Gene Page: RYBP
Summary ?
GeneID | 23429 |
Symbol | RYBP |
Synonyms | AAP1|APAP-1|DEDAF|YEAF1 |
Description | RING1 and YY1 binding protein |
Reference | MIM:607535|HGNC:HGNC:10480|HPRD:09607| |
Gene type | protein-coding |
Map location | 3p13 |
Pascal p-value | 0.235 |
Sherlock p-value | 0.962 |
Fetal beta | 0.544 |
eGene | Myers' cis & trans Meta |
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 | |
GSMA_IIE | Genome scan meta-analysis (European-ancestry samples) | Psr: 0.04359 | |
GSMA_IIA | Genome scan meta-analysis (All samples) | Psr: 0.04047 |
Section I. Genetics and epigenetics annotation
eQTL annotation
SNP ID | Chromosome | Position | eGene | Gene Entrez ID | pvalue | qvalue | TSS distance | eQTL type |
---|---|---|---|---|---|---|---|---|
rs4677155 | chr3 | 72413686 | RYBP | 23429 | 6.735E-8 | cis | ||
rs4677155 | chr3 | 72413686 | RYBP | 23429 | 1.51E-5 | trans |
Section II. Transcriptome annotation
General gene expression (GTEx)

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 |
GNG13 | 0.89 | 0.66 |
CPNE9 | 0.86 | 0.74 |
WNT2 | 0.86 | 0.62 |
RDH12 | 0.85 | 0.64 |
DPYS | 0.83 | 0.60 |
FAM19A4 | 0.83 | 0.62 |
CASQ2 | 0.83 | 0.52 |
NPL | 0.83 | 0.46 |
RGS16 | 0.82 | 0.30 |
CCDC136 | 0.82 | 0.36 |
Top 10 negatively co-expressed genes | ||
Gene | Pearson's Correlation | Spearman's Correlation |
WDR86 | -0.37 | -0.55 |
EMID1 | -0.31 | -0.47 |
PVRL2 | -0.30 | -0.55 |
PLEKHO1 | -0.30 | -0.43 |
OLFM2 | -0.29 | -0.46 |
AC022098.2 | -0.29 | -0.46 |
NR2C2AP | -0.28 | -0.44 |
MARCKSL1 | -0.28 | -0.54 |
TUBB2B | -0.28 | -0.62 |
SHF | -0.28 | -0.42 |
Section III. Gene Ontology annotation
Molecular function | GO term | Evidence | Neuro keywords | PubMed ID |
---|---|---|---|---|
GO:0003677 | DNA binding | IEA | - | |
GO:0003714 | transcription corepressor activity | TAS | 10369680 | |
GO:0008270 | zinc ion binding | IEA | - | |
GO:0046872 | metal ion binding | IEA | - | |
Biological process | GO term | Evidence | Neuro keywords | PubMed ID |
GO:0000122 | negative regulation of transcription from RNA polymerase II promoter | TAS | 10369680 | |
GO:0006355 | regulation of transcription, DNA-dependent | IEA | - | |
GO:0006350 | transcription | IEA | - | |
GO:0006915 | apoptosis | IEA | - | |
GO:0007275 | multicellular organismal development | TAS | 10369680 | |
Cellular component | GO term | Evidence | Neuro keywords | PubMed ID |
GO:0005622 | intracellular | IEA | - | |
GO:0005634 | nucleus | IEA | - | |
GO:0005737 | cytoplasm | IEA | - |
Section IV. Protein-protein interaction annotation
Interactors | Aliases B | Official full name B | Experimental | Source | PubMed ID |
---|---|---|---|---|---|
ABL1 | ABL | JTK7 | bcr/abl | c-ABL | p150 | v-abl | c-abl oncogene 1, receptor tyrosine kinase | Far Western Reconstituted Complex Two-hybrid | BioGRID | 8943360 |
CASP10 | ALPS2 | FLICE2 | MCH4 | caspase 10, apoptosis-related cysteine peptidase | - | HPRD,BioGRID | 11395500 |
CASP8 | ALPS2B | CAP4 | FLICE | FLJ17672 | MACH | MCH5 | MGC78473 | caspase 8, apoptosis-related cysteine peptidase | - | HPRD | 11395500 |
CBX2 | CDCA6 | M33 | MGC10561 | chromobox homolog 2 (Pc class homolog, Drosophila) | Affinity Capture-Western Reconstituted Complex | BioGRID | 10369680 |
E2F2 | E2F-2 | E2F transcription factor 2 | E2F2 interacts with RYBP. | BIND | 12411495 |
E2F2 | E2F-2 | E2F transcription factor 2 | Affinity Capture-Western Two-hybrid | BioGRID | 12411495 |
E2F3 | DKFZp686C18211 | E2F-3 | KIAA0075 | MGC104598 | E2F transcription factor 3 | Affinity Capture-Western Two-hybrid | BioGRID | 12411495 |
E2F3 | DKFZp686C18211 | E2F-3 | KIAA0075 | MGC104598 | E2F transcription factor 3 | E2F3 interacts with RYBP. | BIND | 12411495 |
E2F4 | E2F-4 | E2F transcription factor 4, p107/p130-binding | Two-hybrid | BioGRID | 12411495 |
E2F6 | E2F-6 | MGC111545 | E2F transcription factor 6 | Affinity Capture-Western Reconstituted Complex Two-hybrid | BioGRID | 11171983 |12411495 |
FADD | GIG3 | MGC8528 | MORT1 | Fas (TNFRSF6)-associated via death domain | Affinity Capture-Western | BioGRID | 11395500 |
RING1 | RING1A | RNF1 | ring finger protein 1 | - | HPRD,BioGRID | 10369680 |
YY1 | DELTA | INO80S | NF-E1 | UCRBP | YIN-YANG-1 | YY1 transcription factor | - | HPRD,BioGRID | 10369680 |
Section V. Pathway annotation
Pathway name | Pathway size | # SZGR 2.0 genes in pathway | Info |
---|---|---|---|
PID E2F PATHWAY | 74 | 48 | All SZGR 2.0 genes in this pathway |
NAKAMURA TUMOR ZONE PERIPHERAL VS CENTRAL DN | 634 | 384 | All SZGR 2.0 genes in this pathway |
ONKEN UVEAL MELANOMA DN | 526 | 357 | All SZGR 2.0 genes in this pathway |
GAZDA DIAMOND BLACKFAN ANEMIA MYELOID DN | 38 | 25 | All SZGR 2.0 genes in this pathway |
PUIFFE INVASION INHIBITED BY ASCITES DN | 145 | 91 | All SZGR 2.0 genes in this pathway |
DIAZ CHRONIC MEYLOGENOUS LEUKEMIA UP | 1382 | 904 | All SZGR 2.0 genes in this pathway |
GARGALOVIC RESPONSE TO OXIDIZED PHOSPHOLIPIDS BLUE UP | 136 | 80 | All SZGR 2.0 genes in this pathway |
MULLIGHAN NPM1 MUTATED SIGNATURE 1 UP | 276 | 165 | All SZGR 2.0 genes in this pathway |
MULLIGHAN NPM1 MUTATED SIGNATURE 2 UP | 139 | 83 | All SZGR 2.0 genes in this pathway |
MULLIGHAN NPM1 SIGNATURE 3 UP | 341 | 197 | All SZGR 2.0 genes in this pathway |
UDAYAKUMAR MED1 TARGETS DN | 240 | 171 | All SZGR 2.0 genes in this pathway |
SENESE HDAC3 TARGETS DN | 536 | 332 | All SZGR 2.0 genes in this pathway |
TIEN INTESTINE PROBIOTICS 6HR DN | 167 | 100 | All SZGR 2.0 genes in this pathway |
NAGASHIMA NRG1 SIGNALING DN | 58 | 35 | All SZGR 2.0 genes in this pathway |
NAGASHIMA EGF SIGNALING UP | 58 | 40 | All SZGR 2.0 genes in this pathway |
KIM WT1 TARGETS 8HR UP | 164 | 122 | All SZGR 2.0 genes in this pathway |
ENK UV RESPONSE EPIDERMIS DN | 508 | 354 | All SZGR 2.0 genes in this pathway |
SCHLOSSER SERUM RESPONSE DN | 712 | 443 | All SZGR 2.0 genes in this pathway |
DACOSTA UV RESPONSE VIA ERCC3 DN | 855 | 609 | 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 |
SCHAEFFER PROSTATE DEVELOPMENT 48HR DN | 428 | 306 | All SZGR 2.0 genes in this pathway |
AMIT SERUM RESPONSE 120 MCF10A | 65 | 44 | All SZGR 2.0 genes in this pathway |
KIM GERMINAL CENTER T HELPER DN | 24 | 15 | All SZGR 2.0 genes in this pathway |
JAZAERI BREAST CANCER BRCA1 VS BRCA2 DN | 43 | 31 | All SZGR 2.0 genes in this pathway |
WU HBX TARGETS 2 DN | 16 | 11 | All SZGR 2.0 genes in this pathway |
DEBIASI APOPTOSIS BY REOVIRUS INFECTION UP | 314 | 201 | All SZGR 2.0 genes in this pathway |
WU HBX TARGETS 1 DN | 23 | 14 | All SZGR 2.0 genes in this pathway |
BLALOCK ALZHEIMERS DISEASE UP | 1691 | 1088 | All SZGR 2.0 genes in this pathway |
DAZARD RESPONSE TO UV SCC DN | 123 | 86 | All SZGR 2.0 genes in this pathway |
GENTILE UV RESPONSE CLUSTER D2 | 41 | 30 | All SZGR 2.0 genes in this pathway |
GENTILE UV HIGH DOSE DN | 312 | 203 | All SZGR 2.0 genes in this pathway |
JIANG HYPOXIA NORMAL | 311 | 205 | All SZGR 2.0 genes in this pathway |
MITSIADES RESPONSE TO APLIDIN UP | 439 | 257 | All SZGR 2.0 genes in this pathway |
CHEN HOXA5 TARGETS 9HR UP | 223 | 132 | All SZGR 2.0 genes in this pathway |
LEE DIFFERENTIATING T LYMPHOCYTE | 200 | 115 | All SZGR 2.0 genes in this pathway |
SHEDDEN LUNG CANCER GOOD SURVIVAL A12 | 317 | 177 | All SZGR 2.0 genes in this pathway |
MILI PSEUDOPODIA HAPTOTAXIS UP | 518 | 299 | All SZGR 2.0 genes in this pathway |
ROME INSULIN TARGETS IN MUSCLE UP | 442 | 263 | All SZGR 2.0 genes in this pathway |
KYNG RESPONSE TO H2O2 VIA ERCC6 UP | 40 | 30 | All SZGR 2.0 genes in this pathway |
RAGHAVACHARI PLATELET SPECIFIC GENES | 70 | 46 | All SZGR 2.0 genes in this pathway |
PILON KLF1 TARGETS DN | 1972 | 1213 | All SZGR 2.0 genes in this pathway |
JOHNSTONE PARVB TARGETS 3 DN | 918 | 550 | All SZGR 2.0 genes in this pathway |
KRIEG HYPOXIA NOT VIA KDM3A | 770 | 480 | All SZGR 2.0 genes in this pathway |
RAO BOUND BY SALL4 | 227 | 149 | All SZGR 2.0 genes in this pathway |
ZWANG TRANSIENTLY UP BY 1ST EGF PULSE ONLY | 1839 | 928 | 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-1/206 | 2133 | 2139 | m8 | hsa-miR-1 | UGGAAUGUAAAGAAGUAUGUA |
hsa-miR-206SZ | UGGAAUGUAAGGAAGUGUGUGG | ||||
hsa-miR-613 | AGGAAUGUUCCUUCUUUGCC | ||||
miR-10 | 32 | 38 | 1A | hsa-miR-10a | UACCCUGUAGAUCCGAAUUUGUG |
hsa-miR-10b | UACCCUGUAGAACCGAAUUUGU | ||||
miR-103/107 | 64 | 70 | m8 | hsa-miR-103brain | AGCAGCAUUGUACAGGGCUAUGA |
hsa-miR-107brain | AGCAGCAUUGUACAGGGCUAUCA | ||||
miR-124.1 | 3099 | 3105 | m8 | hsa-miR-124a | UUAAGGCACGCGGUGAAUGCCA |
miR-124/506 | 3099 | 3105 | 1A | hsa-miR-506 | UAAGGCACCCUUCUGAGUAGA |
hsa-miR-124brain | UAAGGCACGCGGUGAAUGCC | ||||
miR-125/351 | 2173 | 2180 | 1A,m8 | hsa-miR-125bbrain | UCCCUGAGACCCUAACUUGUGA |
hsa-miR-125abrain | UCCCUGAGACCCUUUAACCUGUG | ||||
miR-128 | 546 | 553 | 1A,m8 | hsa-miR-128a | UCACAGUGAACCGGUCUCUUUU |
hsa-miR-128b | UCACAGUGAACCGGUCUCUUUC | ||||
hsa-miR-128a | UCACAGUGAACCGGUCUCUUUU | ||||
hsa-miR-128b | UCACAGUGAACCGGUCUCUUUC | ||||
miR-130/301 | 2277 | 2283 | m8 | hsa-miR-130abrain | CAGUGCAAUGUUAAAAGGGCAU |
hsa-miR-301 | CAGUGCAAUAGUAUUGUCAAAGC | ||||
hsa-miR-130bbrain | CAGUGCAAUGAUGAAAGGGCAU | ||||
hsa-miR-454-3p | UAGUGCAAUAUUGCUUAUAGGGUUU | ||||
miR-135 | 2194 | 2200 | 1A | hsa-miR-135a | UAUGGCUUUUUAUUCCUAUGUGA |
hsa-miR-135b | UAUGGCUUUUCAUUCCUAUGUG | ||||
miR-136 | 3241 | 3247 | m8 | hsa-miR-136 | ACUCCAUUUGUUUUGAUGAUGGA |
miR-141/200a | 2864 | 2871 | 1A,m8 | hsa-miR-141 | UAACACUGUCUGGUAAAGAUGG |
hsa-miR-200a | UAACACUGUCUGGUAACGAUGU | ||||
miR-142-5p | 3695 | 3701 | m8 | hsa-miR-142-5p | CAUAAAGUAGAAAGCACUAC |
miR-148/152 | 2278 | 2284 | m8 | hsa-miR-148a | UCAGUGCACUACAGAACUUUGU |
hsa-miR-152brain | UCAGUGCAUGACAGAACUUGGG | ||||
hsa-miR-148b | UCAGUGCAUCACAGAACUUUGU | ||||
miR-15/16/195/424/497 | 65 | 71 | m8 | hsa-miR-15abrain | UAGCAGCACAUAAUGGUUUGUG |
hsa-miR-16brain | UAGCAGCACGUAAAUAUUGGCG | ||||
hsa-miR-15bbrain | UAGCAGCACAUCAUGGUUUACA | ||||
hsa-miR-195SZ | UAGCAGCACAGAAAUAUUGGC | ||||
hsa-miR-424 | CAGCAGCAAUUCAUGUUUUGAA | ||||
hsa-miR-497 | CAGCAGCACACUGUGGUUUGU | ||||
miR-17-5p/20/93.mr/106/519.d | 3694 | 3700 | 1A | 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 | ||||
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-19 | 3 | 9 | 1A | hsa-miR-19a | UGUGCAAAUCUAUGCAAAACUGA |
hsa-miR-19b | UGUGCAAAUCCAUGCAAAACUGA | ||||
miR-208 | 3583 | 3589 | 1A | hsa-miR-208 | AUAAGACGAGCAAAAAGCUUGU |
miR-217 | 2968 | 2974 | m8 | hsa-miR-217 | UACUGCAUCAGGAACUGAUUGGAU |
miR-218 | 2859 | 2865 | m8 | hsa-miR-218brain | UUGUGCUUGAUCUAACCAUGU |
miR-219 | 228 | 234 | 1A | hsa-miR-219brain | UGAUUGUCCAAACGCAAUUCU |
miR-23 | 724 | 730 | m8 | hsa-miR-23abrain | AUCACAUUGCCAGGGAUUUCC |
hsa-miR-23bbrain | AUCACAUUGCCAGGGAUUACC | ||||
miR-27 | 547 | 554 | 1A,m8 | hsa-miR-27abrain | UUCACAGUGGCUAAGUUCCGC |
hsa-miR-27bbrain | UUCACAGUGGCUAAGUUCUGC | ||||
miR-29 | 534 | 540 | m8 | hsa-miR-29aSZ | UAGCACCAUCUGAAAUCGGUU |
hsa-miR-29bSZ | UAGCACCAUUUGAAAUCAGUGUU | ||||
hsa-miR-29cSZ | UAGCACCAUUUGAAAUCGGU | ||||
miR-323 | 724 | 730 | 1A | hsa-miR-323brain | GCACAUUACACGGUCGACCUCU |
miR-324-5p | 1972 | 1979 | 1A,m8 | hsa-miR-324-5p | CGCAUCCCCUAGGGCAUUGGUGU |
miR-330 | 812 | 818 | 1A | hsa-miR-330brain | GCAAAGCACACGGCCUGCAGAGA |
miR-335 | 183 | 189 | 1A | hsa-miR-335brain | UCAAGAGCAAUAACGAAAAAUGU |
miR-376 | 597 | 604 | 1A,m8 | hsa-miR-376a | AUCAUAGAGGAAAAUCCACGU |
hsa-miR-376b | AUCAUAGAGGAAAAUCCAUGUU | ||||
hsa-miR-376a | AUCAUAGAGGAAAAUCCACGU | ||||
hsa-miR-376b | AUCAUAGAGGAAAAUCCAUGUU | ||||
hsa-miR-376a | AUCAUAGAGGAAAAUCCACGU | ||||
hsa-miR-376b | AUCAUAGAGGAAAAUCCAUGUU | ||||
miR-381 | 3457 | 3464 | 1A,m8 | hsa-miR-381 | UAUACAAGGGCAAGCUCUCUGU |
hsa-miR-381 | UAUACAAGGGCAAGCUCUCUGU | ||||
miR-410 | 493 | 499 | 1A | hsa-miR-410 | AAUAUAACACAGAUGGCCUGU |
miR-485-3p | 3285 | 3291 | m8 | hsa-miR-485-3p | GUCAUACACGGCUCUCCUCUCU |
miR-488 | 3035 | 3041 | 1A | hsa-miR-488 | CCCAGAUAAUGGCACUCUCAA |
miR-493-5p | 304 | 310 | m8 | hsa-miR-493-5p | UUGUACAUGGUAGGCUUUCAUU |
miR-495 | 3407 | 3413 | 1A | hsa-miR-495brain | AAACAAACAUGGUGCACUUCUUU |
hsa-miR-495brain | AAACAAACAUGGUGCACUUCUUU | ||||
hsa-miR-495brain | AAACAAACAUGGUGCACUUCUUU | ||||
miR-496 | 2355 | 2362 | 1A,m8 | hsa-miR-496 | AUUACAUGGCCAAUCUC |
miR-499 | 3583 | 3589 | 1A | hsa-miR-499 | UUAAGACUUGCAGUGAUGUUUAA |
hsa-miR-499 | UUAAGACUUGCAGUGAUGUUUAA | ||||
miR-7 | 433 | 439 | 1A | hsa-miR-7SZ | UGGAAGACUAGUGAUUUUGUUG |
miR-9 | 2027 | 2033 | m8 | hsa-miR-9SZ | UCUUUGGUUAUCUAGCUGUAUGA |
- SZ: miRNAs which differentially expressed in brain cortex of schizophrenia patients comparing with control samples using microarray. Click here to see the list of SZ related miRNAs.
- Brain: miRNAs which are expressed in brain based on miRNA microarray expression studies. Click here to see the list of brain related miRNAs.