Overrepresentation analyses subset I

This functional characterisation has been carried out for the 179 significant genes of the “More repressed genes in Alzheimer’s disease females” subset (Subset I from the research article). They are genes downregulated in the SDID comparison (logFC < 0), meaning that are repressed in Alzheimer’s disease females compared to males; and downregulated in the IDF comparison (logFC < 0), meaning that are represesed in Alzheimer’s disease females compared to control females.

Significant results displayed.

Reactome
GO Biological Processes

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Term	Description	Gene ratio	Background ratio	p.value	adjusted p.value	q.value	Genes
				0.000000027520142 0.001377854906396	0.000014695756282 0.038724974737640	0.000012862045711 0.033892940633771
R-HSA-112316	Neuronal System	19/111	410/10891	2.752e-8	0.00001470	0.00001286	ARHGEF9, CACNG3, CAMK2A, DLG3, EPB41L3, GABRA1, GABRA5, GABRG2, GLRB, HOMER1, KCND2, KCNJ6, KCNV1, NBEA, PPM1E, PRKCB, SLITRK3, SLITRK4, SLITRK5
R-HSA-112314	Neurotransmitter receptors and postsynaptic signal transmission	12/111	205/10891	0.000001104	0.0002949	0.0002581	ARHGEF9, CACNG3, CAMK2A, DLG3, GABRA1, GABRA5, GABRG2, GLRB, KCNJ6, NBEA, PPM1E, PRKCB
R-HSA-917977	Transferrin endocytosis and recycling	5/111	31/10891	0.00001382	0.002459	0.002153	ATP6V1A, ATP6V1B2, ATP6V1C1, ATP6V1D, STEAP2
R-HSA-112315	Transmission across Chemical Synapses	12/111	270/10891	0.00001878	0.002507	0.002194	ARHGEF9, CACNG3, CAMK2A, DLG3, GABRA1, GABRA5, GABRG2, GLRB, KCNJ6, NBEA, PPM1E, PRKCB
R-HSA-77387	Insulin receptor recycling	4/111	26/10891	0.0001285	0.01373	0.01201	ATP6V1A, ATP6V1B2, ATP6V1C1, ATP6V1D
R-HSA-9639288	Amino acids regulate mTORC1	5/111	55/10891	0.0002329	0.01705	0.01492	ATP6V1A, ATP6V1B2, ATP6V1C1, ATP6V1D, SEH1L
R-HSA-6794362	Protein-protein interactions at synapses	6/111	86/10891	0.0002374	0.01705	0.01492	DLG3, EPB41L3, HOMER1, SLITRK3, SLITRK4, SLITRK5
R-HSA-5607763	CLEC7A (Dectin-1) induces NFAT activation	3/111	13/10891	0.0002736	0.01705	0.01492	ITPR1, PPP3CB, PPP3R1
R-HSA-917937	Iron uptake and transport	5/111	58/10891	0.0002995	0.01705	0.01492	ATP6V1A, ATP6V1B2, ATP6V1C1, ATP6V1D, STEAP2
R-HSA-111885	Opioid Signalling	6/111	92/10891	0.0003426	0.01705	0.01492	CAMK2A, ITPR1, NBEA, PPP2R5D, PPP3CB, PPP3R1

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Term	Description	Gene ratio	Background ratio	p.value	adjusted p.value	q.value	Genes
				0.000001364156379 0.000666927313524	0.002015102192002 0.047634778120469	0.001852077936333 0.043781065749023
GO:0050808	synapse organization	16/170	419/18800	0.000001364	0.002015	0.001852	CBLN2, FRMPD4, GABRA1, GABRG2, GLRB, HOMER1, INA, LGMN, MEF2C, NRCAM, PRNP, RAB39B, SLITRK3, SLITRK4, SLITRK5, VPS35
GO:0061564	axon development	17/170	479/18800	0.000001710	0.002015	0.001852	B4GALT6, EFNB3, FKBP1B, HSP90AB1, MAP2, MAP2K1, NCAM2, NRCAM, PLXNA2, PPP3CB, SEMA4F, SLITRK3, SLITRK4, SLITRK5, TBR1, THY1, VSTM2L
GO:0007409	axonogenesis	15/170	430/18800	0.000008808	0.006046	0.005557	B4GALT6, EFNB3, HSP90AB1, MAP2, MAP2K1, NRCAM, PLXNA2, PPP3CB, SEMA4F, SLITRK3, SLITRK4, SLITRK5, TBR1, THY1, VSTM2L
GO:0099174	regulation of presynapse organization	5/170	34/18800	0.00001283	0.006046	0.005557	CBLN2, SLITRK3, SLITRK4, SLITRK5, VPS35
GO:1905606	regulation of presynapse assembly	5/170	34/18800	0.00001283	0.006046	0.005557	CBLN2, SLITRK3, SLITRK4, SLITRK5, VPS35
GO:0050807	regulation of synapse organization	10/170	209/18800	0.00002106	0.008272	0.007603	CBLN2, FRMPD4, HOMER1, MEF2C, NRCAM, PRNP, SLITRK3, SLITRK4, SLITRK5, VPS35
GO:0050803	regulation of synapse structure or activity	10/170	215/18800	0.00002684	0.009039	0.008308	CBLN2, FRMPD4, HOMER1, MEF2C, NRCAM, PRNP, SLITRK3, SLITRK4, SLITRK5, VPS35
GO:0007416	synapse assembly	9/170	180/18800	0.00003893	0.01147	0.01054	CBLN2, GABRA1, GABRG2, MEF2C, NRCAM, SLITRK3, SLITRK4, SLITRK5, VPS35
GO:0099003	vesicle-mediated transport in synapse	9/170	197/18800	0.00007834	0.01862	0.01711	AMPH, CADPS, CALY, PACSIN1, PPP3CB, PRKCB, RIMS3, SH3GL2, VPS35
GO:0031503	protein-containing complex localization	8/170	155/18800	0.00008446	0.01862	0.01711	CACNG3, CALY, DLG3, LRRC7, SEH1L, SSX2IP, TERF2, VPS35

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Total evaluated genes: AACS, AASDHPPT, ACAD8, ADAM23, AMPH, ANO3, ARHGEF9, ARL8B, ATP6AP2, ATP6V1A, ATP6V1B2, ATP6V1C1, ATP6V1D, B4GALT6, BBS7, BEND6, BNIP3, BTBD10, BTRC, C11orf87, CAB39, CACNG3, CADPS, CALB1, CALY, CAMK1G, CAMK2A, CBLN2, CCDC3, CCDC6, CDC37L1, CDH12, CELSR2, COPS8, CPNE4, DCAF6, DLG3, DNAJA2, DNAJA4, EBP, EFNB3, EIF2S3, EIF4E3, ELMOD1, EPB41L3, EPDR1, FABP3, FAXC, FBXL16, FBXO28, FBXO33, FBXO34, FKBP1B, FRMPD4, GABRA1, GABRA5, GABRG2, GHITM, GLRB, GOT1, GPR137C, GPR22, GPRASP2, HLF, HOMER1, HSP90AB1, HTR1E, INA, INSIG2, ITPR1, JAZF1, KCND2, KCNJ6, KCNV1, KIF3C, KIFAP3, KLHL2, KLK7, KRT222, LAMP5, LGMN, LMBR1, LNX1, LOC441488, LRRC2, LRRC7, LRRC8B, LZTFL1, MADD, MAL2, MAP2, MAP2K1, MAP2K4, MAST3, MEF2C, MGST3, MMD, MPP1, MRAP2, MYH10, MYO5A, NBEA, NCAM2, NCDN, NCKAP1, NECAB1, NECAP1, NEDD4L, NETO2, NIPSNAP3B, NKRF, NLK, NRCAM, PACSIN1, PCMT1, PCSK2, PHF14, PIP4K2C, PLXNA2, PNMA1, PNMA2, PPM1E, PPP2R5D, PPP3CB, PPP3R1, PRICKLE2, PRKCB, PRNP, PRPS2, PRSS3, PTPRT, RAB39B, REEP1, REEP5, RGS4, RIC3, RIMS3, RSPO2, SCN4B, SEC23A, SEH1L, SELT, SEMA4F, SH3BGRL2, SH3GL2, SLBP, SLC30A3, SLITRK3, SLITRK4, SLITRK5, SNX10, SPATA2, SSX2IP, ST6GALNAC5, STAMBPL1, STEAP2, STK26, STMN3, SUSD4, TBC1D9, TBPL1, TBR1, TCERG1L, TERF2, TESPA1, THY1, TOLLIP, TOMM34, TUSC3, UBE2E2, UBE2T, UBE2W, UQCRC2, VPS35, VSNL1, VSTM2L, VTA1, ZNF189, ZNF385B.