Wnt Pathway Analysis Links

Emage Entries and DOI Links

Links for the original un-mapped Wnt and other gene-expression patterns to corresponding Emage entries and, when available, data DOI links to the original image data. Note the EMAGE pages are not fully functional for all links but the expression patterns can be explored and the original data downloaded. The individual DOIs for each dataset are not yet in the table but the mapped data can be downloaded from Edinburgh DataShare Wnt Pathway Analysis Data.

Section-based views of the mapped expression data (IIP3D viewers)

Links to viewers for each stage analysed:

EMA36, Theiler 15 (9.5 dpc); EMA53, Theiler 17 (10.5dpc); EMA118, Theiler 19 (11.5dpc).

These image data and associated embryo models are available for download from the Edinburgh DataShare repository: DOI:10.7488/ds/3141 .

MARender Visualisation

MARender is a means of rendering 3D anatomy and gene expression domains in a web browser. The links here provide pointcloud views of the full mapped gene-expression data for each stage and to view of Wnt Occupancy compared with the reporter expression TCF-GFP.

WNT Gene Expression Pointclouds

Gene Expression Pointclouds WNT and associated gene expression pointclouds shown on stages TS15, TS17 and TS19.

These pointcloud data and associated browser display software are available for download from the Edinburgh DataShare repository: DOI:10.7488/ds/3142 .

WNT Occupancy

TS17 (EMA53) WNT occupancy and TCF-GFP reporter. WNT occupancy shown from a value of 4 (dark blue) through red to yellow with a value of 11. TCF-GFP is shown in green.
TS17 (EMA53) Left forelimb WNT occupancy and TCF-GFP reporter. WNT occupancy shown from a value of 4 through to 8 red. TCF-GFP is shown in green.
TS17 (EMA53) Left forelimb with WNT5A, WNT11 and remaining WNT genes. WNT5A (red), WNT11 (green) and the the remaining WNT genes (blue) are shown with point density/size/value increasing with expression value. The remaining WNT image is formed by the normalised sum of the remaining WNT gene expresion images.
TS19 (EMA118) WNT occupancy and TCF-GFP reporter. WNT occupancy shown from a value of 4 (dark blue) through red to yellow with a value of 14. TCF-GFP is shown in green.
TS19 (EMA118) Left forelimb WNT occupancy and TCF-GFP reporter. WNT occupancy shown from a value of 4 through to 10 red. TCF-GFP is shown in green.
TS19 (EMA118 Left forelimb with WNT5A, WNT11 and remaining WNT genes. WNT5A (red), WNT11 (green) and the the remaining WNT genes (blue) are shown with point density/size/value increasing with expression value. The remaining WNT image is formed by the normalised sum of the remaining WNT gene expresion images.

Help with MARender

MARender uses WebGL (via three.js) and requires a current web browser (preferably firefox, chrome, safari or chromium). In these tests the following rendering controls are available:

mouse left - rotate
mouse centre/wheel - zoom
mouse right - pan
key '<' - opacity down
key '>' - opacity up
key 'h' - home (if render vanishes use this)
key 'p' - increase point size
key 'q' - decrease point size
key 's' - surfaces
key 'w' - wireframe

EMA36, TS15, 9.5dpc domain intersection analysis visualised using parallel coordinates

Data files: EMA36 data-files: EMA36 Volumes table Excel format (Tab-separated values data file)

Analysis for each domain type:

Analysis of gene-expression data for each compartment:

EMA53, TS17, 10.5dpc domain intersection analysis visualised using parallel coordinates

Data files: EMA53 data-files: EMA53 Volumes table Excel format (Tab-separated values data file)

Analysis for each domain type:

Analysis of gene-expression data for each compartment:

Natural Coordinates analysis:

Data files: EMA53 data-files: EMA53 Natural Coordinates IntersectVolTable xlsx format (Tab-separated-values data file)

EMA53_IntersectAnalysis_NC_AP_axis_ColNorm.js
EMA53_IntersectAnalysis_NC_AP_axis_RowNorm.js
EMA53_IntersectAnalysis_NC_Cyl_Radius_axis_ColNorm.js
EMA53_IntersectAnalysis_NC_Cyl_Radius_axis_RowNorm.js
EMA53_IntersectAnalysis_NC_Cyl_Theta_axis_ColNorm.js
EMA53_IntersectAnalysis_NC_Cyl_Theta_axis_RowNorm.js
EMA53_IntersectAnalysis_NC_DV_axis_ColNorm.js
EMA53_IntersectAnalysis_NC_DV_axis_RowNorm.js
EMA53_IntersectAnalysis_NC_LR_axis_ColNorm.js
EMA53_IntersectAnalysis_NC_LR_axis_RowNorm.js
EMA53_NCIntersectAnalysis_All_ColNorm.js
EMA53_NCIntersectAnalysis_All_RowNorm.js

EMA118, TS19, 11.5dpc domain intersection analysis visualised using parallel coordinates

Data files: EMA118 data-files: EMA118 Volumes table Excel format (Tab-separated values data file)

Analysis for each domain type:

Analysis of gene-expression data for each compartment:

Wnt Gene Regions of High Occupancy (ROHO) Analysis

The regions of high occupancy (ROHO) are defined for each stage by thresholding the Wnt occupancy image (usually at 4 or 5) and selecting regions that include at least an occupancy of 6. The regions have been merged to named domains and analysed in terms of all genes expressed in the domain. The values of "column normalised" i.e. the proportion of the domain that is occupied by the given gene are in the second column and "row-normalised" in the third column of the table.

Select in the table below either the parallels view or the tab-delimited text file which can be downloaded and viewed using e.g. Excel.

ROHO Name	Analysis - column normalised	Analysis - row normalised
ROHO_01_base_of_hindlimb	ROHO_01_cn.js ( ROHO_01_cn.txt )	ROHO_01_rn.js ( ROHO_01_rn.txt )
ROHO_02_distal_hindlimb	ROHO_02_cn.js ( ROHO_02_cn.txt )	ROHO_02_rn.js ( ROHO_02_rn.txt )
ROHO_03_ventral_base_of_forelimb	ROHO_03_cn.js ( ROHO_03_cn.txt )	ROHO_03_rn.js ( ROHO_03_rn.txt )
ROHO_04_dorsal_base_of_forelimb	ROHO_04_cn.js ( ROHO_04_cn.txt )	ROHO_04_rn.js ( ROHO_04_rn.txt )
ROHO_05_base_of_forelimb	ROHO_05_cn.js ( ROHO_05_cn.txt )	ROHO_05_rn.js ( ROHO_05_rn.txt )
ROHO_06_distal_forelimb	ROHO_06_cn.js ( ROHO_06_cn.txt )	ROHO_06_rn.js ( ROHO_06_rn.txt )
ROHO_07_dorsal_forelimb	ROHO_07_cn.js ( ROHO_07_cn.txt )	ROHO_07_rn.js ( ROHO_07_rn.txt )
ROHO_08_branchial_arches	ROHO_08_cn.js ( ROHO_08_cn.txt )	ROHO_08_rn.js ( ROHO_08_rn.txt )
ROHO_09_neck	ROHO_09_cn.js ( ROHO_09_cn.txt )	ROHO_09_rn.js ( ROHO_09_rn.txt )
ROHO_10_interlimb_flank	ROHO_10_cn.js ( ROHO_10_cn.txt )	ROHO_10_rn.js ( ROHO_10_rn.txt )
ROHO_11_hindgut	ROHO_11_cn.js ( ROHO_11_cn.txt )	ROHO_11_rn.js ( ROHO_11_rn.txt )
ROHO_12_tailbud	ROHO_12_cn.js ( ROHO_12_cn.txt )	ROHO_12_rn.js ( ROHO_12_rn.txt )
ROHO_13_genital	ROHO_13_cn.js ( ROHO_13_cn.txt )	ROHO_13_rn.js ( ROHO_13_rn.txt )
ROHO_14_diencephalon_floorplate	ROHO_14_cn.js ( ROHO_14_cn.txt )	ROHO_14_rn.js ( ROHO_14_rn.txt )
ROHO_15_fronto_nasal	ROHO_15_cn.js ( ROHO_15_cn.txt )	ROHO_15_rn.js ( ROHO_15_rn.txt )
ROHO_16_dorsal_diecephalon	ROHO_16_cn.js ( ROHO_16_cn.txt )	ROHO_16_rn.js ( ROHO_16_rn.txt )
ROHO_17_dorsal_telencephalon	ROHO_17_cn.js ( ROHO_17_cn.txt )	ROHO_17_rn.js ( ROHO_17_rn.txt )
ROHO_18_metencephalon	ROHO_18_cn.js ( ROHO_18_cn.txt )	ROHO_18_rn.js ( ROHO_18_rn.txt )
ROHO_19_midbrain_dorsal	ROHO_19_cn.js ( ROHO_19_cn.txt )	ROHO_19_rn.js ( ROHO_19_rn.txt )
ROHO_20_cepahlic_flexure	ROHO_20_cn.js ( ROHO_20_cn.txt )	ROHO_20_rn.js ( ROHO_20_rn.txt )
ROHO_21_cortical_hem	ROHO_21_cn.js ( ROHO_21_cn.txt )	ROHO_21_rn.js ( ROHO_21_rn.txt )
ROHO_22_anterior_neural_tube	ROHO_22_cn.js ( ROHO_22_cn.txt )	ROHO_22_rn.js ( ROHO_22_rn.txt )
ROHO_23_posterior_neural_tube	ROHO_23_cn.js ( ROHO_23_cn.txt )	ROHO_23_rn.js ( ROHO_23_rn.txt )
ROHO_24_eye	ROHO_24_cn.js ( ROHO_24_cn.txt )	ROHO_24_rn.js ( ROHO_24_rn.txt )

Anatomy Domains Temporal Analysis

Anatomy regions that are common to each model are analysed in terms of gene occupancy. The values of "column normalised" i.e. the proportion of the domain that is occupied by the given gene are in the second column and "row-normalised" in the third column of the table.

Select in the table below either the parallels view or the tab-delimited text file which can be downloaded and viewed using e.g. Excel.

Anatomy domain	Analysis - column normalised	Analysis - row normalised
diencephalon	diencephalon_cn.js ( diencephalon_cn.txt )	diencephalon_rn.js ( diencephalon_rn.txt )
diencephalon_floor_plate	diencephalon_floor_plate_cn.js ( diencephalon_floor_plate_cn.txt )	diencephalon_floor_plate_rn.js ( diencephalon_floor_plate_rn.txt )
embryo	embryo_cn.js ( embryo_cn.txt )	embryo_rn.js ( embryo_rn.txt )
eye	eye_cn.js ( eye_cn.txt )	eye_rn.js ( eye_rn.txt )
forelimb_L	forelimb_L_cn.js ( forelimb_L_cn.txt )	forelimb_L_rn.js ( forelimb_L_rn.txt )
forelimb_L_AER	forelimb_L_AER_cn.js ( forelimb_L_AER_cn.txt )	forelimb_L_AER_rn.js ( forelimb_L_AER_rn.txt )
forelimb_L_PZ	forelimb_L_PZ_cn.js ( forelimb_L_PZ_cn.txt )	forelimb_L_PZ_rn.js ( forelimb_L_PZ_rn.txt )
forelimb_L_anterior	forelimb_L_anterior_cn.js ( forelimb_L_anterior_cn.txt )	forelimb_L_anterior_rn.js ( forelimb_L_anterior_rn.txt )
forelimb_L_posterior	forelimb_L_posterior_cn.js ( forelimb_L_posterior_cn.txt )	forelimb_L_posterior_rn.js ( forelimb_L_posterior_rn.txt )
forelimb_L_proximal	forelimb_L_proximal_cn.js ( forelimb_L_proximal_cn.txt )	forelimb_L_proximal_rn.js ( forelimb_L_proximal_rn.txt )
forelimb_R	forelimb_R_cn.js ( forelimb_R_cn.txt )	forelimb_R_rn.js ( forelimb_R_rn.txt )
forelimb_R_AER	forelimb_R_AER_cn.js ( forelimb_R_AER_cn.txt )	forelimb_R_AER_rn.js ( forelimb_R_AER_rn.txt )
forelimb_R_PZ	forelimb_R_PZ_cn.js ( forelimb_R_PZ_cn.txt )	forelimb_R_PZ_rn.js ( forelimb_R_PZ_rn.txt )
forelimb_R_anterior	forelimb_R_anterior_cn.js ( forelimb_R_anterior_cn.txt )	forelimb_R_anterior_rn.js ( forelimb_R_anterior_rn.txt )
forelimb_R_posterior	forelimb_R_posterior_cn.js ( forelimb_R_posterior_cn.txt )	forelimb_R_posterior_rn.js ( forelimb_R_posterior_rn.txt )
forelimb_R_proximal	forelimb_R_proximal_cn.js ( forelimb_R_proximal_cn.txt )	forelimb_R_proximal_rn.js ( forelimb_R_proximal_rn.txt )
heart	heart_cn.js ( heart_cn.txt )	heart_rn.js ( heart_rn.txt )
hyoid_arch	hyoid_arch_cn.js ( hyoid_arch_cn.txt )	hyoid_arch_rn.js ( hyoid_arch_rn.txt )
liver	liver_cn.js ( liver_cn.txt )	liver_rn.js ( liver_rn.txt )
mandibular_arch	mandibular_arch_cn.js ( mandibular_arch_cn.txt )	mandibular_arch_rn.js ( mandibular_arch_rn.txt )
maxillary_process	maxillary_process_cn.js ( maxillary_process_cn.txt )	maxillary_process_rn.js ( maxillary_process_rn.txt )
mesencephalon	mesencephalon_cn.js ( mesencephalon_cn.txt )	mesencephalon_rn.js ( mesencephalon_rn.txt )
metencephalon	metencephalon_cn.js ( metencephalon_cn.txt )	metencephalon_rn.js ( metencephalon_rn.txt )
neural_tube	neural_tube_cn.js ( neural_tube_cn.txt )	neural_tube_rn.js ( neural_tube_rn.txt )
olfactory_placode	olfactory_placode_cn.js ( olfactory_placode_cn.txt )	olfactory_placode_rn.js ( olfactory_placode_rn.txt )
otic_pit	otic_pit_cn.js ( otic_pit_cn.txt )	otic_pit_rn.js ( otic_pit_rn.txt )
rathke_pouch	rathke_pouch_cn.js ( rathke_pouch_cn.txt )	rathke_pouch_rn.js ( rathke_pouch_rn.txt )
tail_bud	tail_bud_cn.js ( tail_bud_cn.txt )	tail_bud_rn.js ( tail_bud_rn.txt )
telencephalon	telencephalon_cn.js ( telencephalon_cn.txt )	telencephalon_rn.js ( telencephalon_rn.txt )