AutismKB 2.0

Annotation Detail for BRCA1


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Basic Information Top
Gene Symbol:BRCA1 ( BRCAI,BRCC1,BROVCA1,IRIS,PNCA4,PSCP,RNF53 )
Gene Full Name: breast cancer 1, early onset
Band: 17q21.31
Quick LinksEntrez ID:672; OMIM: 113705; Uniprot ID:BRCA1_HUMAN; ENSEMBL ID: ENSG00000012048; HGNC ID: 1100
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 body2 / 7076128
blastocyst3 / 6231948
fetus13 / 56401223
neonate0 / 310970 
infant3 / 23620127
juvenile1 / 5555617
adult34 / 193912117
Pool Name Gene EST/Total EST in pool Transcripts per million(TPM) Bar based on TPM
adrenal tumor1 / 1279478
bladder carcinoma2 / 17475114
breast (mammary gland) tumor1 / 9417810
cervical tumor2 / 3436658
chondrosarcoma2 / 8282324
colorectal tumor2 / 11424617
esophageal tumor0 / 172900 
gastrointestinal tumor4 / 11936933
germ cell tumor11 / 26384541
glioma1 / 1068839
head and neck tumor0 / 1363020 
kidney tumor2 / 6895929
leukemia1 / 9584210
liver tumor4 / 9635941
lung tumor3 / 10312729
lymphoma3 / 7175541
non-neoplasia1 / 9725010
normal69 / 336030720
ovarian tumor1 / 7668213
pancreatic tumor0 / 1046160 
primitive neuroectodermal tumor of the CNS6 / 12568047
prostate cancer2 / 10268019
retinoblastoma2 / 4635643
skin tumor20 / 124949160
soft tissue/muscle tissue tumor1 / 1251917
uterine tumor4 / 9025744
Pool Name Gene EST/Total EST in pool Transcripts per million(TPM) Bar based on TPM
adipose tissue0 / 131060 
adrenal gland1 / 3319730
ascites3 / 4001574
bladder2 / 2975767
blood1 / 1234788
bone1 / 7165513
bone marrow2 / 4880140
brain21 / 110098919
cervix2 / 4817141
connective tissue0 / 1492550 
ear0 / 162120 
embryonic tissue7 / 21572232
esophagus0 / 202090 
eye4 / 21105418
heart0 / 896260 
intestine4 / 23447217
kidney3 / 21177714
larynx0 / 241450 
liver8 / 20774338
lung7 / 33697420
lymph2 / 4427045
lymph node15 / 91610163
mammary gland5 / 15327132
mouth0 / 670520 
muscle4 / 10771537
nerve0 / 157680 
ovary4 / 10205139
pancreas4 / 21481218
parathyroid0 / 205390 
pharynx0 / 413280 
pituitary gland0 / 165850 
placenta1 / 2808253
prostate4 / 18934521
salivary gland0 / 201550 
skin20 / 21057494
spleen0 / 539520 
stomach0 / 966190 
testis10 / 33044230
thymus3 / 8113136
thyroid0 / 474730 
tonsil0 / 169990 
trachea0 / 524130 
umbilical cord0 / 136800 
uterus7 / 23287830
vascular0 / 517800 
Microarray in BioGPS Top
Select probe  
  • Microarray Platform: GeneAtlas U133A, gcrma
  • Affymatrix Probe ID: 204531_s_at
Cell line Expression level Expression bar
721_B_lymphoblasts30.45
Adipocyte9
AdrenalCortex10.85
Adrenalgland8.6
Amygdala8.85
Appendix15.55
AtrioventricularNode8.5
BDCA4+_DentriticCells8.95
Bonemarrow10.65
BronchialEpithelialCells8.4
CD105+_Endothelial46.4
CD14+_Monocytes9.05
CD19+_BCells(neg._sel.)9.6
CD33+_Myeloid16.05
CD34+23.5
CD4+_Tcells8.65
CD56+_NKCells9.65
CD71+_EarlyErythroid17.25
CD8+_Tcells7.55
CardiacMyocytes15.1
Caudatenucleus9.2
Cerebellum7.8
CerebellumPeduncles11.8
CiliaryGanglion7.65
CingulateCortex10.1
Colorectaladenocarcinoma19.25
DorsalRootGanglion9.65
FetalThyroid12.1
Fetalbrain8.4
Fetalliver9.1
Fetallung6.8
GlobusPallidus7.45
Heart15.85
Hypothalamus9.65
Kidney7.95
Leukemia_chronicMyelogenousK-56225.6
Leukemia_promyelocytic-HL-6019.9
Leukemialymphoblastic(MOLT-4)60.15
Liver16.35
Lung11
Lymphnode10.45
Lymphoma_burkitts(Daudi)83.35
Lymphoma_burkitts(Raji)20.9
MedullaOblongata8.6
OccipitalLobe8.45
OlfactoryBulb7.1
Ovary7.15
Pancreas7.7
PancreaticIslet10.15
ParietalLobe11.4
Pituitary11
Placenta9
Pons13.1
PrefrontalCortex10.9
Prostate10.25
Salivarygland8.35
SkeletalMuscle13.7
Skin7.9
SmoothMuscle10.6
Spinalcord9.25
SubthalamicNucleus9.5
SuperiorCervicalGanglion23.05
TemporalLobe9.75
Testis8.75
TestisGermCell14.95
TestisIntersitial12.75
TestisLeydigCell19.45
TestisSeminiferousTubule9.95
Thalamus9.4
Thymus7.1
Thyroid11.4
Tongue10.65
Tonsil9.75
Trachea7.7
TrigeminalGanglion13.55
Uterus7.15
UterusCorpus9.1
WholeBlood10.1
Wholebrain7.1
colon10.7
pineal_day10.96
pineal_night10.66
retina11.475
small_intestine8.9
Allen Brain Atlas Top
Human Whole Brain Microarrayview in Allen Brain Atlas
  • Probe id     Donor id      
  • Probe name: CUST_114_PI416408490
  • 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
Amygdala2.87 ± 0.86
Basal Forebrain2.49 ± 0.52
Basal Part of Pons3.09 ± 0.55
Cerebellar Cortex2.26 ± 0.55
Cerebellar Nuclei3.05 ± 0.86
Claustrum2.94 ± 0.6
Epithalamus3.47 ± 0.82
Frontal Lobe2.74 ± 0.71
Globus Pallidus4.45 ± 0.27
Hypothalamus2.76 ± 0.41
Insula2.41 ± 0.64
Limbic Lobe2.5 ± 0.71
Mesencephalon3.09 ± 0.77
Myelencephalon2.84 ± 0.71
Occipital Lobe2.95 ± 0.7
Parietal Lobe3.01 ± 0.64
Pontine Tegmentum2.9 ± 0.85
Striatum3.47 ± 0.4
Subthalamus2.72 ± 0.64
Temporal Lobe2.68 ± 0.86
Thalamus3 ± 0.71
White Matter4.95 ± 0.28
Mouse Brain ISH
Gene Symbol Brain Structure ID Brain Structure Name Express Desity/Level (Meatured by ISH) Express Bar
Brca1CBCerebellum0.99
1.1
Brca1CTXCerebral cortex1.41
1.28
Brca1HIPHippocampal region0.34
0.36
Brca1HPFHippocampal formation0.65
0.58
Brca1HYHypothalamus0.82
0.36
Brca1LSXLateral septal complex0.47
0.19
Brca1MBMidbrain0.92
0.8
Brca1MYMedulla3.54
3.54
Brca1OLFOlfactory bulb3.62
2.51
Brca1PPons1.52
1.16
Brca1PALPallidum0.25
0.12
Brca1RHPRetrohippocampal region1.15
0.89
Brca1sAMYStriatum-like amygdalar nuclei0.86
0.42
Brca1STRStriatum0.53
0.49
Brca1STRdStriatum dorsal region0.35
0.4
Brca1STRvStriatum ventral region0.68
0.65
Brca1THThalamus0.64
1.31
Peptide Top
Peptide Name Peptide Lengh Peptide Start Peptide End Peptide Sequence Source
PAp00497947 25 1531 1555 VVDVEEQQLEESGPHDLTETSYLPR 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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