Summary ?
GeneID4192
SymbolMDK
SynonymsARAP|MK|NEGF2
Descriptionmidkine (neurite growth-promoting factor 2)
ReferenceMIM:162096|HGNC:HGNC:6972|Ensembl:ENSG00000110492|HPRD:01200|Vega:OTTHUMG00000150315
Gene typeprotein-coding
Map location11p11.2
Pascal p-value2.765E-10
Sherlock p-value0.639
Fetal beta0.985
DMG1 (# studies)
eGeneMyers' cis & trans

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:PGCnpGenome-wide Association StudyGWAS
DMG:Wockner_2014Genome-wide DNA methylation analysisThis dataset includes 4641 differentially methylated probes corresponding to 2929 unique genes between schizophrenia patients (n=24) and controls (n=24). 1
PMID:cooccurHigh-throughput literature-searchSystematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
LiteratureHigh-throughput literature-searchCo-occurance with Schizophrenia keywords: schizophrenia,schizophrenic,schizophreniasClick to show details
GO_AnnotationMapping neuro-related keywords to Gene Ontology annotationsHits with neuro-related keywords: 1 

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg000781941146402949MDK2.84E-5-0.20.018DMG:Wockner_2014

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs17195543chr1145509795MDK41920.02cis
rs947242chr158042848MDK41920.05trans
rs631503chr172327801MDK41920.06trans
rs11205098chr1152717431MDK41926.48E-4trans
rs7518178chr1199424428MDK41920.18trans
rs3013450chr1214552423MDK41920.08trans
rs2374323chr241898671MDK41925.147E-4trans
rs17486127chr272111878MDK41920trans
rs17558168chr272151944MDK41920trans
rs7562379chr276693222MDK41920.14trans
rs4338920chr2141325591MDK41920.04trans
rs222809chr2146893189MDK41920.07trans
rs6726013chr2189064570MDK41922.414E-4trans
rs6729020chr2189064719MDK41926.202E-6trans
rs10166301chr2189947813MDK41920trans
rs4680999chr378613401MDK41920.11trans
rs17088743chr458668728MDK41920.01trans
rs4425392chr4133569611MDK41920.17trans
rs35129chr56039853MDK41920.09trans
rs447967chr59999056MDK41920.14trans
rs6874831chr559155059MDK41924.156E-8trans
rs7728346chr559155166MDK41928.123E-10trans
rs16890314chr559158770MDK41924.597E-7trans
rs10214307chr559159746MDK41924.156E-8trans
rs6893381chr559160568MDK41929.95E-7trans
rs10052099chr599324715MDK41920.05trans
rs10074374chr599324809MDK41920.08trans
rs545290chr5152858437MDK41920.08trans
rs2294670chr6625834MDK41920.01trans
rs9451867chr692659609MDK41920.01trans
rs9640055chr78029515MDK41920.05trans
rs17142255chr78075258MDK41920.09trans
rs1014201chr725815736MDK41920.05trans
rs2939687chr856313877MDK41920.11trans
rs10123219chr974156668MDK41920.03trans
rs4601388chr994547922MDK41921.187E-4trans
rs2006996chr9117592637MDK41920.16trans
rs2229360chr108116078MDK41920.15trans
rs2225536chr10110354957MDK41920.16trans
rs7933582chr1191178991MDK41920.14trans
rs7953537chr1244693287MDK41920.07trans
rs17094401chr1244696783MDK41920.19trans
rs17094560chr1244769767MDK41920.07trans
rs8013004chr1441098282MDK41920.01trans
rs8013037chr1441098343MDK41920.11trans
rs17105664chr1468926192MDK41920.18trans
rs1515411chr1490614916MDK41920.16trans
rs4457950chr1535445709MDK41920.06trans
rs16969948chr1578864785MDK41920.14trans
rs4550511chr1753340407MDK41920.18trans
rs8071763chr1767930673MDK41923.829E-4trans
rs7244040chr1813972023MDK41928.92E-8trans
rs17681878chr1834767223MDK41920.18trans
rs515453chr1872483272MDK41920.12trans
rs4536719chr2024397114MDK41928.406E-4trans
rs7887127chrX38436019MDK41921.645E-4trans
rs871948chrX39342814MDK41927.043E-4trans

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
GenePearson's Correlation Spearman's Correlation
NEBL0.870.87
EPB41L20.860.90
MFAP3L0.850.89
ACSL60.850.89
MYLK0.850.82
SYNM0.840.89
SIRPA0.840.91
KIAA04940.840.83
DTNA0.840.87
TACC10.820.88
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
TUBB2B-0.62-0.55
KIAA1949-0.62-0.49
BCL7C-0.62-0.71
NXT1-0.62-0.66
RPS8-0.61-0.75
RPS19P3-0.61-0.78
RPS13P2-0.61-0.73
TRAF4-0.61-0.66
DYNLT1-0.61-0.74
ALKBH2-0.61-0.63

Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0008201heparin bindingIDA9384573 
GO:0008083growth factor activityIEA-
GO:0008083growth factor activityNAS1639750 
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0007399nervous system developmentNASneurite (GO term level: 5)9384573 
GO:0007165signal transductionNAS7835084 
GO:0008283cell proliferationIEA-
GO:0009611response to woundingISS-
GO:0007275multicellular organismal developmentIEA-
GO:0030154cell differentiationNAS1639750 
GO:0030325adrenal gland developmentISS-
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0005576extracellular regionIEA-

Section IV. Protein-protein interaction annotation

InteractorsAliases BOfficial full name BExperimentalSourcePubMed ID
ACTG1ACT | ACTG | DFNA20 | DFNA26actin, gamma 1Affinity Capture-MSBioGRID10772929 
JAK1JAK1A | JAK1B | JTK3Janus kinase 1 (a protein tyrosine kinase)-HPRD9452495 
JAK2JTK10Janus kinase 2 (a protein tyrosine kinase)-HPRD9452495 
LRP1A2MR | APOER | APR | CD91 | FLJ16451 | IGFBP3R | LRP | MGC88725 | TGFBR5low density lipoprotein-related protein 1 (alpha-2-macroglobulin receptor)-HPRD,BioGRID10772929 
LRP2DBS | gp330low density lipoprotein-related protein 2-HPRD10772929 
NCAM1CD56 | MSK39 | NCAMneural cell adhesion molecule 1Affinity Capture-MSBioGRID10772929 
NCLC23 | FLJ45706nucleolin-HPRD,BioGRID12147681 
NID1NIDnidogen 1Affinity Capture-MSBioGRID10772929 
NID2-nidogen 2 (osteonidogen)Affinity Capture-MSBioGRID10772929 
PTPRBDKFZp686E2262 | DKFZp686H15164 | FLJ44133 | HPTP-BETA | HPTPB | MGC142023 | MGC59935 | PTPB | R-PTP-BETA | VEPTPprotein tyrosine phosphatase, receptor type, B-HPRD10706604 
PTPRZ1HPTPZ | HPTPzeta | PTP-ZETA | PTP18 | PTPRZ | PTPZ | RPTPB | RPTPbeta | phosphacanprotein tyrosine phosphatase, receptor-type, Z polypeptide 1-HPRD,BioGRID10212223 |10706604 
RPL18A-ribosomal protein L18aTwo-hybridBioGRID16169070 
SDC1CD138 | SDC | SYND1 | syndecansyndecan 1-HPRD9089390 
SDC3N-syndecan | SDCN | SYND3syndecan 3-HPRD9089390 
SDC4MGC22217 | SYND4syndecan 4-HPRD8621465 
STAT1DKFZp686B04100 | ISGF-3 | STAT91signal transducer and activator of transcription 1, 91kDa-HPRD9452495 
TGM1ICR2 | KTG | LI | LI1 | TGASE | TGKtransglutaminase 1 (K polypeptide epidermal type I, protein-glutamine-gamma-glutamyltransferase)-HPRD9384573 
TUBA1AB-ALPHA-1 | FLJ25113 | LIS3 | TUBA3tubulin, alpha 1aAffinity Capture-MSBioGRID10772929 
TUBB2BDKFZp566F223 | FLJ98847 | MGC8685 | TUBB-PARALOG | bA506K6.1tubulin, beta 2BAffinity Capture-MSBioGRID10772929 


Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
PID INTEGRIN1 PATHWAY 6644All SZGR 2.0 genes in this pathway
PID SYNDECAN 4 PATHWAY 3225All SZGR 2.0 genes in this pathway
PID INTEGRIN A4B1 PATHWAY 3324All SZGR 2.0 genes in this pathway
SCHUETZ BREAST CANCER DUCTAL INVASIVE DN 8453All SZGR 2.0 genes in this pathway
MULLIGHAN MLL SIGNATURE 1 DN 242165All SZGR 2.0 genes in this pathway
MULLIGHAN MLL SIGNATURE 2 DN 281186All SZGR 2.0 genes in this pathway
DELYS THYROID CANCER UP 443294All SZGR 2.0 genes in this pathway
MCBRYAN PUBERTAL BREAST 4 5WK UP 271175All SZGR 2.0 genes in this pathway
HAMAI APOPTOSIS VIA TRAIL DN 186107All SZGR 2.0 genes in this pathway
DACOSTA UV RESPONSE VIA ERCC3 TTD UP 6439All SZGR 2.0 genes in this pathway
ROVERSI GLIOMA COPY NUMBER UP 10075All SZGR 2.0 genes in this pathway
LI AMPLIFIED IN LUNG CANCER 178108All SZGR 2.0 genes in this pathway
LUI THYROID CANCER CLUSTER 1 5133All SZGR 2.0 genes in this pathway
KORKOLA YOLK SAC TUMOR 6233All SZGR 2.0 genes in this pathway
DACOSTA ERCC3 ALLELE XPCS VS TTD UP 2819All SZGR 2.0 genes in this pathway
DACOSTA UV RESPONSE VIA ERCC3 UP 309199All SZGR 2.0 genes in this pathway
HEIDENBLAD AMPLICON 8Q24 DN 4628All SZGR 2.0 genes in this pathway
FURUKAWA DUSP6 TARGETS PCI35 UP 7432All SZGR 2.0 genes in this pathway
NUYTTEN NIPP1 TARGETS DN 848527All SZGR 2.0 genes in this pathway
ROZANOV MMP14 TARGETS SUBSET 3320All SZGR 2.0 genes in this pathway
ROZANOV MMP14 TARGETS UP 266171All SZGR 2.0 genes in this pathway
SHEPARD BMYB MORPHOLINO DN 200112All SZGR 2.0 genes in this pathway
SHEPARD BMYB TARGETS 7441All SZGR 2.0 genes in this pathway
TARTE PLASMA CELL VS PLASMABLAST UP 398262All SZGR 2.0 genes in this pathway
SHEPARD CRUSH AND BURN MUTANT DN 185111All SZGR 2.0 genes in this pathway
HADDAD T LYMPHOCYTE AND NK PROGENITOR UP 7856All SZGR 2.0 genes in this pathway
LEI MYB TARGETS 318215All SZGR 2.0 genes in this pathway
ZHAN MULTIPLE MYELOMA CD1 AND CD2 UP 8951All SZGR 2.0 genes in this pathway
KAAB HEART ATRIUM VS VENTRICLE UP 249170All SZGR 2.0 genes in this pathway
CUI TCF21 TARGETS UP 3727All SZGR 2.0 genes in this pathway
KANG FLUOROURACIL RESISTANCE UP 2215All SZGR 2.0 genes in this pathway
BANDRES RESPONSE TO CARMUSTIN MGMT 24HR DN 3321All SZGR 2.0 genes in this pathway
ZHANG ANTIVIRAL RESPONSE TO RIBAVIRIN UP 3021All SZGR 2.0 genes in this pathway
LEE CALORIE RESTRICTION NEOCORTEX DN 8858All SZGR 2.0 genes in this pathway
CUI TCF21 TARGETS 2 UP 428266All SZGR 2.0 genes in this pathway
JIANG HYPOXIA NORMAL 311205All SZGR 2.0 genes in this pathway
BANDRES RESPONSE TO CARMUSTIN WITHOUT MGMT 48HR DN 3225All SZGR 2.0 genes in this pathway
BANDRES RESPONSE TO CARMUSTIN MGMT 48HR DN 161105All SZGR 2.0 genes in this pathway
BACOLOD RESISTANCE TO ALKYLATING AGENTS UP 2617All SZGR 2.0 genes in this pathway
WANG LSD1 TARGETS UP 2414All SZGR 2.0 genes in this pathway
KANG CISPLATIN RESISTANCE UP 1911All SZGR 2.0 genes in this pathway
SASAI TARGETS OF CXCR6 AND PTCH1 DN 86All SZGR 2.0 genes in this pathway
VART KSHV INFECTION ANGIOGENIC MARKERS DN 13892All SZGR 2.0 genes in this pathway
YAMASHITA LIVER CANCER WITH EPCAM UP 5325All SZGR 2.0 genes in this pathway
YAGI AML WITH T 8 21 TRANSLOCATION 368247All SZGR 2.0 genes in this pathway
CAIRO LIVER DEVELOPMENT UP 166105All SZGR 2.0 genes in this pathway
YAO TEMPORAL RESPONSE TO PROGESTERONE CLUSTER 12 7954All SZGR 2.0 genes in this pathway
CHICAS RB1 TARGETS CONFLUENT 567365All SZGR 2.0 genes in this pathway
JOHNSTONE PARVB TARGETS 2 UP 14094All SZGR 2.0 genes in this pathway
DELACROIX RAR BOUND ES 462273All SZGR 2.0 genes in this pathway
ZWANG TRANSIENTLY UP BY 2ND EGF PULSE ONLY 1725838All SZGR 2.0 genes in this pathway
NABA SECRETED FACTORS 344197All SZGR 2.0 genes in this pathway
NABA MATRISOME ASSOCIATED 753411All SZGR 2.0 genes in this pathway
NABA MATRISOME 1028559All SZGR 2.0 genes in this pathway

Section VI. microRNA annotation

miRNA familyTarget positionmiRNA IDmiRNA seq
UTR startUTR endMatch method
miR-124/5069096m8hsa-miR-506UAAGGCACCCUUCUGAGUAGA
hsa-miR-124brainUAAGGCACGCGGUGAAUGCC