AutismKB 2.0

Annotation Detail for LCN2


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Basic Information Top
Gene Symbol:LCN2 ( 24p3,MSFI,NGAL )
Gene Full Name: lipocalin 2
Band: 9q34.11
Quick LinksEntrez ID:3934; OMIM: 600181; Uniprot ID:NGAL_HUMAN; ENSEMBL ID: ENSG00000148346; HGNC ID: 6526
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 body0 / 707610 
blastocyst0 / 623190 
fetus19 / 56401233
neonate0 / 310970 
infant0 / 236200 
juvenile0 / 555560 
adult180 / 193912192
Pool Name Gene EST/Total EST in pool Transcripts per million(TPM) Bar based on TPM
adrenal tumor0 / 127940 
bladder carcinoma0 / 174750 
breast (mammary gland) tumor1 / 9417810
cervical tumor1 / 3436629
chondrosarcoma0 / 828230 
colorectal tumor36 / 114246315
esophageal tumor4 / 17290231
gastrointestinal tumor26 / 119369217
germ cell tumor0 / 2638450 
glioma0 / 1068830 
head and neck tumor17 / 136302124
kidney tumor0 / 689590 
leukemia40 / 95842417
liver tumor1 / 9635910
lung tumor5 / 10312748
lymphoma0 / 717550 
non-neoplasia4 / 9725041
normal100 / 336030729
ovarian tumor30 / 76682391
pancreatic tumor60 / 104616573
primitive neuroectodermal tumor of the CNS0 / 1256800 
prostate cancer1 / 1026809
retinoblastoma0 / 463560 
skin tumor0 / 1249490 
soft tissue/muscle tissue tumor3 / 12519123
uterine tumor8 / 9025788
Pool Name Gene EST/Total EST in pool Transcripts per million(TPM) Bar based on TPM
adipose tissue0 / 131060 
adrenal gland0 / 331970 
ascites1 / 4001524
bladder0 / 297570 
blood54 / 123478437
bone1 / 7165513
bone marrow9 / 48801184
brain1 / 11009890 
cervix2 / 4817141
connective tissue4 / 14925526
ear0 / 162120 
embryonic tissue1 / 2157224
esophagus5 / 20209247
eye8 / 21105437
heart0 / 896260 
intestine54 / 234472230
kidney2 / 2117779
larynx1 / 2414541
liver1 / 2077434
lung16 / 33697447
lymph0 / 442700 
lymph node8 / 9161087
mammary gland5 / 15327132
mouth5 / 6705274
muscle1 / 1077159
nerve0 / 157680 
ovary30 / 102051293
pancreas65 / 214812302
parathyroid0 / 205390 
pharynx13 / 41328314
pituitary gland0 / 165850 
placenta0 / 2808250 
prostate15 / 18934579
salivary gland0 / 201550 
skin0 / 2105740 
spleen0 / 539520 
stomach48 / 96619496
testis0 / 3304420 
thymus0 / 811310 
thyroid1 / 4747321
tonsil0 / 169990 
trachea3 / 5241357
umbilical cord0 / 136800 
uterus8 / 23287834
vascular0 / 517800 
Microarray in BioGPS Top
Select probe  
  • Microarray Platform: GeneAtlas U133A, gcrma
  • Affymatrix Probe ID: 212531_at
Cell line Expression level Expression bar
721_B_lymphoblasts9.15
Adipocyte29.2
AdrenalCortex24.25
Adrenalgland19.6
Amygdala24.35
Appendix24.3
AtrioventricularNode15.05
BDCA4+_DentriticCells7.3
Bonemarrow8687.25
BronchialEpithelialCells365.5
CD105+_Endothelial16.4
CD14+_Monocytes18.2
CD19+_BCells(neg._sel.)7.65
CD33+_Myeloid22.05
CD34+25.45
CD4+_Tcells8.2
CD56+_NKCells10.15
CD71+_EarlyErythroid18.05
CD8+_Tcells6.8
CardiacMyocytes21.85
Caudatenucleus21
Cerebellum25.45
CerebellumPeduncles40.8
CiliaryGanglion11.3
CingulateCortex28.85
Colorectaladenocarcinoma337.15
DorsalRootGanglion17.05
FetalThyroid19.1
Fetalbrain23.45
Fetalliver60.95
Fetallung1295.4
GlobusPallidus16.9
Heart76.4
Hypothalamus17.8
Kidney31.1
Leukemia_chronicMyelogenousK-56221.05
Leukemia_promyelocytic-HL-6020.5
Leukemialymphoblastic(MOLT-4)18.65
Liver36.4
Lung161.05
Lymphnode19.95
Lymphoma_burkitts(Daudi)21
Lymphoma_burkitts(Raji)32.25
MedullaOblongata25.9
OccipitalLobe20.85
OlfactoryBulb18.4
Ovary15
Pancreas422.95
PancreaticIslet5758.7
ParietalLobe26.55
Pituitary33.7
Placenta24
Pons34.25
PrefrontalCortex29.45
Prostate145.75
Salivarygland1326.75
SkeletalMuscle43.7
Skin17.85
SmoothMuscle23.1
Spinalcord37.65
SubthalamicNucleus21.25
SuperiorCervicalGanglion23.2
TemporalLobe21.3
Testis20.4
TestisGermCell19.75
TestisIntersitial22.1
TestisLeydigCell18.4
TestisSeminiferousTubule20.1
Thalamus23.7
Thymus57.25
Thyroid25.85
Tongue549.6
Tonsil489.6
Trachea3268.2
TrigeminalGanglion22.85
Uterus19.3
UterusCorpus58.05
WholeBlood172.3
Wholebrain16.45
colon297.2
pineal_day17.68
pineal_night16.14
retina28.125
small_intestine22.7
Allen Brain Atlas Top
Human Whole Brain Microarrayview in Allen Brain Atlas
  • Probe id     Donor id      
  • Probe name: CUST_15669_PI416261804
  • 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
Amygdala2.28 ± 1.02
Basal Forebrain1.89 ± 0.27
Basal Part of Pons1.52 ± 0.33
Cerebellar Cortex1.65 ± 0.69
Cerebellar Nuclei2.15 ± 0.71
Claustrum2.73 ± 0.86
Epithalamus1.56 ± 0.77
Frontal Lobe1.68 ± 0.73
Globus Pallidus2.4 ± 0.27
Hypothalamus1.9 ± 0.68
Insula1.77 ± 0.59
Limbic Lobe1.81 ± 0.59
Mesencephalon2 ± 0.67
Myelencephalon1.86 ± 0.67
Occipital Lobe1.83 ± 0.44
Parietal Lobe1.77 ± 0.57
Pontine Tegmentum1.88 ± 0.67
Striatum2.03 ± 0.52
Subthalamus2.04 ± 0.7
Temporal Lobe1.78 ± 0.65
Thalamus1.8 ± 0.57
White Matter2.32 ± 0.24
Mouse Brain ISH
Gene Symbol Brain Structure ID Brain Structure Name Express Desity/Level (Meatured by ISH) Express Bar
Lcn2CBCerebellum0
0
Lcn2CTXCerebral cortex0
0
Lcn2HIPHippocampal region0
0
Lcn2HPFHippocampal formation0
0
Lcn2HYHypothalamus0
0
Lcn2LSXLateral septal complex0
0
Lcn2MBMidbrain0
0
Lcn2MYMedulla0
0
Lcn2OLFOlfactory bulb0
0
Lcn2PPons0
0
Lcn2PALPallidum0
0
Lcn2RHPRetrohippocampal region0
0
Lcn2sAMYStriatum-like amygdalar nuclei0
0
Lcn2STRStriatum0
0
Lcn2STRdStriatum dorsal region0
0
Lcn2STRvStriatum ventral region0
0
Lcn2THThalamus0
0
Peptide Top
Peptide Name Peptide Lengh Peptide Start Peptide End Peptide Sequence Source
NGAL_HUMAN_56 8 56 63 LAGNAILR PRIDE
PAp00024843 13 80 92 EDKSYNVTSVLFR 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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