Supplemental Table 4. Neural Tissues Enriched in the Trisomy 21 and 18 Amniotic Fluid
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Supplemental Table 4. Neural tissues enriched in the Trisomy 21 and 18 amniotic fluid transcriptomes
Supplemental Table 4. Enriched neural tissues from DAVID tissue expression charts for trisomy 18 and 21 amniotic fluid transcriptomesNovel neurodevelopmental information revealed in amniotic fluid supernatant from fetuses with trisomies 18 and 21. Human Genetics. Lisa Hui, Donna K. Slonim, Heather C. Wick, Kirby L. Johnson, Keiko Koide, and Diana W. Bianchi. Corresponding author: Lisa Hui, Mother Infant Research Institute at Tufts Medical Center,
Neural Tissues enriched in the Trisomy 18 AF transcriptome *
DAVID Category / Term / No. of genes / Benjamini-Hochberg corrected P value
GNF_U133A / caudatenucleus / 364 / 1.01E-45
CGAP_SAGE / brain (cell line) / 142 / 6.68E-22
UP_TISSUE / Fetal brain cortex / 50 / 1.37E-20
CGAP_SAGE / cerebellum_large cell medulloblastoma / 130 / 5.09E-20
CGAP_SAGE / cerebellum_medulloblastoma / 152 / 5.63E-19
UP_TISSUE / Cajal-Retzius cell / 44 / 2.39E-17
CGAP_SAGE / cerebellum_anaplastic medulloblastoma / 127 / 2.44E-15
CGAP_SAGE / cerebellum_medulloblastoma cell line / 123 / 6.33E-15
CGAP_SAGE / brain_anaplastic astrocytoma / 120 / 1.39E-14
CGAP_SAGE / retina_Bilateral retinoblastoma, poorly differentiated, left orbit / 122 / 2.44E-13
CGAP_SAGE / brain_ependymoma / 132 / 2.73E-13
CGAP_SAGE / brain_null / 123 / 5.31E-13
CGAP_SAGE / brain_Glioblastoma / 126 / 7.31E-13
CGAP_SAGE / brain_Anaplastic astrocytoma grade III / 120 / 1.26E-11
CGAP_SAGE / brain_benign meningioma of the meningothelial subtype / 90 / 6.65E-11
CGAP_SAGE / brain_anaplastic grade III, primary, brain / 120 / 1.07E-10
CGAP_SAGE / brain_pediatric glioblastoma, cerebral cortex / 100 / 1.80E-10
GNF_U133A / Whole Brain / 264 / 9.46E-10
CGAP_SAGE / brain_glioblastoma, cerebral cortex / 132 / 2.25E-09
CGAP_SAGE / brain_astrocytoma grade II / 102 / 3.30E-09
CGAP_SAGE / brain_atypical meningioma / 104 / 4.66E-09
CGAP_SAGE / cerebellum_medulloblastoma with neuroblastic differentiation / 118 / 4.92E-09
UNIGENE_EST / retinoblastoma_disease / 180 / 5.47E-09
CGAP_EST / nervous_normal (fetus, normal, uncharacterized preparation, EST, whole brain / 33 / 7.87E-08
CGAP_EST / eye_normal / 41 / 8.20E-08
CGAP_SAGE / brain_normal fetal astrocyte, GFAP positive, cerebral cortex / 97 / 1.62E-07
CGAP_SAGE / brain_Malignant Meningioma / 102 / 3.16E-07
GNF_U133A / TemporalLobe / 194 / 4.93E-07
CGAP_EST / brain_neoplasia / 22 / 1.18E-06
CGAP_SAGE / brain_glioblatastoma infected with mutant EGFR, cerebral cortex / 1.70E-06
GNF_U133A / spinal cord / 145 / 1.95E-06
CGAP_SAGE / retina_normal peripheral retina / 95 / 2.57E-06
UNIGENE_EST / pituitary gland_normal / 177 / 3.50E-06
GNF_U133A / Superior Cervical Ganglion / 404 / 3.80E-06
CGAP_SAGE / brain_glioblatastoma infected with LacZ control, cerebral cortex / 4.19E-06
GNF_U133A / globus pallidus / 159 / 4.45E-06
CGAP_EST / brain_normal / 28 / 1.10E-05
CGAP_EST / cerebrum_normal / 29 / 3.20E-05
CGAP_SAGE / spinal cord_normal spinal cord / 114 / 3.40E-05
CGAP_SAGE / retina_normal macula / 87 / 5.58E-05
CGAP_SAGE / brain_oligodendroglioma / 106 / 8.64E-05
UP_TISSUE / Brain / 397 / 9.45E-05
CGAP_SAGE / brain_ependymoma / 91 / 1.03E-04
GNF_U133A / fetal brain / 176 / 1.58E-04
UP_TISSUE / Pituitary / 20 / 1.80E-04
CGAP_SAGE / brain_arachnoid cells, blood vessels, macrophages / 79 / 4.03E-04
CGAP_SAGE / brain_Anaplastic GradeII Astrocytoma / 87 / 4.57E-04
GNF_U133A / Parietal Lobe / 191 / 6.17E-04
CGAP_SAGE / cerebellum_desmoplastic medulloblastoma / 91 / 6.33E-04
GNF_U133A / Olfactory Bulb / 138 / 8.41E-04
CGAP_SAGE / brain_anaplastic astrocytoma / 83 / 0.001391931
CGAP_SAGE / brain_GBM / 80 / 0.003254521
GNF_U133A / Trigeminal Ganglion / 95 / 0.004499928
CGAP_SAGE / brain_normal pediatric cortex / 95 / 0.006593734
GNF_U133A / Thalamus / 124 / 0.011302979
CGAP_SAGE / brain_well-differentiated oligodendroglioma, frontal lobe, cortex / 95 / 0.014168122
GNF_U133A / Amygdala / 167 / 0.014681346
CGAP_SAGE / eye_ / 48 / 0.015403084
GNF_U133A / Cingulate Cortex / 127 / 0.020535875
CGAP_SAGE / brain_pilocytic astrocyoma, cerebellum / 66 / 0.046780169
* redundant SAGE terms removed
Neural tissues enriched in the Trisomy 21 AF transcriptome *DAVID Category / Term / No. of genes / Benjamini-Hochberg corrected P value
GNF_U133A / caudatenucleus / 591 / 3.80E-84
CGAP_SAGE / brain_Glioblastoma / 232 / 8.70E-34
CGAP_SAGE / brain, cell line / 220 / 6.37E-33
CGAP_SAGE / cerebellum_anaplastic medulloblastoma / 216 / 4.56E-31
CGAP_SAGE / brain_ependymoma / 225 / 2.26E-27
CGAP_SAGE / cerebellum_medulloblastoma / 233 / 4.27E-27
CGAP_SAGE / retina_bilateral retinoblastoma, poorly differentiated, left orbit / 207 / 7.35E-27
CGAP_SAGE / cerebellum_large cell medulloblastoma / 193 / 2.10E-26
CGAP_SAGE / brain_Anaplastic astrocytoma grade III / 211 / 2.24E-26
UP_TISSUE / Fetal brain cortex / 63 / 4.24E-22
UP_TISSUE / Cajal-Retzius cell / 59 / 3.20E-21
CGAP_SAGE / brain_benign meningioma of the meningothelial subtype / 156 / 3.54E-20
GNF_U133A / Whole Brain / 430 / 2.46E-19
CGAP_SAGE / cerebellum_medulloblastoma / 170 / 3.79E-18
CGAP_SAGE / brain_anaplastic gradeIII, primary, brain / 177 / 7.96E-18
CGAP_SAGE / brain_astrocytoma grade II / 170 / 2.10E-17
CGAP_SAGE / cerebellum_medulloblastoma with neuroblastic differentiation / 196 / 4.77E-17
CGAP_SAGE / spinal cord_normal spinal cord / 215 / 9.15E-17
CGAP_SAGE / brain_glioblastoma, cerebral cortex / 215 / 1.50E-16
CGAP_EST / nervous_normal (normal fetus whole brain) / 54 / 1.01E-15
CGAP_SAGE / brain_atypical meningioma / 169 / 1.78E-15
CGAP_SAGE / brain_Malignant Meningioma / 176 / 2.44E-15
CGAP_SAGE / brain_pediatric glioblastoma, cerebral cortex / 155 / 2.44E-15
CGAP_EST / brain_normal (embryo, 4 weeks postconception Tissue:anterior rhombomeres 1-4 (4 pooled) / 58 / 3.36E-15
CGAP_SAGE / brain_normal fetal astrocyte, GFAP positive, cerebral cortex / 165 / 5.11E-15
CGAP_EST / brain_neoplasia (neuroblast) / 69 / 5.50E-15
GNF_U133A / globus pallidus / 268 / 2.38E-13
GNF_U133A / Superior Cervical Ganglion / 652 / 2.53E-12
UNIGENE_EST / retinoblastoma_disease / 268 / 1.26E-10
CGAP_SAGE / brain_glioblatastoma infected with LacZ control, cerebral cortex / 181 / 5.42E-10
CGAP_SAGE / retina_normal peripheral retina / 151 / 1.08E-09
CGAP_SAGE / brain_arachnoid cells, blood vessels, macrophages / 140 / 1.75E-09
UNIGENE_EST / pituitary gland_normal / 276 / 5.09E-09
CGAP_EST / pituitary gland_normal / 36 / 7.81E-09
CGAP_EST / cerebellum_normal / 48 / 6.31E-08
CGAP_SAGE / brain_glioblatastoma infected with mutant EGFR, cerebral cortex / 178 / 8.56E-08
GNF_U133A / fetal brain (normal whole brains pooled from 59 spontaneously aborted male/female Caucasian fetuses) / 283 / 9.39E-08
GNF_U133A / Parietal Lobe / 313 / 1.45E-07
CGAP_SAGE / retina_normal macula / 138 / 2.20E-07
CGAP_EST / cerebrum_uncharacterized histology / 27 / 1.06E-06
GNF_U133A / Olfactory Bulb / 224 / 1.23E-06
UP_TISSUE / Brain / 611 / 2.06E-06
GNF_U133A / Trigeminal Ganglion / 156 / 1.69E-05
CGAP_EST / brain_uncharacterized histology / 24 / 3.43E-05
CGAP_EST / pituitary gland_neoplasia / 33 / 6.31E-05
CGAP_SAGE / cerebellum_desmoplastic medulloblastoma / 140 / 7.42E-05
GNF_U133A / spinal cord / 199 / 1.06E-04
CGAP_EST / cerebrum_neoplasia / 36 / 1.48E-04
CGAP_SAGE / brain_normal pediatric cortex (15 months age) / 154 / 1.73E-04
GNF_U133A / Temporal Lobe / 264 / 3.12E-04
GNF_U133A / subthalamic nucleus / 256 / 0.002569571
GNF_U133A / Cingulate Cortex / 198 / 0.004452056
GNF_U133A / Thalamus / 189 / 0.005270858
UP_TISSUE / Glioma / 4 / 0.038678355
* redundant SAGE terms removed