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fid.txt

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proteome_meta.py

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+import collections
+
+# Global profiles
+global_profiles_dict = {"Detectability": "detectability", "Promiscuity": "promiscuity"}
+
+# Task suffixes
+task_suf = collections.OrderedDict()
+
+task_suf["_val_log2fc"] = "Log2FC"
+task_suf["_gauss"] = "Gaussianized score"
+
+task_suf["_bin_hit"] = "Protein hits (custom cutoffs)"
+task_suf["_bin_50"] = "Top 50 proteins"
+task_suf["_bin_100"] = "Top 100 proteins"
+task_suf["_bin_250"] = "Top 250 proteins"
+task_suf["_bin_500"] = "Top 500 proteins"
+task_suf["_top_50"] = "Top 50 proteins"
+task_suf["_top_100"] = "Top 100 proteins"
+task_suf["_top_250"] = "Top 250 proteins"
+task_suf["_top_500"] = "Top 500 proteins"
+task_suf["_bottom_50"] = "Bottom 50 proteins"
+task_suf["_bottom_100"] = "Bottom 100 proteins"
+task_suf["_bottom_250"] = "Bottom 250 proteins"
+task_suf["_bottom_500"] = "Bottom 500 proteins"
+
+# Annotation type dict
+annotation_type_dict = {
+    "Sequence": [
+        "InterPro Superfamily",
+        "InterPro Family",
+        "InterPro Domain",
+        "InterPro Active site",
+        "InterPro Binding site",
+        "InterPro Conserved site",
+        "InterPro Repeat",
+        "InterPro PTM"
+    ],
+    "Functions": [
+        "Panther Protein class",
+        "Protein Atlas Protein class",
+        "Protein Atlas Molecular function",
+        "GO Molecular function",
+    ],
+    "Processes and pathways": [
+        "Reactome Pathways",
+        "KEGG Pathways",
+        "WikiPathways",
+        "Protein Atlas Biological process",
+        "GO Biological process",
+    ],
+    "Localization": [
+        "Protein Atlas Subcellular",
+        "GO Cellular component",
+        "OpenCell Localization",
+    ],
+    "Drugs and Diseases": [
+        "Pharos IDG Category",
+        "Pharos Drug Target Ontology",
+        "Protein Atlas Disease involvement",
+        "Human Phenotype Ontology",
+    ],
+}
+
+# Annotation dict
+annotation_dict = {
+    # Sequence
+    "InterPro Superfamily": "interpro_homologous_superfamily",
+    "InterPro Family": "interpro_family",
+    "InterPro Domain": "interpro_domain",
+    "InterPro Active site": "interpro_active_site",
+    "InterPro Binding site": "interpro_binding_site",
+    "InterPro Conserved site": "interpro_conserved_site",
+    "InterPro Repeat": "interpro_repeat",
+    "InterPro PTM": "interpro_ptm",
+    # Functions
+    "Panther Protein class": "panther_protein_class",
+    "Protein Atlas Protein class": "protein_atlas_protein_class",
+    "Protein Atlas Molecular function": "protein_atlas_molecular_function",
+    "GO Molecular function": "msigdb_gomf",
+    # Pathways
+    "Reactome Pathways": "msigdb_reactome",
+    "KEGG Pathways": "msigdb_kegg",
+    "WikiPathways": "msigdb_wp",
+    "Protein Atlas Biological process": "protein_atlas_biological_process",
+    "GO Biological process": "msigdb_gobp",
+    # Localization
+    "Protein Atlas Subcellular": "protein_atlas_subcellular_location_all", # _main?
+    "GO Cellular component": "msigdb_gocc",
+    "OpenCell Localization": "opencell_localization",
+    # Drugs and Diseases
+    "Pharos IDG Category": "pharos_protein_category",
+    "Pharos Drug Target Ontology": "pharos_dto",
+    "Protein Atlas Disease involvement": "protein_atlas_disease_involvement",
+    "Human Phenotype Ontology": "msigdb_hp",
+}
+
+# Universe dict
+universe_dict = {
+    "Human Proteome": "human_proteome",
+    "HEK293T Core": "hek293t_core",
+    "Bind Degs Detected": "cemm_detected",
+    "Bind Degs Enriched": "cemm_enriched",
+    "Pulldown": "pulldown",
+}