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are all BRD4 inhibitors replicable?
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@niranjchandrasekaran
niranjchandrasekaran committed Jan 4, 2024
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Showing 1 changed file with 321 additions and 13 deletions.
334 changes: 321 additions & 13 deletions benchmark/10.analyze-brd4.ipynb
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"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [],
"source": [
"replicate_retrieval = pd.read_csv(\"output/cellprofiler_replicability_map.csv\").merge(\n",
" other_brd4, on=\"Metadata_broad_sample\"\n",
")"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {},
"outputs": [
{
"data": {
Expand Down Expand Up @@ -676,13 +665,332 @@
"7 compound U2OS long 48 PFI-1 bromodomain inhibitor "
]
},
"execution_count": 10,
"execution_count": 9,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"replicate_retrieval"
"replicate_retrieval_other_brd4 = pd.read_csv(\"output/cellprofiler_replicability_map.csv\").merge(\n",
" other_brd4, on=\"Metadata_broad_sample\"\n",
")\n",
"replicate_retrieval_other_brd4"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {},
"outputs": [],
"source": [
"all_brd4 = metadata.query('pert_iname==\"PFI-1\" or pert_iname==\"TG-101348\" or pert_iname==\"BI-2536\"')"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
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"</style>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>Metadata_broad_sample</th>\n",
" <th>mean_average_precision</th>\n",
" <th>nlog10pvalue</th>\n",
" <th>q_value</th>\n",
" <th>nlog10qvalue</th>\n",
" <th>above_p_threshold</th>\n",
" <th>above_q_threshold</th>\n",
" <th>Description</th>\n",
" <th>Modality</th>\n",
" <th>Cell</th>\n",
" <th>time</th>\n",
" <th>timepoint</th>\n",
" <th>pert_iname</th>\n",
" <th>moa_list</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>BRD-K12502280-001-11-4</td>\n",
" <td>1.000000</td>\n",
" <td>5.000004</td>\n",
" <td>0.000033</td>\n",
" <td>4.482766</td>\n",
" <td>True</td>\n",
" <td>True</td>\n",
" <td>compound_A549_short</td>\n",
" <td>compound</td>\n",
" <td>A549</td>\n",
" <td>short</td>\n",
" <td>24</td>\n",
" <td>TG-101348</td>\n",
" <td>FLT3 inhibitor|JAK inhibitor</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>BRD-K12502280-001-11-4</td>\n",
" <td>1.000000</td>\n",
" <td>5.000004</td>\n",
" <td>0.000021</td>\n",
" <td>4.672645</td>\n",
" <td>True</td>\n",
" <td>True</td>\n",
" <td>compound_A549_long</td>\n",
" <td>compound</td>\n",
" <td>A549</td>\n",
" <td>long</td>\n",
" <td>48</td>\n",
" <td>TG-101348</td>\n",
" <td>FLT3 inhibitor|JAK inhibitor</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>BRD-K12502280-001-11-4</td>\n",
" <td>1.000000</td>\n",
" <td>5.000004</td>\n",
" <td>0.000030</td>\n",
" <td>4.527120</td>\n",
" <td>True</td>\n",
" <td>True</td>\n",
" <td>compound_U2OS_short</td>\n",
" <td>compound</td>\n",
" <td>U2OS</td>\n",
" <td>short</td>\n",
" <td>24</td>\n",
" <td>TG-101348</td>\n",
" <td>FLT3 inhibitor|JAK inhibitor</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>BRD-K12502280-001-11-4</td>\n",
" <td>1.000000</td>\n",
" <td>5.000004</td>\n",
" <td>0.000032</td>\n",
" <td>4.492007</td>\n",
" <td>True</td>\n",
" <td>True</td>\n",
" <td>compound_U2OS_long</td>\n",
" <td>compound</td>\n",
" <td>U2OS</td>\n",
" <td>long</td>\n",
" <td>48</td>\n",
" <td>TG-101348</td>\n",
" <td>FLT3 inhibitor|JAK inhibitor</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>BRD-K13094524-001-04-2</td>\n",
" <td>0.840278</td>\n",
" <td>4.094814</td>\n",
" <td>0.000216</td>\n",
" <td>3.665998</td>\n",
" <td>True</td>\n",
" <td>True</td>\n",
" <td>compound_A549_short</td>\n",
" <td>compound</td>\n",
" <td>A549</td>\n",
" <td>short</td>\n",
" <td>24</td>\n",
" <td>PFI-1</td>\n",
" <td>bromodomain inhibitor</td>\n",
" </tr>\n",
" <tr>\n",
" <th>5</th>\n",
" <td>BRD-K13094524-001-04-2</td>\n",
" <td>1.000000</td>\n",
" <td>5.000004</td>\n",
" <td>0.000021</td>\n",
" <td>4.672645</td>\n",
" <td>True</td>\n",
" <td>True</td>\n",
" <td>compound_A549_long</td>\n",
" <td>compound</td>\n",
" <td>A549</td>\n",
" <td>long</td>\n",
" <td>48</td>\n",
" <td>PFI-1</td>\n",
" <td>bromodomain inhibitor</td>\n",
" </tr>\n",
" <tr>\n",
" <th>6</th>\n",
" <td>BRD-K13094524-001-04-2</td>\n",
" <td>0.298359</td>\n",
" <td>1.287362</td>\n",
" <td>0.063666</td>\n",
" <td>1.196092</td>\n",
" <td>False</td>\n",
" <td>False</td>\n",
" <td>compound_U2OS_short</td>\n",
" <td>compound</td>\n",
" <td>U2OS</td>\n",
" <td>short</td>\n",
" <td>24</td>\n",
" <td>PFI-1</td>\n",
" <td>bromodomain inhibitor</td>\n",
" </tr>\n",
" <tr>\n",
" <th>7</th>\n",
" <td>BRD-K13094524-001-04-2</td>\n",
" <td>0.520889</td>\n",
" <td>2.389472</td>\n",
" <td>0.007899</td>\n",
" <td>2.102408</td>\n",
" <td>True</td>\n",
" <td>True</td>\n",
" <td>compound_U2OS_long</td>\n",
" <td>compound</td>\n",
" <td>U2OS</td>\n",
" <td>long</td>\n",
" <td>48</td>\n",
" <td>PFI-1</td>\n",
" <td>bromodomain inhibitor</td>\n",
" </tr>\n",
" <tr>\n",
" <th>8</th>\n",
" <td>BRD-K64890080-001-02-1</td>\n",
" <td>1.000000</td>\n",
" <td>5.000004</td>\n",
" <td>0.000033</td>\n",
" <td>4.482766</td>\n",
" <td>True</td>\n",
" <td>True</td>\n",
" <td>compound_A549_short</td>\n",
" <td>compound</td>\n",
" <td>A549</td>\n",
" <td>short</td>\n",
" <td>24</td>\n",
" <td>BI-2536</td>\n",
" <td>PLK inhibitor</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9</th>\n",
" <td>BRD-K64890080-001-02-1</td>\n",
" <td>1.000000</td>\n",
" <td>5.000004</td>\n",
" <td>0.000021</td>\n",
" <td>4.672645</td>\n",
" <td>True</td>\n",
" <td>True</td>\n",
" <td>compound_A549_long</td>\n",
" <td>compound</td>\n",
" <td>A549</td>\n",
" <td>long</td>\n",
" <td>48</td>\n",
" <td>BI-2536</td>\n",
" <td>PLK inhibitor</td>\n",
" </tr>\n",
" <tr>\n",
" <th>10</th>\n",
" <td>BRD-K64890080-001-02-1</td>\n",
" <td>1.000000</td>\n",
" <td>5.000004</td>\n",
" <td>0.000030</td>\n",
" <td>4.527120</td>\n",
" <td>True</td>\n",
" <td>True</td>\n",
" <td>compound_U2OS_short</td>\n",
" <td>compound</td>\n",
" <td>U2OS</td>\n",
" <td>short</td>\n",
" <td>24</td>\n",
" <td>BI-2536</td>\n",
" <td>PLK inhibitor</td>\n",
" </tr>\n",
" <tr>\n",
" <th>11</th>\n",
" <td>BRD-K64890080-001-02-1</td>\n",
" <td>1.000000</td>\n",
" <td>5.000004</td>\n",
" <td>0.000032</td>\n",
" <td>4.492007</td>\n",
" <td>True</td>\n",
" <td>True</td>\n",
" <td>compound_U2OS_long</td>\n",
" <td>compound</td>\n",
" <td>U2OS</td>\n",
" <td>long</td>\n",
" <td>48</td>\n",
" <td>BI-2536</td>\n",
" <td>PLK inhibitor</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" Metadata_broad_sample mean_average_precision nlog10pvalue q_value \\\n",
"0 BRD-K12502280-001-11-4 1.000000 5.000004 0.000033 \n",
"1 BRD-K12502280-001-11-4 1.000000 5.000004 0.000021 \n",
"2 BRD-K12502280-001-11-4 1.000000 5.000004 0.000030 \n",
"3 BRD-K12502280-001-11-4 1.000000 5.000004 0.000032 \n",
"4 BRD-K13094524-001-04-2 0.840278 4.094814 0.000216 \n",
"5 BRD-K13094524-001-04-2 1.000000 5.000004 0.000021 \n",
"6 BRD-K13094524-001-04-2 0.298359 1.287362 0.063666 \n",
"7 BRD-K13094524-001-04-2 0.520889 2.389472 0.007899 \n",
"8 BRD-K64890080-001-02-1 1.000000 5.000004 0.000033 \n",
"9 BRD-K64890080-001-02-1 1.000000 5.000004 0.000021 \n",
"10 BRD-K64890080-001-02-1 1.000000 5.000004 0.000030 \n",
"11 BRD-K64890080-001-02-1 1.000000 5.000004 0.000032 \n",
"\n",
" nlog10qvalue above_p_threshold above_q_threshold Description \\\n",
"0 4.482766 True True compound_A549_short \n",
"1 4.672645 True True compound_A549_long \n",
"2 4.527120 True True compound_U2OS_short \n",
"3 4.492007 True True compound_U2OS_long \n",
"4 3.665998 True True compound_A549_short \n",
"5 4.672645 True True compound_A549_long \n",
"6 1.196092 False False compound_U2OS_short \n",
"7 2.102408 True True compound_U2OS_long \n",
"8 4.482766 True True compound_A549_short \n",
"9 4.672645 True True compound_A549_long \n",
"10 4.527120 True True compound_U2OS_short \n",
"11 4.492007 True True compound_U2OS_long \n",
"\n",
" Modality Cell time timepoint pert_iname moa_list \n",
"0 compound A549 short 24 TG-101348 FLT3 inhibitor|JAK inhibitor \n",
"1 compound A549 long 48 TG-101348 FLT3 inhibitor|JAK inhibitor \n",
"2 compound U2OS short 24 TG-101348 FLT3 inhibitor|JAK inhibitor \n",
"3 compound U2OS long 48 TG-101348 FLT3 inhibitor|JAK inhibitor \n",
"4 compound A549 short 24 PFI-1 bromodomain inhibitor \n",
"5 compound A549 long 48 PFI-1 bromodomain inhibitor \n",
"6 compound U2OS short 24 PFI-1 bromodomain inhibitor \n",
"7 compound U2OS long 48 PFI-1 bromodomain inhibitor \n",
"8 compound A549 short 24 BI-2536 PLK inhibitor \n",
"9 compound A549 long 48 BI-2536 PLK inhibitor \n",
"10 compound U2OS short 24 BI-2536 PLK inhibitor \n",
"11 compound U2OS long 48 BI-2536 PLK inhibitor "
]
},
"execution_count": 11,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"replicate_retrieval_all_brd4 = pd.read_csv(\"output/cellprofiler_replicability_map.csv\").merge(\n",
" all_brd4, on=\"Metadata_broad_sample\"\n",
")\n",
"replicate_retrieval_all_brd4"
]
}
],
Expand Down

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