AutismKB 2.0

Annotation Detail for HMGB1


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Basic Information Top
Gene Symbol:HMGB1 ( DKFZp686A04236,HMG1,HMG3,SBP-1 )
Gene Full Name: high-mobility group box 1
Band: 13q12.3
Quick LinksEntrez ID:3146; OMIM: 163905; Uniprot ID:HMGB1_HUMAN; ENSEMBL ID: ENSG00000189403; HGNC ID: 4983
Relate to Another Database: SFARIGene; denovo-db
Unigene EST Top
Pool Name Gene EST/Total EST in pool Transcripts per million(TPM) Bar based on TPM
embryoid body11 / 70761155
blastocyst3 / 6231948
fetus65 / 564012115
neonate0 / 310970 
infant2 / 2362084
juvenile7 / 55556125
adult193 / 193912199
embryoid body25 / 70761353
blastocyst24 / 62319385
fetus38 / 56401267
neonate3 / 3109796
infant1 / 2362042
juvenile7 / 55556125
adult96 / 193912149
embryoid body6 / 7076184
blastocyst4 / 6231964
fetus15 / 56401226
neonate0 / 310970 
infant0 / 236200 
juvenile5 / 5555689
adult94 / 193912148
Pool Name Gene EST/Total EST in pool Transcripts per million(TPM) Bar based on TPM
adrenal tumor3 / 12794234
bladder carcinoma11 / 17475629
breast (mammary gland) tumor8 / 9417884
cervical tumor2 / 3436658
chondrosarcoma1 / 8282312
colorectal tumor16 / 114246140
esophageal tumor1 / 1729057
gastrointestinal tumor15 / 119369125
germ cell tumor40 / 263845151
glioma16 / 106883149
head and neck tumor13 / 13630295
kidney tumor3 / 6895943
leukemia11 / 95842114
liver tumor11 / 96359114
lung tumor7 / 10312767
lymphoma12 / 71755167
non-neoplasia2 / 9725020
normal270 / 336030780
ovarian tumor3 / 7668239
pancreatic tumor8 / 10461676
primitive neuroectodermal tumor of the CNS14 / 125680111
prostate cancer21 / 102680204
retinoblastoma3 / 4635664
skin tumor10 / 12494980
soft tissue/muscle tissue tumor9 / 12519171
uterine tumor16 / 90257177
adrenal tumor6 / 12794468
bladder carcinoma3 / 17475171
breast (mammary gland) tumor5 / 9417853
cervical tumor4 / 34366116
chondrosarcoma3 / 8282336
colorectal tumor18 / 114246157
esophageal tumor2 / 17290115
gastrointestinal tumor18 / 119369150
germ cell tumor85 / 263845322
glioma4 / 10688337
head and neck tumor1 / 1363027
kidney tumor8 / 68959116
leukemia16 / 95842166
liver tumor13 / 96359134
lung tumor14 / 103127135
lymphoma16 / 71755222
non-neoplasia4 / 9725041
normal300 / 336030789
ovarian tumor1 / 7668213
pancreatic tumor11 / 104616105
primitive neuroectodermal tumor of the CNS14 / 125680111
prostate cancer8 / 10268077
retinoblastoma22 / 46356474
skin tumor36 / 124949288
soft tissue/muscle tissue tumor18 / 125191143
uterine tumor3 / 9025733
adrenal tumor1 / 1279478
bladder carcinoma2 / 17475114
breast (mammary gland) tumor8 / 9417884
cervical tumor2 / 3436658
chondrosarcoma9 / 82823108
colorectal tumor14 / 114246122
esophageal tumor0 / 172900 
gastrointestinal tumor9 / 11936975
germ cell tumor15 / 26384556
glioma1 / 1068839
head and neck tumor0 / 1363020 
kidney tumor1 / 6895914
leukemia4 / 9584241
liver tumor8 / 9635983
lung tumor6 / 10312758
lymphoma2 / 7175527
non-neoplasia1 / 9725010
normal101 / 336030730
ovarian tumor0 / 766820 
pancreatic tumor9 / 10461686
primitive neuroectodermal tumor of the CNS10 / 12568079
prostate cancer4 / 10268038
retinoblastoma4 / 4635686
skin tumor4 / 12494932
soft tissue/muscle tissue tumor2 / 12519115
uterine tumor0 / 902570 
Pool Name Gene EST/Total EST in pool Transcripts per million(TPM) Bar based on TPM
adipose tissue1 / 1310676
adrenal gland5 / 33197150
ascites7 / 40015174
bladder11 / 29757369
blood12 / 12347897
bone11 / 71655153
bone marrow4 / 4880181
brain49 / 110098944
cervix3 / 4817162
connective tissue2 / 14925513
ear5 / 16212308
embryonic tissue29 / 215722134
esophagus1 / 2020949
eye7 / 21105433
heart15 / 89626167
intestine33 / 234472140
kidney17 / 21177780
larynx1 / 2414541
liver22 / 207743105
lung38 / 336974112
lymph2 / 4427045
lymph node11 / 91610120
mammary gland16 / 153271104
mouth8 / 67052119
muscle4 / 10771537
nerve2 / 15768126
ovary6 / 10205158
pancreas26 / 214812121
parathyroid12 / 20539584
pharynx2 / 4132848
pituitary gland2 / 16585120
placenta28 / 28082599
prostate32 / 189345169
salivary gland3 / 20155148
skin18 / 21057485
spleen3 / 5395255
stomach13 / 96619134
testis37 / 330442111
thymus4 / 8113149
thyroid6 / 47473126
tonsil4 / 16999235
trachea0 / 524130 
umbilical cord0 / 136800 
uterus34 / 232878145
vascular2 / 5178038
adipose tissue4 / 13106305
adrenal gland6 / 33197180
ascites4 / 4001599
bladder8 / 29757268
blood22 / 123478178
bone1 / 7165513
bone marrow14 / 48801286
brain54 / 110098949
cervix4 / 4817183
connective tissue3 / 14925520
ear0 / 162120 
embryonic tissue88 / 215722407
esophagus2 / 2020998
eye29 / 211054137
heart7 / 8962678
intestine26 / 234472110
kidney13 / 21177761
larynx1 / 2414541
liver34 / 207743163
lung23 / 33697468
lymph14 / 44270316
lymph node4 / 9161043
mammary gland5 / 15327132
mouth0 / 670520 
muscle12 / 107715111
nerve1 / 1576863
ovary6 / 10205158
pancreas16 / 21481274
parathyroid4 / 20539194
pharynx7 / 41328169
pituitary gland4 / 16585241
placenta19 / 28082567
prostate15 / 18934579
salivary gland2 / 2015599
skin41 / 210574194
spleen4 / 5395274
stomach12 / 96619124
testis40 / 330442121
thymus4 / 8113149
thyroid0 / 474730 
tonsil12 / 16999705
trachea1 / 5241319
umbilical cord2 / 13680146
uterus17 / 23287872
vascular3 / 5178057
adipose tissue0 / 131060 
adrenal gland1 / 3319730
ascites3 / 4001574
bladder3 / 29757100
blood3 / 12347824
bone7 / 7165597
bone marrow1 / 4880120
brain21 / 110098919
cervix2 / 4817141
connective tissue10 / 14925566
ear0 / 162120 
embryonic tissue18 / 21572283
esophagus0 / 202090 
eye6 / 21105428
heart4 / 8962644
intestine21 / 23447289
kidney2 / 2117779
larynx4 / 24145165
liver17 / 20774381
lung13 / 33697438
lymph0 / 442700 
lymph node2 / 9161021
mammary gland11 / 15327171
mouth0 / 670520 
muscle5 / 10771546
nerve3 / 15768190
ovary0 / 1020510 
pancreas13 / 21481260
parathyroid0 / 205390 
pharynx0 / 413280 
pituitary gland0 / 165850 
placenta14 / 28082549
prostate5 / 18934526
salivary gland1 / 2015549
skin5 / 21057423
spleen2 / 5395237
stomach2 / 9661920
testis6 / 33044218
thymus0 / 811310 
thyroid0 / 474730 
tonsil1 / 1699958
trachea0 / 524130 
umbilical cord0 / 136800 
uterus7 / 23287830
vascular1 / 5178019
Microarray in BioGPS Top
Select probe  
  • Microarray Platform: GeneAtlas U133A, gcrma
  • Affymatrix Probe ID: 214938_x_at
Cell line Expression level Expression bar
721_B_lymphoblasts6121.05
Adipocyte1251.65
AdrenalCortex1037.1
Adrenalgland626.75
Amygdala2804.2
Appendix1508.45
AtrioventricularNode229.6
BDCA4+_DentriticCells4447.3
Bonemarrow2543.1
BronchialEpithelialCells1871.15
CD105+_Endothelial7744.4
CD14+_Monocytes2895.25
CD19+_BCells(neg._sel.)3529.5
CD33+_Myeloid4727.65
CD34+9755.65
CD4+_Tcells3494.65
CD56+_NKCells4096.9
CD71+_EarlyErythroid5792.6
CD8+_Tcells3085.95
CardiacMyocytes2106.3
Caudatenucleus1510
Cerebellum685.45
CerebellumPeduncles1117.25
CiliaryGanglion455.7
CingulateCortex1243.75
Colorectaladenocarcinoma3873.45
DorsalRootGanglion808.45
FetalThyroid2760.2
Fetalbrain4150.35
Fetalliver2141.55
Fetallung1649.8
GlobusPallidus629.4
Heart132.9
Hypothalamus3225.6
Kidney621.95
Leukemia_chronicMyelogenousK-5621519
Leukemia_promyelocytic-HL-603991.15
Leukemialymphoblastic(MOLT-4)4700.05
Liver224.4
Lung712.95
Lymphnode1741.45
Lymphoma_burkitts(Daudi)3959.5
Lymphoma_burkitts(Raji)2605.35
MedullaOblongata1276.45
OccipitalLobe2137.95
OlfactoryBulb1808.1
Ovary953.8
Pancreas1649.4
PancreaticIslet1404.4
ParietalLobe1303.4
Pituitary2366.6
Placenta884.45
Pons884.7
PrefrontalCortex3844.05
Prostate2571.05
Salivarygland1092.05
SkeletalMuscle593.05
Skin535.75
SmoothMuscle1645.35
Spinalcord2202.5
SubthalamicNucleus1041.45
SuperiorCervicalGanglion486.05
TemporalLobe1163.2
Testis726.75
TestisGermCell1492.55
TestisIntersitial633.4
TestisLeydigCell599.7
TestisSeminiferousTubule822.55
Thalamus1410.95
Thymus2635.95
Thyroid2993.85
Tongue1256.8
Tonsil3143.85
Trachea1606.8
TrigeminalGanglion517.2
Uterus2647
UterusCorpus1080.55
WholeBlood2106.55
Wholebrain1415.7
colon2857.4
pineal_day3267.02
pineal_night3792.08
retina2340.8
small_intestine3251.65
Allen Brain Atlas Top
Human Whole Brain Microarrayview in Allen Brain Atlas
  • Probe id     Donor id      
  • Probe name: A_24_P109962
  • Donor H0351.2001
  • Sex: Male     Age: 24 years     Race/Ethnicity: African American     Handedness: Left
  • Tissue Receipt Date: 7/29/2009     Serology: Pass      Tissue pH :6.72     Additional Medical Information :History of asthma
  • Postmortem Interval: 23 hours (estimated time of death to time that tissue is frozen)
  • Toxicology: Positive for atropine and caffeine, at levels usually not toxicologically significant
Tissue Expression(mean ± stddev) Expression Bar
Amygdala11.05 ± 0.18
Basal Forebrain11.03 ± 0.25
Basal Part of Pons10.68 ± 0.14
Cerebellar Cortex10.87 ± 0.15
Cerebellar Nuclei10.92 ± 0.22
Claustrum11 ± 0.13
Epithalamus11.29 ± 0.15
Frontal Lobe10.83 ± 0.23
Globus Pallidus11.49 ± 0.15
Hypothalamus10.88 ± 0.33
Insula10.86 ± 0.23
Limbic Lobe10.78 ± 0.2
Mesencephalon10.95 ± 0.22
Myelencephalon10.92 ± 0.24
Occipital Lobe10.92 ± 0.17
Parietal Lobe10.89 ± 0.21
Pontine Tegmentum10.96 ± 0.2
Striatum10.92 ± 0.16
Subthalamus10.84 ± 0.16
Temporal Lobe10.9 ± 0.2
Thalamus10.96 ± 0.14
White Matter11.7 ± 0.15
Mouse Brain ISH
Gene Symbol Brain Structure ID Brain Structure Name Express Desity/Level (Meatured by ISH) Express Bar
Hmgb1CBCerebellum17.03
24.69
Hmgb1CTXCerebral cortex100
92.34
Hmgb1HIPHippocampal region100
100
Hmgb1HPFHippocampal formation92.26
100
Hmgb1HYHypothalamus55.56
47.51
Hmgb1LSXLateral septal complex43.64
32.91
Hmgb1MBMidbrain33.79
32.52
Hmgb1MYMedulla21.59
24.71
Hmgb1OLFOlfactory bulb76.93
75.28
Hmgb1PPons28.28
33.12
Hmgb1PALPallidum53.48
49.87
Hmgb1RHPRetrohippocampal region65.79
62.72
Hmgb1sAMYStriatum-like amygdalar nuclei65.45
58.17
Hmgb1STRStriatum56.78
45.46
Hmgb1STRdStriatum dorsal region55.93
44.7
Hmgb1STRvStriatum ventral region60.58
45.46
Hmgb1THThalamus56.85
53.19
Peptide Top
Peptide Name Peptide Lengh Peptide Start Peptide End Peptide Sequence Source
HMGB1_HUMAN_0 0 0 0 GEHPGLSIGDVAK PRIDE
HMGB1_HUMAN_0 0 0 0 IKGEHPGLSIGDVAK PRIDE
HMGB1_HUMAN_0 0 0 0 KHPDASVNFSEFSK PRIDE
HMGB1_HUMAN_0 0 0 0 LGEMWNNTAADDKQPYEK PRIDE
HMGB1_HUMAN_1 9 1 9 GKGDPKKPR PRIDE
HMGB1_HUMAN_112 15 112 126 IKGEHPGLSIGDVAK PRIDE
HMGB1_HUMAN_112 16 112 127 IKGEHPGLSIGDVAKK PRIDE
HMGB1_HUMAN_114 13 114 126 GEHPGLSIGDVAK PRIDE
HMGB1_HUMAN_114 14 114 127 GEHPGLSIGDVAKK PRIDE
HMGB1_HUMAN_12 12 12 23 MSSYAFFVQTCR PRIDE
HMGB1_HUMAN_12 16 12 27 MSSYAFFVQTCREEHK PRIDE
HMGB1_HUMAN_12 17 12 28 MSSYAFFVQTCREEHKK PRIDE
HMGB1_HUMAN_127 14 127 140 KLGEMWNNTAADDK PRIDE
HMGB1_HUMAN_127 19 127 145 KLGEMWNNTAADDKQPYEK PRIDE
HMGB1_HUMAN_128 13 128 140 LGEMWNNTAADDK PRIDE
HMGB1_HUMAN_128 18 128 145 LGEMWNNTAADDKQPYEK PRIDE
HMGB1_HUMAN_128 19 128 146 LGEMWNNTAADDKQPYEKK PRIDE
HMGB1_HUMAN_152 11 152 162 EKYEKDIAAYR PRIDE
HMGB1_HUMAN_154 9 154 162 YEKDIAAYR PRIDE
HMGB1_HUMAN_2 9 2 10 GKGDPKKPR PRIDE
HMGB1_HUMAN_28 15 28 42 KKHPDASVNFSEFSK PRIDE
HMGB1_HUMAN_29 14 29 42 KHPDASVNFSEFSK PRIDE
HMGB1_HUMAN_29 15 29 43 KHPDASVNFSEFSKK PRIDE
HMGB1_HUMAN_30 13 30 42 HPDASVNFSEFSK PRIDE
HMGB1_HUMAN_30 14 30 43 HPDASVNFSEFSKK PRIDE
HMGB1_HUMAN_57 13 57 69 GKFEDMAKADKAR PRIDE
HMGB1_HUMAN_57 8 57 64 GKFEDMAK PRIDE
HMGB1_HUMAN_76 10 76 85 TYIPPKGETK PRIDE
HMGB1_HUMAN_96 16 96 111 RPPSAFFLFCSEYRPK PRIDE
PAp00002481 10 103 112 FLFCSEYRPK Peptide Atlas

Simple Query:


  (e.g. CHD8)

Syndromic Genes

Non-syndromic Genes

AutismKB Statistics

  • Studies: 1,036
  • Genes: 1,379
  • CNVs/SVs: 5,420
  • SNVs/Indels: 11,669
  • de novo Mutations: 5,669
  • Mosaics: 789
  • Linkage Regions: 172
  • Paper Collected: 6/30/2018
  • Last Update: 8/26/2018


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