\n",
" \n",
" | 0 | \n",
- " urn:mavedb:00000041-a-1 | \n",
- " CTGCGGCTGGAGGTCAAGCTGGGCCAGGGCTGCTTTGGCGAGGTGT... | \n",
+ " urn:mavedb:00000001-a-1 | \n",
+ " ATGTCGGGGATCGCCCTCAGCAGACTCGCCCAGGAGAGGAAAGCAT... | \n",
" dna | \n",
- " Src catalytic domain | \n",
- " GCF_000001405.26 | \n",
- " P12931 | \n",
+ " UBE2I | \n",
" Protein coding | \n",
+ " P63279 | \n",
+ " Homo sapiens | \n",
"
\n",
" \n",
" | 1 | \n",
- " urn:mavedb:00000048-a-1 | \n",
- " GAGGGGATCAGTATATACACTTCAGATAACTACACCGAGGAAATGG... | \n",
+ " urn:mavedb:00000001-a-2 | \n",
+ " ATGTCGGGGATCGCCCTCAGCAGACTCGCCCAGGAGAGGAAAGCAT... | \n",
" dna | \n",
- " CXCR4 | \n",
- " GCF_000001405.26 | \n",
- " P61073 | \n",
+ " UBE2I | \n",
" Protein coding | \n",
+ " P63279 | \n",
+ " Homo sapiens | \n",
"
\n",
" \n",
" | 2 | \n",
- " urn:mavedb:00000068-b-1 | \n",
- " ATGGAGGAGCCGCAGTCAGATCCTAGCGTCGAGCCCCCTCTGAGTC... | \n",
+ " urn:mavedb:00000001-a-3 | \n",
+ " ATGTCGGGGATCGCCCTCAGCAGACTCGCCCAGGAGAGGAAAGCAT... | \n",
" dna | \n",
- " TP53 (P72R) | \n",
- " GCF_000001405.26 | \n",
- " NaN | \n",
+ " UBE2I | \n",
" Protein coding | \n",
+ " P63279 | \n",
+ " Homo sapiens | \n",
"
\n",
" \n",
" | 3 | \n",
- " urn:mavedb:00000045-c-1 | \n",
- " ATGGATGTATTCATGAAAGGACTTTCAAAGGCCAAGGAGGGAGTTG... | \n",
+ " urn:mavedb:00000001-a-4 | \n",
+ " ATGTCGGGGATCGCCCTCAGCAGACTCGCCCAGGAGAGGAAAGCAT... | \n",
" dna | \n",
- " alpha-synuclein | \n",
- " GCF_000001405.10 | \n",
- " P37840 | \n",
+ " UBE2I | \n",
" Protein coding | \n",
+ " P63279 | \n",
+ " Homo sapiens | \n",
"
\n",
" \n",
" | 4 | \n",
- " urn:mavedb:00000018-a-1 | \n",
- " GGTGTCTGTTTGAGGTTGCTAGTGAACACAGTTGTGTCAGAAGCAA... | \n",
+ " urn:mavedb:00000001-b-1 | \n",
+ " ATGTCTGACCAGGAGGCAAAACCTTCAACTGAGGACTTGGGGGATA... | \n",
" dna | \n",
- " HBB promoter | \n",
- " GCF_000001405.26 | \n",
- " NaN | \n",
- " Regulatory | \n",
+ " SUMO1 | \n",
+ " Protein coding | \n",
+ " P63165 | \n",
+ " Homo sapiens | \n",
"
\n",
" \n",
"\n",
@@ -136,25 +136,18 @@
],
"text/plain": [
" urn target_sequence \\\n",
- "0 urn:mavedb:00000041-a-1 CTGCGGCTGGAGGTCAAGCTGGGCCAGGGCTGCTTTGGCGAGGTGT... \n",
- "1 urn:mavedb:00000048-a-1 GAGGGGATCAGTATATACACTTCAGATAACTACACCGAGGAAATGG... \n",
- "2 urn:mavedb:00000068-b-1 ATGGAGGAGCCGCAGTCAGATCCTAGCGTCGAGCCCCCTCTGAGTC... \n",
- "3 urn:mavedb:00000045-c-1 ATGGATGTATTCATGAAAGGACTTTCAAAGGCCAAGGAGGGAGTTG... \n",
- "4 urn:mavedb:00000018-a-1 GGTGTCTGTTTGAGGTTGCTAGTGAACACAGTTGTGTCAGAAGCAA... \n",
- "\n",
- " target_sequence_type target assembly_id uniprot_id \\\n",
- "0 dna Src catalytic domain GCF_000001405.26 P12931 \n",
- "1 dna CXCR4 GCF_000001405.26 P61073 \n",
- "2 dna TP53 (P72R) GCF_000001405.26 NaN \n",
- "3 dna alpha-synuclein GCF_000001405.10 P37840 \n",
- "4 dna HBB promoter GCF_000001405.26 NaN \n",
+ "0 urn:mavedb:00000001-a-1 ATGTCGGGGATCGCCCTCAGCAGACTCGCCCAGGAGAGGAAAGCAT... \n",
+ "1 urn:mavedb:00000001-a-2 ATGTCGGGGATCGCCCTCAGCAGACTCGCCCAGGAGAGGAAAGCAT... \n",
+ "2 urn:mavedb:00000001-a-3 ATGTCGGGGATCGCCCTCAGCAGACTCGCCCAGGAGAGGAAAGCAT... \n",
+ "3 urn:mavedb:00000001-a-4 ATGTCGGGGATCGCCCTCAGCAGACTCGCCCAGGAGAGGAAAGCAT... \n",
+ "4 urn:mavedb:00000001-b-1 ATGTCTGACCAGGAGGCAAAACCTTCAACTGAGGACTTGGGGGATA... \n",
"\n",
- " target_type \n",
- "0 Protein coding \n",
- "1 Protein coding \n",
- "2 Protein coding \n",
- "3 Protein coding \n",
- "4 Regulatory "
+ " target_sequence_type target target_type uniprot_id organism \n",
+ "0 dna UBE2I Protein coding P63279 Homo sapiens \n",
+ "1 dna UBE2I Protein coding P63279 Homo sapiens \n",
+ "2 dna UBE2I Protein coding P63279 Homo sapiens \n",
+ "3 dna UBE2I Protein coding P63279 Homo sapiens \n",
+ "4 dna SUMO1 Protein coding P63165 Homo sapiens "
]
},
"execution_count": 2,
@@ -163,8 +156,7 @@
}
],
"source": [
- "mave_dat = pd.read_csv(\"analysis_files/mave_dat.csv\", index_col=[0])\n",
- "mave_dat = mave_dat.iloc[:-5]\n",
+ "mave_dat = pd.read_csv(\"analysis_files/mave_metadata_20241114.csv\", index_col=0)\n",
"mave_dat.head()"
]
},
@@ -185,7 +177,7 @@
{
"data": {
"text/plain": [
- "'The number of score sets with DNA target sequences is: 176'"
+ "'The number of score sets with DNA target sequences is: 482'"
]
},
"execution_count": 3,
@@ -215,7 +207,7 @@
{
"data": {
"text/plain": [
- "'The number of score sets with protein target sequences is: 33'"
+ "'The number of score sets with protein target sequences is: 582'"
]
},
"execution_count": 4,
@@ -245,7 +237,7 @@
{
"data": {
"text/plain": [
- "'The number of protein coding score sets: 168'"
+ "'The number of protein coding score sets: 1023'"
]
},
"execution_count": 5,
@@ -305,7 +297,7 @@
{
"data": {
"text/plain": [
- "'95 score sets have UniProt IDs'"
+ "'897 score sets have UniProt IDs'"
]
},
"execution_count": 7,
@@ -334,7 +326,7 @@
{
"data": {
"text/plain": [
- "'The number of score sets with protein target sequences is: 33'"
+ "'The number of score sets with protein target sequences is: 582'"
]
},
"execution_count": 8,
@@ -363,7 +355,7 @@
{
"data": {
"text/plain": [
- "'The number of coding score sets with DNA target sequences is: 135'"
+ "'The number of coding score sets with DNA target sequences is: 441'"
]
},
"execution_count": 9,
@@ -421,7 +413,7 @@
{
"data": {
"text/plain": [
- "'The average length of protein target sequences is: 573.060606060606 amino acids'"
+ "'The average length of protein target sequences is: 105.39003436426117 amino acids'"
]
},
"execution_count": 11,
@@ -452,7 +444,7 @@
{
"data": {
"text/plain": [
- "'The average length of protein coding DNA target sequences is: 1337.6296296296296 nucleotides'"
+ "'The average length of protein coding DNA target sequences is: 635.2448979591836 nucleotides'"
]
},
"execution_count": 12,
@@ -514,7 +506,7 @@
{
"data": {
"text/plain": [
- "'The number of protein coding score sets with gene symbols/aliases is: 126'"
+ "'The number of protein coding score sets with gene symbols/aliases is: 348'"
]
},
"execution_count": 14,
@@ -545,7 +537,7 @@
{
"data": {
"text/plain": [
- "'The number of protein coding score sets with descriptive targets is: 42'"
+ "'The number of protein coding score sets with descriptive targets is: 675'"
]
},
"execution_count": 15,
@@ -607,7 +599,7 @@
{
"data": {
"text/plain": [
- "'The number of unique gene symbols across examined score set targets is: 71'"
+ "'The number of unique gene symbols across examined score set targets is: 526'"
]
},
"execution_count": 17,
@@ -641,90 +633,9 @@
"execution_count": 18,
"id": "4ef61ec4",
"metadata": {},
- "outputs": [
- {
- "data": {
- "text/plain": [
- "{'ACE2',\n",
- " 'AICDA',\n",
- " 'ALDOB',\n",
- " 'Aβ42',\n",
- " 'BCL11A',\n",
- " 'BRAF',\n",
- " 'BRCA1',\n",
- " 'CALM1',\n",
- " 'CBS',\n",
- " 'CCR5',\n",
- " 'CD86',\n",
- " 'CXCR4',\n",
- " 'CYP2C19',\n",
- " 'CYP2C9',\n",
- " 'DLG4',\n",
- " 'ECR11',\n",
- " 'ERBB2',\n",
- " 'F9',\n",
- " 'FOXE1',\n",
- " 'GABBR1',\n",
- " 'GCK',\n",
- " 'GDI1',\n",
- " 'GP1BB',\n",
- " 'Glycophorin',\n",
- " 'HBB',\n",
- " 'HBG1',\n",
- " 'HMBS',\n",
- " 'HMGCR',\n",
- " 'HNF4A',\n",
- " 'IGHG1',\n",
- " 'IRF4',\n",
- " 'IRF6',\n",
- " 'KCNQ1',\n",
- " 'KCNQ4',\n",
- " 'LDLR',\n",
- " 'LDLRAP1',\n",
- " 'MAPK1',\n",
- " 'MPL',\n",
- " 'MSH2',\n",
- " 'MSMB',\n",
- " 'MTHFR',\n",
- " 'MYC',\n",
- " 'NCS1',\n",
- " 'NUDT15',\n",
- " 'PARP1',\n",
- " 'PKLR',\n",
- " 'PSAT1',\n",
- " 'PTEN',\n",
- " 'RET',\n",
- " 'RHO',\n",
- " 'Ras',\n",
- " 'SCN5A',\n",
- " 'SORT1',\n",
- " 'SRC',\n",
- " 'SUMO1',\n",
- " 'TARDBP',\n",
- " 'TCF7L2',\n",
- " 'TECR',\n",
- " 'TERT',\n",
- " 'TP53',\n",
- " 'TPK1',\n",
- " 'TPMT',\n",
- " 'UBE2I',\n",
- " 'UC88',\n",
- " 'VKORC1',\n",
- " 'WT1',\n",
- " 'YAP1',\n",
- " 'ZFAND3',\n",
- " 'ZHX2',\n",
- " 'ZRS',\n",
- " 'alpha-synuclein'}"
- ]
- },
- "execution_count": 18,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
+ "outputs": [],
"source": [
- "set(unique_genes)"
+ "#set(unique_genes)"
]
},
{
@@ -768,7 +679,7 @@
"