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BRAIN SUBSTANTIA NIGRA Show tissue menu
AMYGDALA BASAL GANGLIA CEREBELLUM CEREBRAL CORTEX CHOROID PLEXUS HIPPOCAMPAL FORMATION HYPOTHALAMUS MEDULLA OBLONGATA
MIDBRAIN OLFACTORY BULB PITUITARY GLAND PONS RETINA SPINAL CORD THALAMUS WHITE MATTER
PRIMARY MOUSE DATA
ANTIBODIES
AND
VALIDATION
Brain proteome
SUBSTANTIA NIGRA - Expression summary
Protein expression
Substantia nigrai

On the top, protein expression in current human tissue, based on all annotated cell types, is reported with the units not detected (n), low (l), medium (m) and high (h). Underneath, protein expression in each annotated cell type are reported using the same units.

Protein expression data is based on knowledge-based annotation. For genes where more than one antibody has been used, a collective score is set.

If knowledge-based annotation could not be performed for a gene, no data is displayed here. View antibody staining data further down this page.

h
m
l
n
Glial cells: Not detected
Neuronal cells: High
Neuronal projections: High
Synapses: High
RNA expressioni

A summary of mRNA expression data available for current tissue based on several datasets. The mRNA expression levels in human tissues are based on RNA-seq data generated by the Human Protein Atlas (HPA), Genotype-Tissue Expression (GTEx) portal and CAGE data generated by the FANTOM5 consortium. Consensus normalized expression levels for human tissues was created by combining the data from HPA and GTEx datasets.

The mRNA expression levels in pig are based on RNA-seq data generated by the Human Protein Atlas (HPA), and for mouse, HPA data and in situ hybridization generated by the Allen brain atlas are reported.

Scroll down to view mRNA expression data in more detail.
HPA Brain:133.7 nTPM
GTEx:95.8 nTPM
FANTOM5:1.7 Scaled Tags Per Million
Pig:393.2 nTPM

SUBSTANTIA NIGRA - Extended tissue profilei

For selected proteins extended tissue profiling is performed in addition to standard tissue microarrays. The section below contains results from the extended profiling.

, antibody HPA012763
Glial cells Not detected
Neuronal cells Not detected
Neuronal projections Medium
Synapses Not detected

SUBSTANTIA NIGRA - Extended tissue profilei

For selected proteins extended tissue profiling is performed in addition to standard tissue microarrays. The section below contains results from the extended profiling.

, antibody CAB016249
Glial cells Not detected
Neuronal cells Not detected
Neuronal projections High
Synapses Medium

SUBSTANTIA NIGRA - Extended tissue profilei

For selected proteins extended tissue profiling is performed in addition to standard tissue microarrays. The section below contains results from the extended profiling.

, antibody CAB078172
Glial cells Not detected
Neuronal cells High
Neuronal projections High
Synapses High

SUBSTANTIA NIGRA - HPA Brain RNA-seq
Max subtype nTPMi

Max subtype nTPM is the value for the subtype with the largest average nTPM across the subtype samples.

133.7
Sample id Sample description nTPM
Substantia nigra
nTPM: 133.7
2699 Male, age 18, unknown 306.5
1916 Female, age 42, unknown 279.1
2665 Male, age 74, both hemispheres 244.3
2241 Male, age 72, unknown 122.9
1851 Male, age 51, unknown 120.5
1941 Male, age 53, unknown 117.4
2409 Female, age 72, unknown 96.4
2590 Female, age 75, unknown 21.5
1889 Female, age 72, unknown 20.2
2583 Male, age 75, right hemisphere 7.6

SUBSTANTIA NIGRA - GTEx RNA-seqi

RNA-Seq data generated by the Genotype-Tissue Expression (GTEx) project from human tissues is reported as mean nTPM. More information can be found on the GTEx portal.

Distribution across the dataset is visualized with box plots, shown as median and 25th and 75th percentiles. Points are displayed as outliers if they are above or below 1.5 times the interquartile range. nTPM values of the individual samples are presented next to the box plot.
Max subtype nTPMi

Max subtype nTPM is the value for the subtype with the largest average nTPM across the subtype samples.

95.8
GTEx sample id Sample description nTPM
Brain - Substantia nigra
Average nTPM: 95.8
Samples: 139

Max nTPM: 423.7
Min nTPM: 0.0
Std nTPM: 112.4
Median nTPM: 50.3
GTEX-13OW6-0011-R2a-SM-5L3HG 50-59 years, male 423.7
GTEX-1313W-0011-R2a-SM-5EGLF 50-59 years, female 413.1
GTEX-1B8L1-0011-R2a-SM-9OSVL 60-69 years, male 387.2
GTEX-15ER7-0011-R2a-SM-6M46O 20-29 years, female 364.1
GTEX-13O3Q-0011-R2b-SM-5KM3K 50-59 years, male 363.3
GTEX-1LH75-0011-R2b-SM-EYYWQ 50-59 years, female 357.0
GTEX-15DYW-0011-R2b-SM-7KUKY 60-69 years, female 353.8
GTEX-15CHQ-0011-R2b-SM-6AJAD 60-69 years, male 324.3
GTEX-1HB9E-0011-R2b-SM-A96RW 50-59 years, male 323.2
GTEX-1EMGI-0011-R2b-SM-9OSVS 60-69 years, male 322.7
GTEX-1GN73-0011-R2a-SM-CJI2V 60-69 years, male 322.5
GTEX-11GSP-0011-R2b-SM-9QEGE 60-69 years, female 321.1
GTEX-1399T-0011-R2b-SM-5DUXM 60-69 years, male 319.1
GTEX-12WSD-0011-R2a-SM-5LZWB 60-69 years, female 308.0
GTEX-14BIN-0011-R2a-SM-5S2RJ 50-59 years, female 303.7
GTEX-12ZZX-0011-R2a-SM-5EGLG 40-49 years, female 282.8
GTEX-1B933-0011-R2b-SM-7IGNM 50-59 years, female 279.4
GTEX-1EKGG-0011-R2a-SM-CE6R8 60-69 years, male 263.2
GTEX-13OW8-0011-R2a-SM-5L3G2 60-69 years, male 254.7
GTEX-13G51-0011-R2b-SM-5LZXS 60-69 years, male 243.1
GTEX-13SLX-0011-R2b-SM-5S2VP 50-59 years, female 224.0
GTEX-XLM4-0011-R2B-SM-4AT5Z 60-69 years, male 214.3
GTEX-13O3O-0011-R2b-SM-5P9H1 60-69 years, female 213.3
GTEX-13FXS-0011-R2b-SM-5K7XX 50-59 years, male 210.3
GTEX-14BIM-0011-R2b-SM-69LQ6 60-69 years, female 197.4
GTEX-WHSE-0011-R2A-SM-3P5ZL 20-29 years, male 192.9
GTEX-X585-0011-R2B-SM-46MVF 50-59 years, male 183.1
GTEX-12WSF-0011-R2a-SM-5DUVU 70-79 years, male 182.8
GTEX-1F6I4-0011-R2a-SM-CL536 60-69 years, male 178.3
GTEX-T6MN-0011-R2A-SM-32QOW 50-59 years, male 168.9
GTEX-13RTJ-0011-R2a-SM-5PNW9 60-69 years, male 167.2
GTEX-11GSO-0011-R2a-SM-57WDF 60-69 years, male 163.6
GTEX-QMR6-0011-R2A-SM-32PKV 50-59 years, male 160.9
GTEX-T2IS-0011-R2A-SM-32QPF 20-29 years, female 160.1
GTEX-1LSNL-0011-R2a-SM-EZ6MK 50-59 years, male 149.7
GTEX-1GMR8-0011-R2a-SM-CE6RD 50-59 years, female 142.6
GTEX-14C5O-0011-R2a-SM-5ZZV2 60-69 years, male 142.5
GTEX-145LS-0011-R2a-SM-5PNZI 60-69 years, female 138.6
GTEX-15DCD-0011-R2b-SM-6LPIE 70-79 years, female 138.4
GTEX-11WQC-0011-R2a-SM-DO927 60-69 years, male 133.1
GTEX-1CB4G-0011-R2a-SM-9QEGQ 60-69 years, male 125.5
GTEX-1E1VI-0011-R2a-SM-9QEGS 50-59 years, male 122.0
GTEX-14ASI-0011-R2b-SM-5YY9H 60-69 years, male 115.7
GTEX-13N2G-0011-R2a-SM-5MR4Q 60-69 years, male 113.8
GTEX-1A3MX-0011-R2b-SM-7EWFL 60-69 years, male 110.3
GTEX-YFC4-0011-R2a-SM-4V6DZ 40-49 years, female 106.8
GTEX-13NYS-0011-R2b-SM-5MR4G 60-69 years, male 105.5
GTEX-11PRG-0011-R2a-SM-69LQ5 50-59 years, male 105.4
GTEX-T5JC-0011-R2A-SM-32PLZ 20-29 years, male 104.4
GTEX-15RJE-0011-R2b-SM-79OMP 40-49 years, male 96.8
GTEX-13QJC-0011-R2b-SM-5PNUN 60-69 years, female 91.0
GTEX-1IY9M-0011-R2a-SM-D4P29 60-69 years, male 90.7
GTEX-147GR-0011-R2b-SM-5S2RQ 60-69 years, male 88.1
GTEX-17EVP-0011-R2a-SM-7LG4W 40-49 years, male 77.5
GTEX-14JG1-0011-R2a-SM-5ZZVE 40-49 years, male 77.2
GTEX-14PJO-0011-R2a-SM-5ZZVF 60-69 years, male 75.8
GTEX-18464-0011-R2a-SM-731AL 50-59 years, male 74.7
GTEX-16Z82-0011-R2b-SM-79OK9 60-69 years, male 72.2
GTEX-1B996-0011-R2a-SM-7IGON 60-69 years, male 64.4
GTEX-1I1CD-0011-R2a-SM-CM2T3 60-69 years, female 64.2
GTEX-1GN2E-0011-R2a-SM-9WG7D 60-69 years, male 63.4
GTEX-NPJ7-0011-R2a-SM-2I3GF 60-69 years, female 62.0
GTEX-14PN4-0011-R2a-SM-6EU2Y 50-59 years, male 61.7
GTEX-1F6IF-0011-R2b-SM-9QEHB 60-69 years, male 58.7
GTEX-1H3O1-0011-R2b-SM-CKZOT 60-69 years, male 57.5
GTEX-1A8G7-0011-R2a-SM-7IGQI 60-69 years, male 55.4
GTEX-S7SE-0011-R2A-SM-2XCDC 50-59 years, male 55.3
GTEX-17HG3-0011-R2a-SM-7MGVX 30-39 years, female 54.5
GTEX-ZV68-0011-R2a-SM-4YCDK 50-59 years, female 51.0
GTEX-11EMC-0011-R2b-SM-DO114 60-69 years, female 50.3
GTEX-R55E-0011-R2A-SM-EYYV9 20-29 years, male 48.8
GTEX-13CF2-0011-R2a-SM-5L3DC 60-69 years, male 44.8
GTEX-QDT8-0011-R2A-SM-32PKQ 30-39 years, female 44.5
GTEX-P44G-0011-R2A-SM-2XCD2 30-39 years, male 41.8
GTEX-XMD1-0011-R2B-SM-4AT5N 60-69 years, male 37.8
GTEX-1LVAO-0011-R2a-SM-EYYX1 60-69 years, male 36.3
GTEX-1H1ZS-0011-R2b-SM-CL54Q 70-79 years, male 36.1
GTEX-NL4W-0011-R2a-SM-2I5GV 50-59 years, male 34.9
GTEX-11ZTS-0011-R2b-SM-5BC75 60-69 years, female 33.6
GTEX-RU72-0011-R2A-SM-2TF6O 50-59 years, female 33.1
GTEX-11GS4-0011-R2a-SM-DO942 60-69 years, male 29.7
GTEX-1I1GV-0011-R2a-SM-ARZLF 60-69 years, male 28.8
GTEX-1B8SG-0011-R2b-SM-79OOT 50-59 years, male 28.3
GTEX-1IL2U-0011-R2a-SM-ARU6V 60-69 years, male 28.2
GTEX-13X6K-0011-R2b-SM-5P9K3 60-69 years, female 27.8
GTEX-YJ89-0011-R2b-SM-4RGLT 60-69 years, male 27.6
GTEX-1EU9M-0011-R2b-SM-9QEH7 60-69 years, male 26.2
GTEX-NPJ8-0011-R2a-SM-2TC6M 40-49 years, male 22.0
GTEX-1C6VR-0011-R2a-SM-7RHGZ 60-69 years, male 20.6
GTEX-PWO3-0011-R2A-SM-2S1OX 60-69 years, female 19.1
GTEX-1IGQW-0011-R2b-SM-D4P26 60-69 years, male 17.8
GTEX-15EO6-0011-R2a-SM-6M46R 50-59 years, male 17.2
GTEX-12WSA-0011-R2a-SM-57WDK 60-69 years, male 16.9
GTEX-12WSH-0011-R2a-SM-5GU68 50-59 years, male 16.9
GTEX-13PDP-0011-R2b-SM-5O9DH 60-69 years, male 13.7
GTEX-ZAB4-0011-R2a-SM-4RGNP 40-49 years, male 12.4
GTEX-11TUW-0011-R2b-SM-DO92T 60-69 years, male 11.4
GTEX-1F48J-0011-R2a-SM-CL535 50-59 years, female 10.9
GTEX-13OVJ-0011-R2b-SM-5L3GP 50-59 years, female 10.8
GTEX-13X6I-0011-R2b-SM-5PNWQ 60-69 years, male 10.7
GTEX-131XH-0011-R2b-SM-5DUVY 50-59 years, male 10.5
GTEX-132Q8-0011-R2b-SM-5EQ5Z 60-69 years, male 8.1
GTEX-ZDXO-0011-R2b-SM-4WKFG 60-69 years, male 7.1
GTEX-1H23P-0011-R2a-SM-CKZP3 60-69 years, male 6.5
GTEX-1445S-0011-R2b-SM-5PNUH 60-69 years, male 5.7
GTEX-1GTWX-0011-R2b-SM-ADEH5 60-69 years, male 5.1
GTEX-1GZ2Q-0011-R2b-SM-9OSWO 40-49 years, male 4.9
GTEX-13SLW-0011-R2b-SM-5O9C6 70-79 years, male 4.1
GTEX-1H3VE-0011-R2a-SM-CE6SA 40-49 years, male 4.0
GTEX-1IKJJ-0011-R2b-SM-ARZLJ 60-69 years, male 3.9
GTEX-1F75B-0011-R2a-SM-ARL8I 50-59 years, male 3.1
GTEX-1HT8W-0011-R2a-SM-CMKH9 30-39 years, male 2.3
GTEX-1LVA9-0011-R2a-SM-EZ6MJ 50-59 years, male 2.2
GTEX-1IKOH-0011-R2a-SM-CMKHO 60-69 years, female 1.9
GTEX-1GN1U-0011-R2a-SM-CL53A 50-59 years, female 1.6
GTEX-1I1GS-0011-R2b-SM-CMKHG 60-69 years, male 1.6
GTEX-OHPN-0011-R2A-SM-2I5FB 60-69 years, female 1.5
GTEX-1MA7X-0011-R2b-SM-EZ6MT 60-69 years, male 1.4
GTEX-UTHO-0011-R2A-SM-3GIKC 60-69 years, male 1.2
GTEX-1RLM8-0011-R2a-SM-EZ6N4 50-59 years, male 1.2
GTEX-1HFI6-0011-R2a-SM-CMKH5 40-49 years, male 1.0
GTEX-1J1OQ-0011-R2b-SM-ARU88 40-49 years, female 0.9
GTEX-Z93S-0011-R2a-SM-4RGNG 50-59 years, male 0.7
GTEX-1JMQK-0011-R2a-SM-EYYXQ 60-69 years, male 0.6
GTEX-11UD1-0011-R2b-SM-5BC6O 40-49 years, female 0.4
GTEX-Q2AG-0011-R2A-SM-2HMIT 40-49 years, female 0.2
GTEX-1H1DG-0011-R2a-SM-ADEIQ 70-79 years, male 0.2
GTEX-1HR98-0011-R2a-SM-ARL7A 60-69 years, male 0.2
GTEX-139TS-0011-R2b-SM-5J1MX 60-69 years, male 0.1
GTEX-N7MS-0011-R2a-SM-2HML6 60-69 years, male 0.1
GTEX-N7MT-0011-R2a-SM-2I3GI 60-69 years, female 0.1
GTEX-OXRO-0011-R2A-SM-3NB1W 60-69 years, female 0.1
GTEX-11DZ1-0011-R2a-SM-DNZZM 50-59 years, male 0.1
GTEX-13NYB-0011-R2a-SM-5MR3C 40-49 years, male 0.0
GTEX-X4XX-0011-R2A-SM-3P623 60-69 years, male 0.0
GTEX-ZE9C-0011-R2a-SM-4WKGH 60-69 years, male 0.0
GTEX-1HSMO-0011-R2a-SM-CL553 60-69 years, male 0.0
GTEX-1J8Q2-0011-R2b-SM-EAZ2X 60-69 years, male 0.0
GTEX-1LB8K-0011-R2a-SM-EZ6MQ 50-59 years, male 0.0
Show allShow less

SUBSTANTIA NIGRA - FANTOM5 CAGEi

RNA expression in human tissues obtained through Cap Analysis of Gene Expression (CAGE) generated by the FANTOM5 project are reported as Scaled Tags Per Million.

Max subtype Scaled Tags Per Millioni

Max subtype Scaled Tags Per Million is the value for the subtype with the largest average Scaled Tags Per Million across the subtype samples.

1.7
FANTOM5 sample id Sample description Scaled Tags Per Million
Substantia nigra
Scaled Tags Per Million: 1.7
FF:10158-103A5 76 years, female 1.7

SUBSTANTIA NIGRA - Pig RNA-seqi

RNA-seq data obtained from pig brain is reported as nTPM .

Normal distribution across the dataset is visualized with box plots, shown as median and 25th and 75th percentiles. Points are displayed as outliers if they are above or below 1.5 times the interquartile range. nTPM values of the individual samples are presented next to the box plot.
Max subtype nTPMi

Max subtype nTPM is the value for the subtype with the largest average nTPM across the subtype samples.

393.2
Pig sample Sample description nTPM
Substantia nigra
nTPM: 393.2
Samples: 4

Max nTPM: 746.3
Min nTPM: 4.3
Sample A Female 569.0
Sample B Female 253.2
Sample C Male 746.3
Sample D Male 4.3

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