Gene Page:ABCA1

Summary?
GeneID 19
Symbol ABCA1
Synonyms ABC-1|ABC1|CERP|HDLDT1|TGD
Description ATP binding cassette subfamily A member 1
Reference MIM:600046|HGNC:HGNC:29|Ensembl:ENSG00000165029|HPRD:02501|Vega:OTTHUMG00000020417
Gene type protein-coding
Map location 9q31.1
Pascal p-value 0.243
Sherlock p-value 0.383
DEG p-value DEG:Maycox_2009:CC_BA10_fold_change=1.14:CC_BA10_disease_P=0.0337:HBB_BA9_fold_change=1.28:HBB_BA9_disease_P=0.0220
Fetal beta 1.893
DMG 1 (# studies)

Gene in Data Sources
Gene set name Method of gene set Description Info
CV:GWASdb Genome-wide Association Studies GWASdb records for schizophrenia
CV:PGCnp Genome-wide Association Study GWAS
DEG:Maycox_2009 Microarray to determine the expression of over 30000 mRNA transcripts in post-mortem tissue We included 51 genes whose expression changes are common between two schizophrenia cohorts.
DMG:vanEijk_2014 Genome-wide DNA methylation analysis This dataset includes 432 differentially methylated CpG sites corresponding to 391 unique transcripts between schizophrenia patients (n=260) and unaffected controls (n=250). 1
PMID:cooccur High-throughput literature-search Systematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
Literature High-throughput literature-search Co-occurance with Schizophrenia keywords: schizophrenia,schizophrenias Click to show details
GO_Annotation Mapping neuro-related keywords to Gene Ontology annotations Hits with neuro-related keywords: 1
Network Shortest path distance of core genes in the Human protein-protein interaction network Contribution to shortest path in PPI network: 0.0323

部分即遗传学和表观遗传学注释

@Differentially methylated gene

Probe Chromosome Position Nearest gene P (dis) Beta (dis) FDR (dis) Study
cg13160888 9 107526516 ABCA1 0.016 -7.686 DMG:vanEijk_2014


Section II. Transcriptome annotation

General gene expression (GTEx)

Not available

Gene expression during devlopment (BrainCloud)

Footnote:
A total of 269 time points ploted, with n=38 fetal samples (x=1:38). Each triangle represents one time point.

Gene expression of temporal and spatial changes (BrainSpan)

Footnote:
SC: sub-cortical regions; SM: sensory-motor regions; FC: frontal cortex; and TP: temporal-parietal cortex
ST1: fetal (13 - 26 postconception weeks), ST2: early infancy to late childhood (4 months to 11 years), and ST3: adolescence to adulthood (13 - 23 years)
The bar shown representes the lower 25% and upper 25% of the expression distribution.

Top co-expressed genes in brain regions

Top 10 positively co-expressed genes
Gene Pearson's Correlation Spearman's Correlation
DHX15 0.94 0.91
SF3B1 0.93 0.92
ZNF22 0.93 0.90
ELP2 0.93 0.91
CDKAL1 0.93 0.89
METAP2 0.92 0.92
C2orf67 0.92 0.91
DHX9 0.92 0.88
DDX5 0.92 0.91
UHRF2 0.92 0.89
Top 10 negatively co-expressed genes
Gene Pearson's Correlation Spearman's Correlation
AF347015.27 -0.70 -0.81
MT-CO2 -0.69 -0.82
AF347015.31 -0.69 -0.82
IFI27 -0.67 -0.82
AF347015.33 -0.67 -0.78
HLA-F -0.67 -0.72
AF347015.8 -0.67 -0.81
MT-CYB -0.67 -0.80
AIFM3 -0.66 -0.72
PTH1R -0.66 -0.73

Section III. Gene Ontology annotation

Molecular function GO term Evidence Neuro keywords PubMed ID
GO:0000166 nucleotide binding IEA -
GO:0005543 phospholipid binding IC 16702602
GO:0005548 phospholipid transporter activity IDA 16702602
GO:0005515 protein binding 新闻学会 16192269
GO:0005524 ATP binding IEA -
GO:0008509 anion transmembrane transporter activity IEA -
GO:0017127 cholesterol transporter activity IDA 12084722
去:0016887 ATPase activity IEA -
GO:0015485 cholesterol binding IC 12084722
GO:0031267 small GTPase binding 新闻学会 16443932
GO:0030349 syntaxin-13 binding 新闻学会 15469992
GO:0034188 apolipoprotein A-I receptor activity IDA 16443932
Biological process GO term Evidence Neuro keywords PubMed ID
GO:0060155 platelet dense granule organization IMP serotonin (GO term level: 7) 15163665
GO:0002790 peptide secretion IEA -
GO:0007186 G-protein coupled receptor protein signaling pathway IMP 16443932
GO:0006497 protein amino acid lipidation IEA -
GO:0008202 steroid metabolic process IEA -
GO:0008203 cholesterol metabolic process IEA -
GO:0006810 transport IEA -
GO:0007040 lysosome organization IDA 15163665
GO:0006629 lipid metabolic process IEA -
GO:0006911 phagocytosis, engulfment IEA -
GO:0016197 endosome transport IDA 14747463
GO:0033344 cholesterol efflux IEA -
GO:0032367 intracellular cholesterol transport IMP 10431236
GO:0030819 positive regulation of cAMP biosynthetic process IMP 14701824
GO:0032488 Cdc42 protein signal transduction IMP 16443932
去:0033700 phospholipid efflux IDA 10431236|11162594
去:0033700 phospholipid efflux IMP 16702602
GO:0042632 cholesterol homeostasis IDA 10431236
GO:0045332 phospholipid translocation IEA -
GO:0050702 interleukin-1 beta secretion IMP 11855831
GO:0043691 reverse cholesterol transport IEA -
GO:0055091 phospholipid homeostasis IMP 16702602
Cellular component GO term Evidence Neuro keywords PubMed ID
GO:0005794 Golgi apparatus IEA -
GO:0005624 membrane fraction IDA 10525055
GO:0005886 plasma membrane IEA -
GO:0005887 integral to plasma membrane IEA -
GO:0045335 phagocytic vesicle IDA 15469992
GO:0045121 膜筏 IDA 15469992

Section V. Pathway annotation

Pathway name Pathway size # SZGR 2.0 genes in pathway Info
KEGG ABC TRANSPORTERS 44 29 All SZGR 2.0 genes in this pathway
PID RXR VDR PATHWAY 26 24 All SZGR 2.0 genes in this pathway
REACTOME PPARA ACTIVATES GENE EXPRESSION 104 72 All SZGR 2.0 genes in this pathway
REACTOME HDL MEDIATED LIPID TRANSPORT 15 12 All SZGR 2.0 genes in this pathway
REACTOME METABOLISM OF LIPIDS AND LIPOPROTEINS 478 302 All SZGR 2.0 genes in this pathway
REACTOME FATTY ACID TRIACYLGLYCEROL AND KETONE BODY METABOLISM 168 115 All SZGR 2.0 genes in this pathway
REACTOME LIPID DIGESTION MOBILIZATION AND TRANSPORT 46 37 All SZGR 2.0 genes in this pathway
REACTOME LIPOPROTEIN METABOLISM 28 24 All SZGR 2.0 genes in this pathway
NAKAMURA TUMOR ZONE PERIPHERAL VS CENTRAL UP 285 181 All SZGR 2.0 genes in this pathway
ZHOU INFLAMMATORY RESPONSE LIVE UP 485 293 All SZGR 2.0 genes in this pathway
SAMOLS TARGETS OF KHSV MIRNAS DN 62 35 All SZGR 2.0 genes in this pathway
CASORELLI ACUTE PROMYELOCYTIC LEUKEMIA UP 177 110 All SZGR 2.0 genes in this pathway
HUTTMANN B CLL POOR SURVIVAL DN 60 39 All SZGR 2.0 genes in this pathway
HORIUCHI WTAP TARGETS UP 306 188 All SZGR 2.0 genes in this pathway
SMIRNOV CIRCULATING ENDOTHELIOCYTES IN CANCER UP 158 103 All SZGR 2.0 genes in this pathway
HOEBEKE LYMPHOID STEM CELL UP 95 64 All SZGR 2.0 genes in this pathway
RHEIN ALL GLUCOCORTICOID THERAPY UP 78 41 All SZGR 2.0 genes in this pathway
KINSEY TARGETS OF EWSR1 FLII FUSION DN 329 219 All SZGR 2.0 genes in this pathway
MARKEY RB1 ACUTE LOF UP 215 137 All SZGR 2.0 genes in this pathway
GAUSSMANN MLL AF4 FUSION TARGETS E UP 97 60 All SZGR 2.0 genes in this pathway
PEREZ TP53 TARGETS 1174 695 All SZGR 2.0 genes in this pathway
HERNANDEZ MITOTIC ARREST BY DOCETAXEL 2 UP 64 45 All SZGR 2.0 genes in this pathway
XU HGF TARGETS REPRESSED BY AKT1 DN 95 58 All SZGR 2.0 genes in this pathway
DAUER STAT3 TARGETS UP 49 35 All SZGR 2.0 genes in this pathway
NUYTTEN NIPP1 TARGETS DN 848 527 All SZGR 2.0 genes in this pathway
BUYTAERT PHOTODYNAMIC THERAPY STRESS UP 811 508 All SZGR 2.0 genes in this pathway
PASQUALUCCI LYMPHOMA BY GC STAGE UP 283 177 All SZGR 2.0 genes in this pathway
MORI MATURE B LYMPHOCYTE UP 90 62 All SZGR 2.0 genes in this pathway
BYSTRYKH HEMATOPOIESIS STEM CELL AND BRAIN QTL TRANS 185 114 All SZGR 2.0 genes in this pathway
MANALO HYPOXIA UP 207 145 All SZGR 2.0 genes in this pathway
YU MYC TARGETS DN 55 38 All SZGR 2.0 genes in this pathway
GERY CEBP TARGETS 126 90 All SZGR 2.0 genes in this pathway
AFFAR YY1 TARGETS UP 214 133 All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE INCIPIENT UP 390 242 All SZGR 2.0 genes in this pathway
RUAN RESPONSE TO TNF UP 12 10 All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE UP 1691 1088 All SZGR 2.0 genes in this pathway
BURTON ADIPOGENESIS 3 101 64 All SZGR 2.0 genes in this pathway
RUAN RESPONSE TO TNF TROGLITAZONE UP 17 11 All SZGR 2.0 genes in this pathway
MCLACHLAN DENTAL CARIES DN 245 144 All SZGR 2.0 genes in this pathway
SARTIPY NORMAL AT INSULIN RESISTANCE DN 21 11 All SZGR 2.0 genes in this pathway
WANG SMARCE1 TARGETS UP 280 183 All SZGR 2.0 genes in this pathway
HAN JNK SINGALING DN 39 27 All SZGR 2.0 genes in this pathway
MCLACHLAN DENTAL CARIES UP 253 147 All SZGR 2.0 genes in this pathway
BURTON ADIPOGENESIS 6 189 112 All SZGR 2.0 genes in this pathway
《图片报》极品致癌标记TURE 261 166 All SZGR 2.0 genes in this pathway
JEPSEN SMRT TARGETS 33 23 All SZGR 2.0 genes in this pathway
MASSARWEH TAMOXIFEN RESISTANCE UP 578 341 All SZGR 2.0 genes in this pathway
BOCHKIS FOXA2 TARGETS 425 261 All SZGR 2.0 genes in this pathway
MATZUK POST-IMPLANTATION AND POST-PARTUM 14 13 All SZGR 2.0 genes in this pathway
WEST ADRENOCORTICAL TUMOR DN 546 362 All SZGR 2.0 genes in this pathway
BREDEMEYER RAG SIGNALING NOT VIA ATM DN 57 34 All SZGR 2.0 genes in this pathway
BEIER GLIOMA STEM CELL UP 39 17 All SZGR 2.0 genes in this pathway
SWEET LUNG CANCER KRAS DN 435 289 All SZGR 2.0 genes in this pathway
HOFFMANN LARGE TO SMALL PRE BII LYMPHOCYTE DN 72 47 All SZGR 2.0 genes in this pathway
MCMURRAY TP53 HRAS COOPERATION RESPONSE DN 67 46 All SZGR 2.0 genes in this pathway
WONG ADULT TISSUE STEM MODULE 721 492 All SZGR 2.0 genes in this pathway
YAO TEMPORAL RESPONSE TO PROGESTERONE CLUSTER 0 76 54 All SZGR 2.0 genes in this pathway
NAKAMURA ADIPOGENESIS EARLY UP 66 44 All SZGR 2.0 genes in this pathway
NAKAMURA ADIPOGENESIS LATE UP 104 67 All SZGR 2.0 genes in this pathway
HIRSCH CELLULAR TRANSFORMATION SIGNATURE UP 242 159 All SZGR 2.0 genes in this pathway
DUTERTRE ESTRADIOL RESPONSE 24HR DN 505 328 All SZGR 2.0 genes in this pathway
WIERENGA STAT5A TARGETS UP 217 131 All SZGR 2.0 genes in this pathway
WIERENGA STAT5A TARGETS GROUP2 60 38 All SZGR 2.0 genes in this pathway
PILON KLF1 TARGETS UP 504 321 All SZGR 2.0 genes in this pathway
JOHNSTONE PARVB TARGETS 3 UP 430 288 All SZGR 2.0 genes in this pathway
LEE BMP2 TARGETS UP 745 475 All SZGR 2.0 genes in this pathway
PURBEY施的目标P1 NOT SATB1 UP 344 215 All SZGR 2.0 genes in this pathway
GOBERT CORE OLIGODENDROCYTE DIFFERENTIATION 40 28 All SZGR 2.0 genes in this pathway
SCHMIDT POR TARGETS IN LIMB BUD DN 8 7 All SZGR 2.0 genes in this pathway
YANG BCL3 TARGETS UP 364 236 All SZGR 2.0 genes in this pathway
PHONG TNF RESPONSE NOT VIA P38 337 236 All SZGR 2.0 genes in this pathway
RAO BOUND BY SALL4 ISOFORM A 182 108 All SZGR 2.0 genes in this pathway

Section VI. microRNA annotation

miRNA family Target position miRNA ID miRNA seq
UTR start UTR end Match method
miR-101 2687 2693 1A hsa-miR-101 UACAGUACUGUGAUAACUGAAG
miR-124/506 185 191 m8 hsa-miR-506 UAAGGCACCCUUCUGAGUAGA
hsa-miR-124brain UAAGGCACGCGGUGAAUGCC
miR-128 2593 2599 1A hsa-miR-128a UCACAGUGAACCGGUCUCUUUU
hsa-miR-128b UCACAGUGAACCGGUCUCUUUC
miR-130/301 3111 3117 m8 hsa-miR-130abrain CAGUGCAAUGUUAAAAGGGCAU
hsa-miR-301 CAGUGCAAUAGUAUUGUCAAAGC
hsa-miR-130bbrain CAGUGCAAUGAUGAAAGGGCAU
hsa-miR-454-3p UAGUGCAAUAUUGCUUAUAGGGUUU
miR-142-5p 3223 3230 1A,m8 hsa-miR-142-5p CAUAAAGUAGAAAGCACUAC
miR-144 2687 2693 1A hsa-miR-144 UACAGUAUAGAUGAUGUACUAG
miR-145 3115 3121 1A hsa-miR-145 GUCCAGUUUUCCCAGGAAUCCCUU
hsa-miR-145 GUCCAGUUUUCCCAGGAAUCCCUU
miR-148/152 3112 3118 m8 hsa-miR-148a UCAGUGCACUACAGAACUUUGU
hsa-miR-152brain UCAGUGCAUGACAGAACUUGGG
hsa-miR-148b UCAGUGCAUCACAGAACUUUGU
miR-17-5p/20/93.mr/106/519.d 3079 3086 1A,m8 hsa-miR-17-5p CAAAGUGCUUACAGUGCAGGUAGU
hsa-miR-20abrain UAAAGUGCUUAUAGUGCAGGUAG
hsa-miR-106a AAAAGUGCUUACAGUGCAGGUAGC
hsa-miR-106bSZ UAAAGUGCUGACAGUGCAGAU
hsa-miR-20bSZ CAAAGUGCUCAUAGUGCAGGUAG
hsa-miR-519d CAAAGUGCCUCCCUUUAGAGUGU
miR-183 1367 1373 m8 hsa-miR-183 UAUGGCACUGGUAGAAUUCACUG
miR-19 3110 3116 m8 hsa-miR-19a UGUGCAAAUCUAUGCAAAACUGA
hsa-miR-19b UGUGCAAAUCCAUGCAAAACUGA
miR-199 3114 3120 1A hsa-miR-199a CCCAGUGUUCAGACUACCUGUUC
hsa-miR-199b CCCAGUGUUUAGACUAUCUGUUC
miR-23 255 261 1A hsa-miR-23abrain AUCACAUUGCCAGGGAUUUCC
hsa-miR-23bbrain AUCACAUUGCCAGGGAUUACC
miR-26 227 233 1A hsa-miR-26abrain UUCAAGUAAUCCAGGAUAGGC
hsa-miR-26bSZ UUCAAGUAAUUCAGGAUAGGUU
miR-27 2593 2600 1A,m8 hsa-miR-27abrain UUCACAGUGGCUAAGUUCCGC
hsa-miR-27bbrain UUCACAGUGGCUAAGUUCUGC
miR-324-3p 181 187 m8 hsa-miR-324-3p CCACUGCCCCAGGUGCUGCUGG
miR-33 150 157 1A,m8 hsa-miR-33 GUGCAUUGUAGUUGCAUUG
hsa-miR-33b GUGCAUUGCUGUUGCAUUGCA
hsa-miR-33 GUGCAUUGUAGUUGCAUUG
hsa-miR-33b GUGCAUUGCUGUUGCAUUGCA
hsa-miR-33 GUGCAUUGUAGUUGCAUUG
hsa-miR-33b GUGCAUUGCUGUUGCAUUGCA
miR-376c 3252 3258 m8 hsa-miR-376c AACAUAGAGGAAAUUCCACG
miR-381 2808 2814 1A hsa-miR-381 UAUACAAGGGCAAGCUCUCUGU
hsa-miR-381 UAUACAAGGGCAAGCUCUCUGU
miR-9 2833 2839 1A hsa-miR-9SZ UCUUUGGUUAUCUAGCUGUAUGA
miR-93.hd/291-3p/294/295/302/372/373/520 3078 3084 m8 hsa-miR-93brain AAAGUGCUGUUCGUGCAGGUAG
hsa-miR-302a UAAGUGCUUCCAUGUUUUGGUGA
hsa-miR-302b UAAGUGCUUCCAUGUUUUAGUAG
hsa-miR-302c UAAGUGCUUCCAUGUUUCAGUGG
hsa-miR-302d UAAGUGCUUCCAUGUUUGAGUGU
hsa-miR-372 AAAGUGCUGCGACAUUUGAGCGU
hsa-miR-373 GAAGUGCUUCGAUUUUGGGGUGU
hsa-miR-520e AAAGUGCUUCCUUUUUGAGGG
hsa-miR-520a AAAGUGCUUCCCUUUGGACUGU
hsa-miR-520b AAAGUGCUUCCUUUUAGAGGG
hsa-miR-520c AAAGUGCUUCCUUUUAGAGGGUU
hsa-miR-520d AAAGUGCUUCUCUUUGGUGGGUU
miR-96 499 505 m8 hsa-miR-96brain UUUGGCACUAGCACAUUUUUGC