E16.5_E1S1.MOSTA Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Adipose tissue 9.6544e-01 6.9921e-01
Adrenal gland 3.6902e-01 4.4669e-01
Bone 9.9280e-01 6.9308e-01
Brain 5.1527e-26 1.2053e-15
Cartilage 9.9993e-01 2.4000e-01
Cartilage primordium 2.2454e-05 3.3773e-02
Cavity 9.9996e-01 8.0438e-01
Choroid plexus 6.9592e-10 5.1547e-06
Connective tissue 2.2180e-03 3.5259e-01
Dorsal root ganglion 1.1088e-11 6.5161e-09
Epidermis 1.0000e+00 9.9235e-01
GI tract 2.9548e-03 2.7980e-01
Heart 7.0407e-01 5.6915e-01
Inner ear 2.2317e-05 1.4350e-03
Jaw and tooth 1.0891e-05 7.7011e-02
Kidney 3.8745e-03 4.7718e-02
Liver 9.9691e-01 9.4123e-01
Lung 5.4170e-03 2.9359e-02
Meninges 7.2034e-05 1.4966e-01
Mucosal epithelium 1.5267e-05 7.6137e-03
Muscle 4.6005e-05 7.8008e-03
Smooth muscle 9.9938e-01 9.4992e-01
Spinal cord 1.9761e-21 1.6149e-13
Submandibular gland 9.9864e-01 7.8465e-01
Sympathetic nerve 8.2282e-09 5.4611e-07

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
MAP2 Expression Distribution
Gene Specificity Score (GSS)
MAP2 GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
MAP2 Spinal cord 6.8789 0.9471
DCX Brain 6.0938 0.9255
CDK5R1 Brain 5.4141 0.9223
NSG2 Brain 6.0117 0.9220
ELAVL3 Brain 5.3438 0.9217
CNIH2 Spinal cord 5.6523 0.9195
CRMP1 Spinal cord 6.4258 0.9174
CELF4 Brain 5.9609 0.9151
MYT1L Brain 4.6562 0.9138
MLLT11 Spinal cord 6.0703 0.9120
MAPT Spinal cord 7.7773 0.9118
RAB3C Spinal cord 4.4414 0.9087
ACTL6B Brain 2.7930 0.9074
SNRPN Spinal cord 7.1953 0.9061
SOGA3 Dorsal root ganglion 3.4609 0.9052
PAK5 Brain 2.4902 0.9047
APBA2 Brain 2.8574 0.9045
RUFY3 Brain 4.3672 0.9043
HECW1 Brain 2.9980 0.9043
ATCAY Brain 2.4355 0.9034
NOL4 Brain 2.2656 0.8993
DPYSL5 Brain 3.8086 0.8990
RTN1 Spinal cord 6.7461 0.8964
FNBP1L Brain 4.4648 0.8960
GNAO1 Spinal cord 5.2656 0.8958
KIF5C Sympathetic nerve 3.8438 0.8954
NSG1 Spinal cord 4.8867 0.8942
INA Spinal cord 7.1406 0.8936
GNG3 Dorsal root ganglion 6.4727 0.8930
APC2 Brain 2.7285 0.8915
JAKMIP2 Dorsal root ganglion 2.6504 0.8914
ASTN1 Brain 2.6270 0.8906
CTNNA2 Dorsal root ganglion 6.6250 0.8905
GABRB3 Spinal cord 2.9238 0.8901
HDGFL3 Spinal cord 3.4902 0.8899
GPM6A Spinal cord 5.2148 0.8898
RAB3A Spinal cord 5.2773 0.8897
CSRNP3 Brain 3.1992 0.8887
GDAP1 Brain 2.4219 0.8886
TUBB3 Sympathetic nerve 6.2031 0.8878
ATAT1 Brain 3.1367 0.8873
GNG2 Brain 3.9102 0.8867
GPRIN1 Spinal cord 2.5977 0.8866
GDI1 Brain 3.6328 0.8866
SCG5 Spinal cord 3.1426 0.8862
MAPK10 Sympathetic nerve 2.9941 0.8853
STMN4 Brain 4.8750 0.8848
MAP9 Brain 2.5508 0.8835
SBK1 Brain 4.1855 0.8825
PAK3 Spinal cord 3.7188 0.8823

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.70

Parameters:

  • Sample Name: E16.5_E1S1.MOSTA
  • Trait Name: IQ
  • Summary Statistics File: gsMap_example_data/GWAS/IQ_NG_2018.sumstats.gz
  • HDF5 Path: example/Mouse_Embryo/E16.5_E1S1.MOSTA/find_latent_representations/E16.5_E1S1.MOSTA_add_latent.h5ad
  • Annotation: annotation
  • Spatial LDSC Save Directory: example/Mouse_Embryo/E16.5_E1S1.MOSTA/spatial_ldsc
  • Cauchy Directory: example/Mouse_Embryo/E16.5_E1S1.MOSTA/cauchy_combination
  • Report Directory: example/Mouse_Embryo/E16.5_E1S1.MOSTA/report/IQ
  • gsMap Report File: example/Mouse_Embryo/E16.5_E1S1.MOSTA/report/IQ/E16.5_E1S1.MOSTA_IQ_gsMap_Report.html
  • Gene Diagnostic Info File: example/Mouse_Embryo/E16.5_E1S1.MOSTA/report/IQ/E16.5_E1S1.MOSTA_IQ_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2024-09-23 11:30:16