Gene Page:HMGA1

Summary?
GeneID 3159
Symbol HMGA1
Synonyms HMG-R|HMGA1A|HMGIY
Description high mobility group AT-hook 1
Reference MIM:600701|HGNC:HGNC:5010|Ensembl:ENSG00000137309|HPRD:02829|Vega:OTTHUMG00000014539
Gene type protein-coding
Map location 6p21
Pascal p-value 0.732
Sherlock p-value 0.532
Fetal beta 0.629
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
DMG:Jaffe_2016 Genome-wide DNA methylation analysis This dataset includes 2,104 probes/CpGs associated with SZ patients (n=108) compared to 136 controls at Bonferroni-adjusted P < 0.05. 1
GSMA_I Genome scan meta-analysis Psr: 0.033
GSMA_IIE Genome scan meta-analysis (European-ancestry samples) Psr: 0.04433

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

Probe Chromosome Position Nearest gene P (dis) Beta (dis) FDR (dis) Study
cg23193153 6 34192178 HMGA1 3.54E-8 -0.014 1.04E-5 DMG:Jaffe_2016


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:分皮质区域;SM:感觉运动区域s; 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.

No co-expressed genes in brain regions


Section III. Gene Ontology annotation

Molecular function GO term Evidence Neuro keywords PubMed ID
GO:0003677 DNA binding IEA -
GO:0003680 AT DNA binding TAS 10428834
GO:0003700 transcription factor activity IMP 10428834
GO:0042975 peroxisome proliferator activated receptor binding IDA 10428834
GO:0030374 ligand-dependent nuclear receptor transcription coactivator activity IMP 10428834
GO:0046965 retinoid X receptor binding IDA 10428834
Biological process GO term Evidence Neuro keywords PubMed ID
GO:0006337 nucleosome disassembly TAS 10428834
GO:0006345 loss of chromatin silencing TAS 10428834
GO:0006355 regulation of transcription, DNA-dependent IEA -
GO:0006355 regulation of transcription, DNA-dependent TAS 10871404
GO:0007169 跨膜受体蛋白酪氨酸激酶e signaling pathway NAS 15609325
GO:0006461 protein complex assembly TAS 10428834
GO:0006268 DNA unwinding during replication NAS 10428834
GO:0019047 provirus integration EXP 16291214
GO:0019059 initiation of viral infection EXP 12091904
GO:0045941 positive regulation of transcription IMP 10428834
GO:0044419 interspecies interaction between organisms IEA -
Cellular component GO term Evidence Neuro keywords PubMed ID
GO:0000785 chromatin IEA -
GO:0005829 cytosol EXP 12228227|15479846
GO:0005634 nucleus IEA -
GO:0005667 transcription factor complex TAS 10428834
GO:0005694 chromosome IEA -

Section IV. Protein-protein interaction annotation

Interactors Aliases B Official full name B Experimental Source PubMed ID
ATF2 CRE-BP1 | CREB2 | HB16 | MGC111558 | TREB7 activating transcription factor 2 - HPRD,BioGRID 10357819
CEBPB C/EBP-beta | CRP2 | IL6DBP | LAP | MGC32080 | NF-IL6 | TCF5 CCAAT/enhancer binding protein (C/EBP), beta - HPRD,BioGRID 12665574
ELF1 - E74-like factor 1 (ets domain transcription factor) Reconstituted Complex BioGRID 7862168
EWSR1 EWS Ewing sarcoma breakpoint region 1 Two-hybrid BioGRID 16189514
HIPK2 DKFZp686K02111 | FLJ23711 | PRO0593 homeodomain interacting protein kinase 2 - HPRD 11593421
INSR CD220 | HHF5 insulin receptor HMGA1 interacts with INSR locus. BIND 15924147
IRF1 IRF-1 | MAR interferon regulatory factor 1 - HPRD,BioGRID 10357819
JUN AP-1 | AP1 | c-Jun jun oncogene - HPRD,BioGRID 10357819
NFYA CBF-A | CBF-B | FLJ11236 | HAP2 | NF-YA nuclear transcription factor Y, alpha - HPRD,BioGRID 9388234
POU3F1 OCT6 | OTF6 | SCIP POU class 3 homeobox 1 - HPRD,BioGRID 7791781
RNF4 RES4-26 | SNURF ring finger protein 4 - HPRD 10713105
SP1 - Sp1 transcription factor - HPRD,BioGRID 12665574
SUFU PRO1280 | SUFUH | SUFUXL suppressor of fused homolog (Drosophila) - HPRD 14611647


Section V. Pathway annotation

Pathway name Pathway size # SZGR 2.0 genes in pathway Info
PID IL4 2PATHWAY 65 43 All SZGR 2.0 genes in this pathway
PID MYC ACTIV PATHWAY 79 62 All SZGR 2.0 genes in this pathway
REACTOME HIV INFECTION 207 122 All SZGR 2.0 genes in this pathway
REACTOME HIV LIFE CYCLE 125 69 All SZGR 2.0 genes in this pathway
REACTOME EARLY PHASE OF HIV LIFE CYCLE 21 8 All SZGR 2.0 genes in this pathway
REACTOME HOST INTERACTIONS OF HIV FACTORS 132 81 All SZGR 2.0 genes in this pathway
REACTOME INTERACTIONS OF VPR WITH HOST CELLULAR PROTEINS 33 21 All SZGR 2.0 genes in this pathway
LIU SOX4 TARGETS DN 309 191 All SZGR 2.0 genes in this pathway
GARY CD5 TARGETS UP 473 314 All SZGR 2.0 genes in this pathway
BORCZUK MALIGNANT MESOTHELIOMA UP 305 185 All SZGR 2.0 genes in this pathway
HORIUCHI WTAP TARGETS DN 310 188 All SZGR 2.0 genes in this pathway
VECCHI GASTRIC CANCER EARLY UP 430 232 All SZGR 2.0 genes in this pathway
RHEIN ALL GLUCOCORTICOID THERAPY DN 362 238 All SZGR 2.0 genes in this pathway
SENESE HDAC1 TARGETS UP 457 269 All SZGR 2.0 genes in this pathway
SENESE HDAC1 AND HDAC2 TARGETS UP 238 144 All SZGR 2.0 genes in this pathway
SENESE HDAC2 TARGETS UP 114 66 All SZGR 2.0 genes in this pathway
SENESE HDAC3 TARGETS UP 501 327 All SZGR 2.0 genes in this pathway
LEE NEURAL CREST STEM CELL UP 146 99 All SZGR 2.0 genes in this pathway
KIM WT1 TARGETS UP 214 155 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 KERATINOCYTE UP 530 342 All SZGR 2.0 genes in this pathway
GRAESSMANN APOPTOSIS BY DOXORUBICIN UP 1142 669 All SZGR 2.0 genes in this pathway
MARKS ACETYLATED NON HISTONE PROTEINS 15 9 All SZGR 2.0 genes in this pathway
MYLLYKANGAS AMPLIFICATION HOT SPOT 15 13 9 All SZGR 2.0 genes in this pathway
ROSTY CERVICAL CANCER PROLIFERATION CLUSTER 140 73 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 SIGNALING NOT VIA AKT1 48HR UP 35 20 All SZGR 2.0 genes in this pathway
PATIL LIVER CANCER 747 453 All SZGR 2.0 genes in this pathway
OXFORD RALA OR RALB TARGETS UP 48 23 All SZGR 2.0 genes in this pathway
JAZAG TGFB1 SIGNALING VIA SMAD4 UP 108 66 All SZGR 2.0 genes in this pathway
PUJANA BRCA1 PCC NETWORK 1652 1023 All SZGR 2.0 genes in this pathway
LIAO METASTASIS 539 324 All SZGR 2.0 genes in this pathway
BENPORATH ES 1 379 235 All SZGR 2.0 genes in this pathway
BENPORATH ES CORE NINE CORRELATED 100 68 All SZGR 2.0 genes in this pathway
AMIT EGF RESPONSE 480 HELA 164 118 All SZGR 2.0 genes in this pathway
MORI MATURE B LYMPHOCYTE DN 75 43 All SZGR 2.0 genes in this pathway
SHEPARD BMYB MORPHOLINO DN 200 112 All SZGR 2.0 genes in this pathway
SHEPARD BMYB TARGETS 74 41 All SZGR 2.0 genes in this pathway
SHEPARD CRUSH AND BURN MUTANT DN 185 111 All SZGR 2.0 genes in this pathway
SHEPARD BMYB MORPHOLINO UP 205 126 All SZGR 2.0 genes in this pathway
MANALO HYPOXIA DN 289 166 All SZGR 2.0 genes in this pathway
POMEROY MEDULLOBLASTOMA PROGNOSIS DN 43 28 All SZGR 2.0 genes in this pathway
SHIPP DLBCL VS FOLLICULAR LYMPHOMA UP 45 30 All SZGR 2.0 genes in this pathway
PEART HDAC PROLIFERATION CLUSTER DN 76 57 All SZGR 2.0 genes in this pathway
BHATTACHARYA EMBRYONIC STEM CELL 89 60 All SZGR 2.0 genes in this pathway
FERRANDO T ALL WITH MLL ENL FUSION DN 87 57 All SZGR 2.0 genes in this pathway
THEILGAARD NEUTROPHIL AT SKIN WOUND UP 77 52 All SZGR 2.0 genes in this pathway
FAELT B CLL WITH VH3 21 UP 44 30 All SZGR 2.0 genes in this pathway
WEIGEL OXIDATIVE STRESS RESPONSE 35 28 All SZGR 2.0 genes in this pathway
WANG SMARCE1 TARGETS DN 371 218 All SZGR 2.0 genes in this pathway
LINDVALL IMMORTALIZED BY TERT UP 78 48 All SZGR 2.0 genes in this pathway
YAMAZAKI TCEB3 TARGETS DN 215 132 All SZGR 2.0 genes in this pathway
ZHOU TNF SIGNALING 30MIN 54 36 All SZGR 2.0 genes in this pathway
JACKSON DNMT1 TARGETS UP 77 57 All SZGR 2.0 genes in this pathway
BURTON ADIPOGENESIS PEAK AT 16HR 40 24 All SZGR 2.0 genes in this pathway
DOUGLAS BMI1 TARGETS UP 566 371 All SZGR 2.0 genes in this pathway
LEIN MIDBRAIN MARKERS 82 55 All SZGR 2.0 genes in this pathway
LEIN PONS MARKERS 89 59 All SZGR 2.0 genes in this pathway
LEIN MEDULLA MARKERS 81 48 All SZGR 2.0 genes in this pathway
JEPSEN SMRT TARGETS 33 23 All SZGR 2.0 genes in this pathway
DAIRKEE CANCER PRONE RESPONSE BPA E2 118 65 All SZGR 2.0 genes in this pathway
SMID BREAST CANCER BASAL UP 648 398 All SZGR 2.0 genes in this pathway
BONOME OVARIAN CANCER SURVIVAL SUBOPTIMAL DEBULKING 510 309 All SZGR 2.0 genes in this pathway
MATZUK MALE REPRODUCTION SERTOLI 28 23 All SZGR 2.0 genes in this pathway
GRADE COLON CANCER UP 871 505 All SZGR 2.0 genes in this pathway
HUPER BREAST BASAL VS LUMINAL DN 59 44 All SZGR 2.0 genes in this pathway
MUELLER PLURINET 299 189 All SZGR 2.0 genes in this pathway
GRESHOCK CANCER COPY NUMBER UP 323 240 All SZGR 2.0 genes in this pathway
YOSHIMURA MAPK8 TARGETS UP 1305 895 All SZGR 2.0 genes in this pathway
SHEDDEN LUNG CANCER POOR SURVIVAL A6 456 285 All SZGR 2.0 genes in this pathway
HAN SATB1 TARGETS UP 395 249 All SZGR 2.0 genes in this pathway
CHEN METABOLIC SYNDROM NETWORK 1210 725 All SZGR 2.0 genes in this pathway
CROONQUIST IL6 DEPRIVATION DN 98 69 All SZGR 2.0 genes in this pathway
CROONQUIST NRAS SIGNALING DN 72 47 All SZGR 2.0 genes in this pathway
ZHAN V1 LATE DIFFERENTIATION GENES DN 15 13 All SZGR 2.0 genes in this pathway
KAPOSI LIVER CANCER MET UP 18 11 All SZGR 2.0 genes in this pathway
WOO LIVER CANCER RECURRENCE UP 105 75 All SZGR 2.0 genes in this pathway
MEISSNER NPC HCP WITH H3K4ME2 491 319 All SZGR 2.0 genes in this pathway
CAIRO HEPATOBLASTOMA CLASSES UP 605 377 All SZGR 2.0 genes in this pathway
ZHAN MULTIPLE MYELOMA CD2 DN 46 29 All SZGR 2.0 genes in this pathway
DANG MYC TARGETS UP 143 100 All SZGR 2.0 genes in this pathway
DANG BOUND BY MYC 1103 714 All SZGR 2.0 genes in this pathway
MARTENS BOUND BY PML RARA FUSION 456 287 All SZGR 2.0 genes in this pathway
MARTENS TRETINOIN RESPONSE DN 841 431 All SZGR 2.0 genes in this pathway
CHICAS RB1 TARGETS CONFLUENT 567 365 All SZGR 2.0 genes in this pathway
MIYAGAWA TARGETS OF EWSR1 ETS FUSIONS DN 229 135 All SZGR 2.0 genes in this pathway
DELACROIX RARG BOUND MEF 367 231 All SZGR 2.0 genes in this pathway
DELACROIX RAR TARGETS UP 48 33 All SZGR 2.0 genes in this pathway
VANOEVELEN MYOGENESIS SIN3A TARGETS 220 133 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
let-7/98 960 966 m8 hsa-let-7abrain UGAGGUAGUAGGUUGUAUAGUU
hsa-let-7bbrain UGAGGUAGUAGGUUGUGUGGUU
hsa-let-7cbrain UGAGGUAGUAGGUUGUAUGGUU
hsa-let-7dbrain AGAGGUAGUAGGUUGCAUAGU
hsa-let-7ebrain UGAGGUAGGAGGUUGUAUAGU
hsa-let-7fbrain UGAGGUAGUAGAUUGUAUAGUU
hsa-miR-98brain UGAGGUAGUAAGUUGUAUUGUU
hsa-let-7gSZ UGAGGUAGUAGUUUGUACAGU
hsa-let-7ibrain UGAGGUAGUAGUUUGUGCUGU
miR-103/107 1178 1185 1A,m8 hsa-miR-103brain AGCAGCAUUGUACAGGGCUAUGA
hsa-miR-107brain AGCAGCAUUGUACAGGGCUAUCA
miR-124.1 435 441 1A hsa-miR-124a UUAAGGCACGCGGUGAAUGCCA
miR-138 168 174 m8 hsa-miR-138brain AGCUGGUGUUGUGAAUC
miR-142-3p 155 162 1A,m8 hsa-miR-142-3p UGUAGUGUUUCCUACUUUAUGGA
miR-143 457 463 1A hsa-miR-143brain UGAGAUGAAGCACUGUAGCUCA
miR-15/16/195/424/497 1019 1025 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
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-196 959 965 m8 hsa-miR-196a UAGGUAGUUUCAUGUUGUUGG
hsa-miR-196b UAGGUAGUUUCCUGUUGUUGG
miR-26 1317 1324 1A,m8 hsa-miR-26abrain UUCAAGUAAUCCAGGAUAGGC
hsa-miR-26bSZ UUCAAGUAAUUCAGGAUAGGUU