
RIBOSOMAL SMALL SUBUNIT BIOGENESIS%GOBP%GO:0042274 | 2.29E-03 | −2.00 | 0 | 63 | RNA translation + ribosomes |
RNA SPLICING%GOBP%GO:0008380 | 2.29E-03 | −1.99 | 0 | 198 | RNA processing + translation |
HALLMARK_OXIDATIVE_PHOSPHORYLATION%MSIGDB_C2%HALLMARK_OXIDATIVE_PHOSPHORYLATION | 2.29E-03 | −1.97 | 0 | 178 | Metabolism: Ox-Phos |
RIBONUCLEOPROTEIN COMPLEX ASSEMBLY%GOBP%GO:0022618 | 2.29E-03 | −1.94 | 0 | 187 | RNA processing + translation |
PID_MYC_ACTIV_PATHWAY%MSIGDB_C2%PID_MYC_ACTIV_PATHWAY | 2.29E-03 | −1.93 | 0 | 66 | DNA + cell cycle |
PROGRAMMED CELL DEATH%REACTOME%R-HSA-5357801.2 | 2.29E-03 | −1.93 | 0 | 139 | Miscellaneous |
PROTEIN REFOLDING%GOBP%GO:0042026 | 2.29E-03 | −1.92 | 0 | 23 | Protein processing |
G2 M CHECKPOINTS%REACTOME%R-HSA-69481.3 | 2.29E-03 | −1.92 | 0 | 122 | DNA + cell cycle |
TOXIN TRANSPORT%GOBP%GO:1901998 | 2.29E-03 | −1.92 | 0 | 34 | Miscellaneous |
PROTEIN FOLDING%GOBP%GO:0006457 | 2.29E-03 | −1.91 | 0 | 101 | Protein processing |
HALLMARK_E2F_TARGETS%MSIGDB_C2%HALLMARK_E2F_TARGETS | 2.29E-03 | −1.91 | 0 | 193 | DNA + cell cycle |
MITOTIC ANAPHASE%REACTOME DATABASE ID RELEASE 71%68882 | 2.29E-03 | −1.90 | 0 | 161 | DNA + cell cycle |
PROTEIN LOCALIZATION TO MITOCHONDRION%GOBP%GO:0070585 | 2.29E-03 | −1.90 | 0 | 67 | Protein processing |
G1 S TRANSITION%REACTOME DATABASE ID RELEASE 71%69206 | 2.29E-03 | −1.89 | 0 | 123 | DNA + cell cycle |
TRANSCRIPTIONAL REGULATION BY RUNX1%REACTOME%R-HSA-8878171.3 | 2.29E-03 | −1.88 | 0 | 156 | Transcriptional regulation |
NEGATIVE REGULATION OF MRNA METABOLIC PROCESS%GOBP%GO:1903312 | 2.29E-03 | −1.88 | 0 | 72 | RNA processing + translation |
RNA POLYMERASE II TRANSCRIPTION TERMINATION%REACTOME%R-HSA-73856.4 | 2.29E-03 | −1.87 | 0 | 55 | Transcriptional regulation |
G2 M TRANSITION%REACTOME%R-HSA-69275.5 | 2.29E-03 | −1.86 | 0 | 164 | DNA + cell cycle |
NUCLEOSIDE TRIPHOSPHATE BIOSYNTHETIC PROCESS%GOBP%GO:0009142 | 2.29E-03 | −1.86 | 0 | 62 | DNA + cell cycle |
GENE AND PROTEIN EXPRESSION BY JAK-STAT SIGNALING AFTER INTERLEUKIN-12 STIMULATION%REACTOME%R-HSA-8950505.3 | 2.29E-03 | −1.84 | 0 | 27 | Signaling |
EUKARYOTIC TRANSCRIPTION INITIATION%WIKIPATHWAYS_20191210%WP567%MUS MUSCULUS | 2.29E-03 | −1.83 | 0 | 41 | Transcriptional regulation |
NADH DEHYDROGENASE COMPLEX ASSEMBLY%GOBP%GO:0010257 | 2.29E-03 | −1.82 | 0 | 45 | Metabolism: Ox-Phos |
RIBONUCLEOPROTEIN COMPLEX LOCALIZATION%GOBP%GO:0071166 | 2.29E-03 | −1.82 | 0 | 54 | RNA processing + translation |
RNA LOCALIZATION%GOBP%GO:0006403 | 2.29E-03 | −1.81 | 0 | 104 | RNA processing + translation |
PROTEIN TRANSMEMBRANE TRANSPORT%GOBP%GO:0071806 | 2.29E-03 | −1.81 | 0 | 51 | Protein processing |
TAT-MEDIATED ELONGATION OF THE HIV-1 TRANSCRIPT%REACTOME DATABASE ID RELEASE 71%167246 | 2.29E-03 | −1.80 | 0 | 40 | IR |
HALLMARK_MTORC1_SIGNALING%MSIGDB_C2%HALLMARK_MTORC1_SIGNALING | 2.29E-03 | −1.80 | 0 | 188 | Signaling |
ELECTRON TRANSPORT CHAIN%WIKIPATHWAYS_20191210%WP295%MUS MUSCULUS | 2.29E-03 | −1.79 | 0 | 94 | Metabolism: Ox-Phos |
NUCLEOTIDE EXCISION REPAIR%REACTOME DATABASE ID RELEASE 71%5696398 | 2.29E-03 | −1.78 | 0 | 101 | DNA + cell cycle |
MITOCHONDRIAL RESPIRATORY CHAIN COMPLEX ASSEMBLY%GOBP%GO:0033108 | 2.29E-03 | −1.77 | 0 | 75 | Metabolism: Ox-Phos |
REGULATION OF MRNA SPLICING, VIA SPLICEOSOME%GOBP%GO:0048024 | 2.29E-03 | −1.76 | 0 | 92 | RNA processing + translation |
POSITIVE REGULATION OF VIRAL GENOME REPLICATION%GOBP%GO:0045070 | 2.29E-03 | −1.76 | 0 | 30 | IR |
TNF-ALPHA NF-KB SIGNALING PATHWAY%WIKIPATHWAYS_20191210%WP246%MUS MUSCULUS | 2.29E-03 | −1.75 | 0 | 165 | Signaling |
OXIDATIVE PHOSPHORYLATION%WIKIPATHWAYS_20191210%WP1248%MUS MUSCULUS | 2.29E-03 | −1.75 | 0 | 57 | Metabolism: Ox-Phos |
REGULATION OF UBIQUITIN-PROTEIN TRANSFERASE ACTIVITY%GOBP%GO:0051438 | 2.29E-03 | −1.73 | 0 | 45 | Protein processing |
MITOCHONDRIAL GENE EXPRESSION%GOBP%GO:0140053 | 2.29E-03 | −1.73 | 0 | 75 | Transcriptional regulation |
HALLMARK_DNA_REPAIR%MSIGDB_C2%HALLMARK_DNA_REPAIR | 2.29E-03 | −1.71 | 0 | 143 | DNA + cell cycle |
HALLMARK_UNFOLDED_PROTEIN_RESPONSE%MSIGDB_C2%HALLMARK_UNFOLDED_PROTEIN_RESPONSE | 2.29E-03 | −1.70 | 0 | 108 | Protein processing |
HIV LIFE CYCLE%REACTOME%R-HSA-162587.2 | 2.29E-03 | −1.69 | 0 | 132 | IR |
CELLULAR RESPONSE TO HEAT STRESS%REACTOME%R-HSA-3371556.1 | 2.29E-03 | −1.69 | 0 | 79 | Miscellaneous |
THE CITRIC ACID (TCA) CYCLE AND RESPIRATORY ELECTRON TRANSPORT%REACTOME%R-HSA-1428517.1 | 2.29E-03 | −1.68 | 0 | 149 | Metabolism: Ox-Phos |
ATP METABOLIC PROCESS%GOBP%GO:0046034 | 2.29E-03 | −1.67 | 0 | 121 | Metabolism |
NUCLEOSIDE TRIPHOSPHATE METABOLIC PROCESS%GOBP%GO:0009141 | 2.29E-03 | −1.67 | 0 | 161 | DNA + cell cycle |
HALLMARK_G2M_CHECKPOINT%MSIGDB_C2%HALLMARK_G2M_CHECKPOINT | 2.29E-03 | −1.66 | 0 | 180 | DNA + cell cycle |
PROTEIN-DNA COMPLEX SUBUNIT ORGANIZATION%GOBP%GO:0071824 | 2.29E-03 | −1.62 | 0 | 127 | Transcriptional regulation |
NUCLEOSIDE MONOPHOSPHATE METABOLIC PROCESS%GOBP%GO:0009123 | 2.29E-03 | −1.62 | 0 | 150 | DNA + cell cycle |
PROTEIN STABILIZATION%GOBP%GO:0050821 | 2.29E-03 | −1.59 | 0 | 156 | Protein processing |
CILIUM ASSEMBLY%REACTOME DATABASE ID RELEASE 71%5617833 | 2.29E-03 | −1.58 | 0 | 169 | Miscellaneous |
PROTEIN TARGETING%GOBP%GO:0006605 | 2.29E-03 | −1.58 | 0 | 183 | Protein processing |
METHYLATION%GOBP%GO:0032259 | 2.29E-03 | −1.51 | 0 | 191 | Miscellaneous |
HALLMARK_GLYCOLYSIS%MSIGDB_C2%HALLMARK_GLYCOLYSIS | 2.29E-03 | −1.49 | 0 | 172 | Metabolism |
PROTEASOMAL UBIQUITIN-INDEPENDENT PROTEIN CATABOLIC PROCESS%GOBP%GO:0010499 | 2.30E-03 | −2.27 | 0 | 21 | Protein processing |
ATP SYNTHESIS COUPLED PROTON TRANSPORT%GOBP%GO:0015986 | 2.30E-03 | −2.08 | 0 | 16 | Metabolism: Ox-Phos |
CELLULAR RESPONSE TO INTERLEUKIN-7%GOBP%GO:0098761 | 2.30E-03 | −2.07 | 0 | 16 | Signaling |
FORMATION OF TUBULIN FOLDING INTERMEDIATES BY CCT TRIC%REACTOME%R-HSA-389960.2 | 2.30E-03 | −2.03 | 0 | 17 | Miscellaneous |
CELLULAR RESPONSE TO INTERLEUKIN-4%GOBP%GO:0071353 | 2.30E-03 | −1.94 | 0 | 18 | Signaling |
SPERM-EGG RECOGNITION%GOBP%GO:0035036 | 2.30E-03 | −1.97 | 0 | 15 | IR |
ER TO GOLGI VESICLE-MEDIATED TRANSPORT%GOBP%GO:0006888 | 3.91E-03 | −1.61 | 1 | 93 | Protein processing |
HALLMARK_MYC_TARGETS_V2%MSIGDB_C2%HALLMARK_MYC_TARGETS_V2 | 3.95E-03 | −1.75 | 1 | 56 | DNA + cell cycle |
REGULATION OF SIGNAL TRANSDUCTION BY P53 CLASS MEDIATOR%GOBP%GO:1901796 | 3.95E-03 | −1.72 | 1 | 58 | Signaling |
CELLULAR RESPONSE TO HEAT%GOBP%GO:0034605 | 3.98E-03 | −1.69 | 1 | 46 | Miscellaneous |
CRISTAE FORMATION%REACTOME DATABASE ID RELEASE 71%8949613 | 4.17E-03 | −1.83 | 1 | 24 | Miscellaneous |
RIBOSOMAL SMALL SUBUNIT ASSEMBLY%GOBP%GO:0000028 | 4.18E-03 | −1.89 | 1 | 18 | RNA processing + translation |
PROTEIN PEPTIDYL-PROLYL ISOMERIZATION%GOBP%GO:0000413 | 4.18E-03 | −1.83 | 1 | 18 | Protein processing |
POSITIVE REGULATION OF TRANSCRIPTION INITIATION FROM RNA POLYMERASE II PROMOTER%GOBP%GO:0060261 | 4.18E-03 | −1.81 | 1 | 20 | Transcriptional regulation |
VIRAL GENE EXPRESSION%GOBP%GO:0019080 | 4.18E-03 | −1.81 | 1 | 20 | IR |
BBSOME-MEDIATED CARGO-TARGETING TO CILIUM%REACTOME DATABASE ID RELEASE 71%5620922 | 4.18E-03 | −1.79 | 1 | 21 | Miscellaneous |
MITOTIC PROMETAPHASE%REACTOME%R-HSA-68877.5 | 5.40E-03 | −1.48 | 2 | 167 | DNA + cell cycle |
POSITIVE REGULATION OF TRANSLATION%GOBP%GO:0045727 | 5.40E-03 | −1.62 | 2 | 104 | RNA processing + translation |
DNA REPLICATION%GOBP%GO:0006260 | 5.40E-03 | −1.57 | 2 | 117 | DNA + cell cycle |
RNA CATABOLIC PROCESS%GOBP%GO:0006401 | 5.40E-03 | −1.54 | 2 | 112 | RNA processing + translation |
MITOCHONDRIAL PROTEIN IMPORT%REACTOME DATABASE ID RELEASE 71%1268020 | 5.50E-03 | −1.69 | 2 | 57 | Miscellaneous |
DEADENYLATION-DEPENDENT MRNA DECAY%REACTOME DATABASE ID RELEASE 71%429914 | 5.50E-03 | −1.69 | 2 | 55 | RNA processing + translation |
NEGATIVE REGULATION OF PROTEIN POLYMERIZATION%GOBP%GO:0032272 | 5.52E-03 | −1.67 | 2 | 52 | Protein processing |
RNA MODIFICATION%GOBP%GO:0009451 | 6.86E-03 | −1.55 | 3 | 114 | RNA processing + translation |
DNA RECOMBINATION%GOBP%GO:0006310 | 6.86E-03 | −1.53 | 3 | 142 | DNA + cell cycle |
REGULATION OF NUCLEAR DIVISION%GOBP%GO:0051783 | 6.86E-03 | −1.53 | 3 | 144 | DNA + cell cycle |
INTERSPECIES INTERACTION BETWEEN ORGANISMS%GOBP%GO:0044419 | 6.86E-03 | −1.46 | 3 | 173 | IR |
CHROMOSOME MAINTENANCE%REACTOME%R-HSA-73886.2 | 6.97E-03 | −1.65 | 3 | 72 | DNA + cell cycle |
SIG_REGULATION_OF_THE_ACTIN_CYTOSKELETON_BY_RHO_GTPASES%MSIGDB_C2%SIG_REGULATION_OF_THE_ACTIN_CYTOSKELETON_BY_RHO_GTPASES | 7.29E-03 | −1.73 | 3 | 28 | Signaling |
NEGATIVE REGULATION OF UBIQUITIN-PROTEIN TRANSFERASE ACTIVITY%GOBP%GO:0051444 | 7.60E-03 | −1.76 | 3 | 16 | Protein processing |
TRNA METABOLIC PROCESS%GOBP%GO:0006399 | 8.03E-03 | −1.51 | 4 | 137 | RNA processing + translation |
REGULATION OF TP53 ACTIVITY%REACTOME%R-HSA-5633007.3 | 9.43E-03 | −1.50 | 5 | 138 | Miscellaneous |
AUTOPHAGY%REACTOME%R-HSA-9612973.1 | 9.46E-03 | −1.52 | 5 | 107 | Miscellaneous |
NEGATIVE REGULATION OF PROTEOLYSIS INVOLVED IN CELLULAR PROTEIN CATABOLIC PROCESS%GOBP%GO:1903051 | 9.65E-03 | −1.62 | 5 | 67 | Protein 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.