PAX4 (human): Bgee expression evidence

Generated by projects/BGEEDB_EXPRESSION/scripts/gene_report.py; do not edit. Source: Bgee 15.2 (human simple call files for present/absent calls with stages merged; REST API for stage-resolved present calls). Method and tier definitions: projects/BGEEDB_EXPRESSION/methods.md.

Command:

uv run python projects/BGEEDB_EXPRESSION/scripts/gene_report.py human PAX4 --paralog PAX6 --focus UBERON:0001264 --focus UBERON:0000970 --focus UBERON:0001905 --focus UBERON:0001890 --focus UBERON:0000160

1. Where the gene and its paralogs are expressed

gene	Bgee id	present / sampled entities	breadth	top present tissues (score)
PAX4	ENSG00000106331	32 / 258	0.12	male germ line stem cell (sensu Vertebrata) in testis (80); rectum (62); mucosa of transverse colon (61); duodenum (52); tibialis anterior (52); deltoid (51); islet of Langerhans (51); muscle tissue (46)
PAX6	ENSG00000007372	201 / 288	0.70	palpebral conjunctiva (100); type B pancreatic cell (99); ventricular zone (99); paraflocculus (99); ganglionic eminence (98); cerebellum (98); cerebellar vermis (98); cerebellar cortex (98)

2. GO terms with a GO anatomy, scored for the gene and each paralog

Tier per gene: ENRICHED (present in the term's anatomy and in the gene's own top 10%), CONSISTENT, ABSENT (calls exist there, all absent), ABSENT_DEVELOPMENTAL (absent, but the term is developmental and calls merge stages), NO_DATA. A paralog that is detected where the gene is absent shows the anatomy was sampled.

GO term	anatomy	PAX4	PAX6
GO:0003309 type B pancreatic cell differentiation	type B pancreatic cell	CONSISTENT (UBERON:0000006 islet of Langerhans (50.6))	ENRICHED (CL:0000169 type B pancreatic cell (99.3))
GO:0007420 brain development	brain	CONSISTENT (UBERON:0004023 ganglionic eminence (45.2))	ENRICHED (UBERON:0003053 ventricular zone (99.3))
GO:0007423 sensory organ development	sense organ	ABSENT_DEVELOPMENTAL (absent in UBERON:0005384 nasal cavity epithelium, UBERON:0006919 tongue squamous epithelium)	ENRICHED (UBERON:0001812 palpebral conjunctiva (99.5))
GO:0030900 forebrain development	forebrain	CONSISTENT (UBERON:0004023 ganglionic eminence (45.2))	ENRICHED (UBERON:0002476 lateral globus pallidus (93.2))
GO:0060041 retina development in camera-type eye	retina	ABSENT_DEVELOPMENTAL (absent in UBERON:0001782 pigmented layer of retina)	ENRICHED (UBERON:0001782 pigmented layer of retina (88.7))
GO:7770019 negative regulation of enteroendocrine cell differentiation	enteroendocrine cell	ABSENT_DEVELOPMENTAL (absent in CL:0000169 type B pancreatic cell)	ENRICHED (CL:0000169 type B pancreatic cell (99.3))
GO:7770020 intestinal enterochromaffin enteroendocrine cell differentiation	type EC enteroendocrine cell	ENRICHED (UBERON:0001052 rectum (61.8))	CONSISTENT (UBERON:0001826 nasal cavity mucosa (78.8))

4. Stage-resolved present calls in anatomies of interest

Present calls only (the API reports no absent calls); a missing stage means no call, not absence. Stages broader than one developmental window (life cycle, organogenesis stage) are omitted.

UBERON:0001264 pancreas and its parts

gene	entity	stage	start (dpc)	score	data types
—	no stage-resolved present call

Stage-merged calls (present and absent) in pancreas and its parts:

PAX4: pancreatic ductal cell absent (silver, 50); epithelial cell of pancreas absent (gold, 49); type B pancreatic cell absent (gold, 49); body of pancreas absent (gold, 30); islet of Langerhans present (gold, 51); pancreas present (gold, 38)
PAX6: pancreatic ductal cell absent (silver, 58); type B pancreatic cell present (gold, 99); islet of Langerhans present (gold, 97); pancreas present (gold, 83); body of pancreas present (gold, 76); epithelial cell of pancreas present (silver, 71)

UBERON:0000970 eye and its parts

gene	entity	stage	start (dpc)	score	data types
PAX6	palpebral conjunctiva	juvenile stage	42.5	99.5	Affymetrix

Stage-merged calls (present and absent) in eye and its parts:

PAX4: palpebral conjunctiva absent (gold, 44); pigmented layer of retina absent (gold, 39)
PAX6: palpebral conjunctiva present (gold, 100); eye present (gold, 97); pigmented layer of retina present (gold, 89); retina present (gold, 89); lens of camera-type eye present (silver, 66)

UBERON:0001905 pineal body and its parts

gene	entity	stage	start (dpc)	score	data types
—	no stage-resolved present call

Stage-merged calls (present and absent) in pineal body and its parts:

PAX4: no calls
PAX6: no calls

UBERON:0001890 forebrain and its parts

gene	entity	stage	start (dpc)	score	data types
PAX6	lateral globus pallidus	life cycle	0.5	93.2	Affymetrix
PAX6	medial globus pallidus	life cycle	0.5	81.2	Affymetrix
PAX6	lateral nuclear group of thalamus	life cycle	0.5	74.5	Affymetrix
PAX6	frontal cortex	infant stage	23.5	80.9	RNA-Seq
PAX6	caudate nucleus	infant stage	23.5	81.0	Affymetrix
PAX6	dorsolateral prefrontal cortex	infant stage	23.5	81.4	Affymetrix
PAX6	frontal cortex	juvenile stage	42.5	80.8	Affymetrix
PAX6	caudate nucleus	juvenile stage	42.5	83.8	Affymetrix
PAX6	Ammon's horn	juvenile stage	42.5	85.6	Affymetrix
PAX6	corpus callosum	juvenile stage	42.5	77.8	RNA-Seq
PAX6	superior frontal gyrus	juvenile stage	42.5	77.5	Affymetrix
PAX6	dorsolateral prefrontal cortex	juvenile stage	42.5	79.0	Affymetrix

Stage-merged calls (present and absent) in forebrain and its parts:

PAX4: Brodmann (1909) area 10 absent (gold, 69); frontal pole absent (gold, 50); middle frontal gyrus absent (gold, 50); Brodmann (1909) area 46 absent (gold, 49); olfactory bulb absent (gold, 49); CA1 field of hippocampus absent (gold, 48); orbitofrontal cortex absent (gold, 48); lateral globus pallidus absent (gold, 48); lateral nuclear group of thalamus absent (gold, 46); middle temporal gyrus absent (gold, 44); dorsal plus ventral thalamus absent (gold, 42); Brodmann (1909) area 23 absent (gold, 42); globus pallidus absent (gold, 42); subthalamic nucleus absent (gold, 41); cortical plate absent (gold, 40); parietal lobe absent (gold, 40); postcentral gyrus absent (gold, 40); entorhinal cortex absent (gold, 39); medial globus pallidus absent (gold, 39); superior frontal gyrus absent (gold, 38); occipital lobe absent (gold, 37); primary visual cortex absent (gold, 35); prefrontal cortex absent (gold, 32); frontal cortex absent (gold, 32); temporal lobe absent (gold, 29); corpus callosum absent (gold, 29); Ammon's horn absent (gold, 28); hypothalamus absent (silver, 27); dorsolateral prefrontal cortex absent (gold, 27); cingulate cortex absent (gold, 25); anterior cingulate cortex absent (gold, 25); Brodmann (1909) area 9 absent (gold, 25); putamen absent (gold, 24); caudate nucleus absent (gold, 22); nucleus accumbens absent (gold, 22); amygdala absent (gold, 22); right frontal lobe absent (gold, 20); pituitary gland absent (gold, 18); adenohypophysis absent (gold, 16)
PAX6: olfactory bulb absent (gold, 77); lateral globus pallidus present (gold, 93); CA1 field of hippocampus present (gold, 92); middle frontal gyrus present (gold, 91); entorhinal cortex present (gold, 88); putamen present (gold, 87); temporal lobe present (gold, 87); caudate nucleus present (gold, 87); amygdala present (gold, 87); Brodmann (1909) area 10 present (gold, 86); frontal pole present (gold, 86); cingulate cortex present (gold, 85); anterior cingulate cortex present (gold, 85); Brodmann (1909) area 46 present (gold, 85); orbitofrontal cortex present (gold, 85); nucleus accumbens present (gold, 85); telencephalon present (gold, 84); right frontal lobe present (gold, 84); corpus callosum present (gold, 84); parietal lobe present (gold, 84); superior frontal gyrus present (gold, 84); Ammon's horn present (gold, 84); cerebral cortex present (gold, 83); postcentral gyrus present (gold, 83); forebrain present (gold, 83); globus pallidus present (gold, 83); Brodmann (1909) area 9 present (gold, 83); neocortex present (gold, 83); dorsolateral prefrontal cortex present (gold, 83); frontal cortex present (gold, 82); subthalamic nucleus present (gold, 82); medial globus pallidus present (gold, 81); occipital lobe present (gold, 81); prefrontal cortex present (gold, 80); dorsal plus ventral thalamus present (silver, 80); hypothalamus present (gold, 78); primary visual cortex present (gold, 78); Brodmann (1909) area 23 present (gold, 77); cortical plate present (gold, 77); pituitary gland present (gold, 76); adenohypophysis present (gold, 75); lateral nuclear group of thalamus present (silver, 75); middle temporal gyrus present (gold, 73)

UBERON:0000160 intestine and its parts

gene	entity	stage	start (dpc)	score	data types
PAX4	duodenum	life cycle	0.5	51.9	Affymetrix
PAX6	colonic epithelium	life cycle	0.5	57.9	RNA-Seq
PAX6	jejunal mucosa	life cycle	0.5	64.7	Affymetrix
PAX6	duodenum	life cycle	0.5	67.5	Affymetrix

Stage-merged calls (present and absent) in intestine and its parts:

PAX4: ileal mucosa absent (silver, 49); jejunum absent (gold, 43); colonic epithelium absent (gold, 41); jejunal mucosa absent (gold, 41); mucosa of sigmoid colon absent (gold, 40); rectum present (gold, 62); mucosa of transverse colon present (gold, 61); duodenum present (gold, 52); transverse colon present (gold, 46); small intestine present (gold, 45); small intestine Peyer's patch present (gold, 44); colonic mucosa present (gold, 42); intestine present (gold, 41); large intestine present (gold, 39); colon present (gold, 39); vermiform appendix present (silver, 36); sigmoid colon present (gold, 30); muscle layer of sigmoid colon present (gold, 28)
PAX6: mucosa of sigmoid colon absent (gold, 59); ileal mucosa absent (silver, 50); duodenum present (gold, 68); jejunal mucosa present (gold, 65); jejunum present (gold, 64); rectum present (gold, 58); colonic epithelium present (silver, 58); small intestine present (gold, 56); small intestine Peyer's patch present (gold, 54); mucosa of transverse colon present (gold, 53); intestine present (gold, 51); transverse colon present (gold, 51); large intestine present (gold, 49); caecum present (silver, 49); colon present (gold, 49); vermiform appendix present (gold, 45); sigmoid colon present (gold, 44); muscle layer of sigmoid colon present (gold, 41)