Added variants to classification.json: human H3.6, H3.7, H3.8

intbio · Nov 19, 2024 · 629f48d · 629f48d
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commit 629f48d
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Showing 6 changed files with 2,623 additions and 33 deletions.
diff --git a/CURATED_SET/classification.json b/CURATED_SET/classification.json
@@ -271,9 +271,9 @@
             "H3.5_(Hominidae)": {
                 "H3.5_(Homo_sapiens)": "null"
             },
-            "H3.6_(Mammals?)?": "null",
-            "H3.7_(Mammals?)?": "null",
-            "H3.8_(Mammals?)?": "null",
+            "H3.6_(Homo_sapiens)": "null",
+            "H3.7_(Homo_sapiens)": "null",
+            "H3.8_(Homo_sapiens)": "null",
             "H3.B_(Giardia?)": "null",
             "H3.P_(Moneuplotes?)": "null",
             "H3.V_(Trypanosomatidae)": "null"
@@ -4892,10 +4892,10 @@
             "alternate_names": [],
             "publications": []
         },
-        "H3.6_(Mammals?)?": {
+        "H3.6_(Homo_sapiens)": {
             "level": "variant_group",
             "description": {
-                "summary": "null",
+                "summary": "H3.6_(Homo_sapiens) is a human histone variant, similar to histone variant H3.3 in amino acid sequence, encoded by the H3F3AP6 gene. Expression levels of H3F3AP6 are extremely low, as compared to H3F3B gene (encodes histone H3.3) [taguchi_crystal_2017]. H3.6 nucleosomes are substantially unstable due to the Val62 residue, which weakens interactions with H4 [taguchi_crystal_2017].",
                 "taxonomy": "null",
                 "genes": "null",
                 "evolution": "null",
@@ -4905,20 +4905,22 @@
                 "sequence": "null",
                 "localization": "null",
                 "deposition": "null",
-                "structure": "null",
+                "structure": "H3.6 nucleosomes are substantially unstable due to the Val62 residue, which weakens interactions with H4 [taguchi_crystal_2017].",
                 "interactions": "null",
                 "disease": "null",
                 "caveats": "null"
             },
             "taxonomic_span": "null",
             "taxonomic_span_id": "null",
             "alternate_names": [],
-            "publications": []
+            "publications": [
+                "taguchi_crystal_2017"
+            ]
         },
-        "H3.7_(Mammals?)?": {
+        "H3.7_(Homo_sapiens)": {
             "level": "variant_group",
             "description": {
-                "summary": "null",
+                "summary": "H3.7_(Homo_sapiens) is a human histone variant, similar to histone variant H3.1 in amino acid sequence, encoded by the HIST2H3PS2 gene. Expression levels of HIST2H3PS2 are extremely low, as compared to H3F3B gene (encodes histone H3.3) [taguchi_crystal_2017]. In vitro results showed that H3.7 failed to form nucleosomes [taguchi_crystal_2017].",
                 "taxonomy": "null",
                 "genes": "null",
                 "evolution": "null",
@@ -4928,20 +4930,22 @@
                 "sequence": "null",
                 "localization": "null",
                 "deposition": "null",
-                "structure": "null",
+                "structure": "In vitro results showed that H3.7 failed to form nucleosomes [taguchi_crystal_2017].",
                 "interactions": "null",
                 "disease": "null",
                 "caveats": "null"
             },
             "taxonomic_span": "null",
             "taxonomic_span_id": "null",
             "alternate_names": [],
-            "publications": []
+            "publications": [
+                "taguchi_crystal_2017"
+            ]
         },
-        "H3.8_(Mammals?)?": {
+        "H3.8_(Homo_sapiens)": {
             "level": "variant_group",
             "description": {
-                "summary": "null",
+                "summary": "H3.8_(Homo_sapiens) is a human histone variant, similar to histone variant H3.3 in amino acid sequence, encoded by the H3F3AP5 gene. Expression levels of H3F3AP5 are extremely low, as compared to H3F3B gene (encodes histone H3.3) [taguchi_crystal_2017]. H3.8 nucleosomes are extremely unstable [taguchi_crystal_2017].",
                 "taxonomy": "null",
                 "genes": "null",
                 "evolution": "null",
@@ -4951,15 +4955,17 @@
                 "sequence": "null",
                 "localization": "null",
                 "deposition": "null",
-                "structure": "null",
+                "structure": "H3.8 nucleosomes are extremely unstable [taguchi_crystal_2017].",
                 "interactions": "null",
                 "disease": "null",
                 "caveats": "null"
             },
             "taxonomic_span": "null",
             "taxonomic_span_id": "null",
             "alternate_names": [],
-            "publications": []
+            "publications": [
+                "taguchi_crystal_2017"
+            ]
         },
         "H3.B_(Giardia?)": {
             "level": "variant_group",

diff --git a/CURATED_SET/curated_service/curatedDB/UPD_curatedDB_241018.ipynb b/CURATED_SET/curated_service/curatedDB/UPD_curatedDB_241018.ipynb
@@ -484,7 +484,6 @@
    "cell_type": "markdown",
    "id": "42fed33b-1181-4f30-917a-d835b96d24b9",
    "metadata": {
-    "jp-MarkdownHeadingCollapsed": true,
     "tags": []
    },
    "source": [

diff --git a/CURATED_SET/curated_service/curatedDB/UPD_curatedDB_241113.ipynb b/CURATED_SET/curated_service/curatedDB/UPD_curatedDB_241113.ipynb
@@ -2364,7 +2364,10 @@
   {
    "cell_type": "markdown",
    "id": "e8fd8805-c640-415d-94a0-da21a6e9ccf3",
-   "metadata": {},
+   "metadata": {
+    "jp-MarkdownHeadingCollapsed": true,
+    "tags": []
+   },
    "source": [
     "# Delete GBG59214.1 and GBG60584.1\n",
     "\n",