py-CellCall 0.1.0__py3-none-any.whl

cellcall/correlation.py

@@ -0,0 +1,93 @@
+"""TF-target gene correlation filtering using Spearman correlation."""
+
+from __future__ import annotations
+import numpy as np
+import pandas as pd
+from scipy import stats
+
+
+def get_correlated_genes(
+    data: pd.DataFrame,
+    cell_type: str,
+    tf: str,
+    target_list: list[str],
+    p_value: float = 0.05,
+    cor_value: float = 0.0,
+    top_gene: float = 0.1,
+) -> list[str]:
+    """Filter target genes of a TF by Spearman correlation.
+
+    Parameters
+    ----------
+    data : pd.DataFrame
+        Expression matrix (genes x cells).
+    cell_type : str
+        Cell type to subset.
+    tf : str
+        Transcription factor gene name.
+    target_list : list[str]
+        Candidate target genes.
+    p_value : float
+        P-value threshold.
+    cor_value : float
+        Correlation threshold.
+    top_gene : float
+        Fraction of top correlated genes to keep (1.0 = keep all).
+
+    Returns
+    -------
+    list[str]
+        Filtered target gene names.
+    """
+    if tf not in data.index:
+        return []
+
+    ct_cols = data.columns[data.columns == cell_type]
+    if len(ct_cols) == 0:
+        return []
+
+    expr_tmp = data[ct_cols]
+
+    tf_expr = expr_tmp.loc[tf].values.astype(float)
+    target_expr = expr_tmp.loc[expr_tmp.index.isin(target_list)]
+
+    if target_expr.empty:
+        return []
+
+    # Compute Spearman correlation: tf vs each target
+    valid_targets = []
+    valid_corr = []
+    valid_p = []
+
+    for gene in target_expr.index:
+        gene_expr = target_expr.loc[gene].values.astype(float)
+        if np.std(gene_expr) == 0 or np.std(tf_expr) == 0:
+            continue
+        corr, p = stats.spearmanr(tf_expr, gene_expr)
+        if np.isnan(corr):
+            continue
+        valid_targets.append(gene)
+        valid_corr.append(corr)
+        valid_p.append(p)
+
+    if not valid_targets:
+        return []
+
+    corr_df = pd.DataFrame({"gene": valid_targets, "corr": valid_corr, "p": valid_p})
+
+    # Filter by p-value and correlation
+    filtered = corr_df[(corr_df["p"] < p_value) & (corr_df["corr"] > cor_value)]
+
+    if len(filtered) <= 1:
+        return []
+
+    # Sort by correlation descending
+    filtered = filtered.sort_values("corr", ascending=False)
+
+    # Take top fraction (skip the first one which is TF itself if present)
+    n_top = int(np.floor(top_gene * len(filtered)))
+    genes = filtered["gene"].tolist()
+
+    if len(genes) > n_top + 1:
+        genes = genes[1 : n_top + 1]
+    return genes

cellcall/distance.py

@@ -0,0 +1,72 @@
+"""KEGG pathway distance computation between ligand-receptor pairs and TFs.
+
+Vectorized implementation for speed.
+"""
+
+from __future__ import annotations
+import numpy as np
+import pandas as pd
+
+
+def get_distance_kegg(
+    triple_relation: pd.DataFrame,
+    method: str = "mean",
+) -> pd.DataFrame:
+    """Compute distance between LR pairs and TFs from KEGG pathway data.
+
+    Parameters
+    ----------
+    triple_relation : pd.DataFrame
+        Must contain columns at indices 4, 5 for Ligand_Symbol, Receptor_Symbol,
+        TF_Symbol, and a column with KEGG path distances (index 3, comma-separated
+        path_distance pairs like "path1_3,path2_5").
+    method : str
+        "mean" or "median" to aggregate multiple path distances.
+
+    Returns
+    -------
+    pd.DataFrame
+        Distance matrix (LR pairs x TFs).
+    """
+    lr_inter = triple_relation.iloc[:, [4, 5]].drop_duplicates()
+    lr_labels = (lr_inter.iloc[:, 0].astype(str) + "-" + lr_inter.iloc[:, 1].astype(str)).values
+
+    tf_symbols = triple_relation["TF_Symbol"].unique()
+
+    dist_matrix = pd.DataFrame(0.0, index=lr_labels, columns=tf_symbols)
+
+    # Vectorized: group by LR-TF pair and compute mean distance
+    triple_relation = triple_relation.copy()
+    triple_relation["_lr_key"] = (
+        triple_relation.iloc[:, 4].astype(str) + "-" + triple_relation.iloc[:, 5].astype(str)
+    )
+
+    # Parse distances vectorized
+    def _parse_distances(path_str: str, method: str = "mean") -> float:
+        if not path_str or path_str == "nan":
+            return 0.0
+        parts = str(path_str).split(",")
+        distances = []
+        for part in parts:
+            if "_" in part:
+                try:
+                    d = float(part.rsplit("_", 1)[1])
+                    distances.append(d)
+                except (ValueError, IndexError):
+                    continue
+        if not distances:
+            return 0.0
+        return float(np.mean(distances)) if method == "mean" else float(np.median(distances))
+
+    # Apply vectorized
+    path_col = triple_relation.iloc[:, 3]
+    distances = path_col.apply(lambda x: _parse_distances(x, method))
+
+    for i, row in triple_relation.iterrows():
+        lr_key = row["_lr_key"]
+        tf_key = row["TF_Symbol"]
+        d = distances[i]
+        if lr_key in dist_matrix.index and tf_key in dist_matrix.columns:
+            dist_matrix.loc[lr_key, tf_key] = d
+
+    return dist_matrix

cellcall/extdata/KEGG_SYMBOL_ID.txt

@@ -0,0 +1,336 @@
+hsa01100	Metabolic pathways	Metabolism	Global and overview maps
+hsa01200	Carbon metabolism	Metabolism	Global and overview maps
+hsa01210	2-Oxocarboxylic acid metabolism	Metabolism	Global and overview maps
+hsa01212	Fatty acid metabolism	Metabolism	Global and overview maps
+hsa01230	Biosynthesis of amino acids	Metabolism	Global and overview maps
+hsa00010	Glycolysis / Gluconeogenesis	Metabolism	Carbohydrate metabolism
+hsa00020	Citrate cycle (TCA cycle)	Metabolism	Carbohydrate metabolism
+hsa00030	Pentose phosphate pathway	Metabolism	Carbohydrate metabolism
+hsa00040	Pentose and glucuronate interconversions	Metabolism	Carbohydrate metabolism
+hsa00051	Fructose and mannose metabolism	Metabolism	Carbohydrate metabolism
+hsa00052	Galactose metabolism	Metabolism	Carbohydrate metabolism
+hsa00053	Ascorbate and aldarate metabolism	Metabolism	Carbohydrate metabolism
+hsa00500	Starch and sucrose metabolism	Metabolism	Carbohydrate metabolism
+hsa00520	Amino sugar and nucleotide sugar metabolism	Metabolism	Carbohydrate metabolism
+hsa00620	Pyruvate metabolism	Metabolism	Carbohydrate metabolism
+hsa00630	Glyoxylate and dicarboxylate metabolism	Metabolism	Carbohydrate metabolism
+hsa00640	Propanoate metabolism	Metabolism	Carbohydrate metabolism
+hsa00650	Butanoate metabolism	Metabolism	Carbohydrate metabolism
+hsa00562	Inositol phosphate metabolism	Metabolism	Carbohydrate metabolism
+hsa00190	Oxidative phosphorylation	Metabolism	Energy metabolism
+hsa00910	Nitrogen metabolism	Metabolism	Energy metabolism
+hsa00920	Sulfur metabolism	Metabolism	Energy metabolism
+hsa00061	Fatty acid biosynthesis	Metabolism	Lipid metabolism
+hsa00062	Fatty acid elongation	Metabolism	Lipid metabolism
+hsa00071	Fatty acid degradation	Metabolism	Lipid metabolism
+hsa00072	Synthesis and degradation of ketone bodies	Metabolism	Lipid metabolism
+hsa00100	Steroid biosynthesis	Metabolism	Lipid metabolism
+hsa00120	Primary bile acid biosynthesis	Metabolism	Lipid metabolism
+hsa00140	Steroid hormone biosynthesis	Metabolism	Lipid metabolism
+hsa00561	Glycerolipid metabolism	Metabolism	Lipid metabolism
+hsa00564	Glycerophospholipid metabolism	Metabolism	Lipid metabolism
+hsa00565	Ether lipid metabolism	Metabolism	Lipid metabolism
+hsa00600	Sphingolipid metabolism	Metabolism	Lipid metabolism
+hsa00590	Arachidonic acid metabolism	Metabolism	Lipid metabolism
+hsa00591	Linoleic acid metabolism	Metabolism	Lipid metabolism
+hsa00592	alpha-Linolenic acid metabolism	Metabolism	Lipid metabolism
+hsa01040	Biosynthesis of unsaturated fatty acids	Metabolism	Lipid metabolism
+hsa00230	Purine metabolism	Metabolism	Nucleotide metabolism
+hsa00240	Pyrimidine metabolism	Metabolism	Nucleotide metabolism
+hsa00250	Alanine, aspartate and glutamate metabolism	Metabolism	Amino acid metabolism
+hsa00260	Glycine, serine and threonine metabolism	Metabolism	Amino acid metabolism
+hsa00270	Cysteine and methionine metabolism	Metabolism	Amino acid metabolism
+hsa00280	Valine, leucine and isoleucine degradation	Metabolism	Amino acid metabolism
+hsa00290	Valine, leucine and isoleucine biosynthesis	Metabolism	Amino acid metabolism
+hsa00310	Lysine degradation	Metabolism	Amino acid metabolism
+hsa00220	Arginine biosynthesis	Metabolism	Amino acid metabolism
+hsa00330	Arginine and proline metabolism	Metabolism	Amino acid metabolism
+hsa00340	Histidine metabolism	Metabolism	Amino acid metabolism
+hsa00350	Tyrosine metabolism	Metabolism	Amino acid metabolism
+hsa00360	Phenylalanine metabolism	Metabolism	Amino acid metabolism
+hsa00380	Tryptophan metabolism	Metabolism	Amino acid metabolism
+hsa00400	Phenylalanine, tyrosine and tryptophan biosynthesis	Metabolism	Amino acid metabolism
+hsa00410	beta-Alanine metabolism	Metabolism	Metabolism of other amino acids
+hsa00430	Taurine and hypotaurine metabolism	Metabolism	Metabolism of other amino acids
+hsa00440	Phosphonate and phosphinate metabolism	Metabolism	Metabolism of other amino acids
+hsa00450	Selenocompound metabolism	Metabolism	Metabolism of other amino acids
+hsa00471	D-Glutamine and D-glutamate metabolism	Metabolism	Metabolism of other amino acids
+hsa00472	D-Arginine and D-ornithine metabolism	Metabolism	Metabolism of other amino acids
+hsa00480	Glutathione metabolism	Metabolism	Metabolism of other amino acids
+hsa00510	N-Glycan biosynthesis	Metabolism	Glycan biosynthesis and metabolism
+hsa00513	Various types of N-glycan biosynthesis	Metabolism	Glycan biosynthesis and metabolism
+hsa00512	Mucin type O-glycan biosynthesis	Metabolism	Glycan biosynthesis and metabolism
+hsa00515	Mannose type O-glycan biosynthesis	Metabolism	Glycan biosynthesis and metabolism
+hsa00514	Other types of O-glycan biosynthesis	Metabolism	Glycan biosynthesis and metabolism
+hsa00532	Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate	Metabolism	Glycan biosynthesis and metabolism
+hsa00534	Glycosaminoglycan biosynthesis - heparan sulfate / heparin	Metabolism	Glycan biosynthesis and metabolism
+hsa00533	Glycosaminoglycan biosynthesis - keratan sulfate	Metabolism	Glycan biosynthesis and metabolism
+hsa00531	Glycosaminoglycan degradation	Metabolism	Glycan biosynthesis and metabolism
+hsa00563	Glycosylphosphatidylinositol (GPI)-anchor biosynthesis	Metabolism	Glycan biosynthesis and metabolism
+hsa00601	Glycosphingolipid biosynthesis - lacto and neolacto series	Metabolism	Glycan biosynthesis and metabolism
+hsa00603	Glycosphingolipid biosynthesis - globo and isoglobo series	Metabolism	Glycan biosynthesis and metabolism
+hsa00604	Glycosphingolipid biosynthesis - ganglio series	Metabolism	Glycan biosynthesis and metabolism
+hsa00511	Other glycan degradation	Metabolism	Glycan biosynthesis and metabolism
+hsa00730	Thiamine metabolism	Metabolism	Metabolism of cofactors and vitamins
+hsa00740	Riboflavin metabolism	Metabolism	Metabolism of cofactors and vitamins
+hsa00750	Vitamin B6 metabolism	Metabolism	Metabolism of cofactors and vitamins
+hsa00760	Nicotinate and nicotinamide metabolism	Metabolism	Metabolism of cofactors and vitamins
+hsa00770	Pantothenate and CoA biosynthesis	Metabolism	Metabolism of cofactors and vitamins
+hsa00780	Biotin metabolism	Metabolism	Metabolism of cofactors and vitamins
+hsa00785	Lipoic acid metabolism	Metabolism	Metabolism of cofactors and vitamins
+hsa00790	Folate biosynthesis	Metabolism	Metabolism of cofactors and vitamins
+hsa00670	One carbon pool by folate	Metabolism	Metabolism of cofactors and vitamins
+hsa00830	Retinol metabolism	Metabolism	Metabolism of cofactors and vitamins
+hsa00860	Porphyrin and chlorophyll metabolism	Metabolism	Metabolism of cofactors and vitamins
+hsa00130	Ubiquinone and other terpenoid-quinone biosynthesis	Metabolism	Metabolism of cofactors and vitamins
+hsa00900	Terpenoid backbone biosynthesis	Metabolism	Metabolism of terpenoids and polyketides
+hsa00232	Caffeine metabolism	Metabolism	Biosynthesis of other secondary metabolites
+hsa00524	Neomycin, kanamycin and gentamicin biosynthesis	Metabolism	Biosynthesis of other secondary metabolites
+hsa00980	Metabolism of xenobiotics by cytochrome P450	Metabolism	Xenobiotics biodegradation and metabolism
+hsa00982	Drug metabolism - cytochrome P450	Metabolism	Xenobiotics biodegradation and metabolism
+hsa00983	Drug metabolism - other enzymes	Metabolism	Xenobiotics biodegradation and metabolism
+hsa03020	RNA polymerase	Genetic Information Processing	Transcription
+hsa03022	Basal transcription factors	Genetic Information Processing	Transcription
+hsa03040	Spliceosome	Genetic Information Processing	Transcription
+hsa03010	Ribosome	Genetic Information Processing	Translation
+hsa00970	Aminoacyl-tRNA biosynthesis	Genetic Information Processing	Translation
+hsa03013	RNA transport	Genetic Information Processing	Translation
+hsa03015	mRNA surveillance pathway	Genetic Information Processing	Translation
+hsa03008	Ribosome biogenesis in eukaryotes	Genetic Information Processing	Translation
+hsa03060	Protein export	Genetic Information Processing	Folding, sorting and degradation
+hsa04141	Protein processing in endoplasmic reticulum	Genetic Information Processing	Folding, sorting and degradation
+hsa04130	SNARE interactions in vesicular transport	Genetic Information Processing	Folding, sorting and degradation
+hsa04120	Ubiquitin mediated proteolysis	Genetic Information Processing	Folding, sorting and degradation
+hsa04122	Sulfur relay system	Genetic Information Processing	Folding, sorting and degradation
+hsa03050	Proteasome	Genetic Information Processing	Folding, sorting and degradation
+hsa03018	RNA degradation	Genetic Information Processing	Folding, sorting and degradation
+hsa03030	DNA replication	Genetic Information Processing	Replication and repair
+hsa03410	Base excision repair	Genetic Information Processing	Replication and repair
+hsa03420	Nucleotide excision repair	Genetic Information Processing	Replication and repair
+hsa03430	Mismatch repair	Genetic Information Processing	Replication and repair
+hsa03440	Homologous recombination	Genetic Information Processing	Replication and repair
+hsa03450	Non-homologous end-joining	Genetic Information Processing	Replication and repair
+hsa03460	Fanconi anemia pathway	Genetic Information Processing	Replication and repair
+hsa02010	ABC transporters	Environmental Information Processing	Membrane transport
+hsa04014	Ras signaling pathway	Environmental Information Processing	Signal transduction
+hsa04015	Rap1 signaling pathway	Environmental Information Processing	Signal transduction
+hsa04010	MAPK signaling pathway	Environmental Information Processing	Signal transduction
+hsa04012	ErbB signaling pathway	Environmental Information Processing	Signal transduction
+hsa04310	Wnt signaling pathway	Environmental Information Processing	Signal transduction
+hsa04330	Notch signaling pathway	Environmental Information Processing	Signal transduction
+hsa04340	Hedgehog signaling pathway	Environmental Information Processing	Signal transduction
+hsa04350	TGF-beta signaling pathway	Environmental Information Processing	Signal transduction
+hsa04390	Hippo signaling pathway	Environmental Information Processing	Signal transduction
+hsa04392	Hippo signaling pathway - multiple species	Environmental Information Processing	Signal transduction
+hsa04370	VEGF signaling pathway	Environmental Information Processing	Signal transduction
+hsa04371	Apelin signaling pathway	Environmental Information Processing	Signal transduction
+hsa04630	Jak-STAT signaling pathway	Environmental Information Processing	Signal transduction
+hsa04064	NF-kappa B signaling pathway	Environmental Information Processing	Signal transduction
+hsa04668	TNF signaling pathway	Environmental Information Processing	Signal transduction
+hsa04066	HIF-1 signaling pathway	Environmental Information Processing	Signal transduction
+hsa04068	FoxO signaling pathway	Environmental Information Processing	Signal transduction
+hsa04020	Calcium signaling pathway	Environmental Information Processing	Signal transduction
+hsa04070	Phosphatidylinositol signaling system	Environmental Information Processing	Signal transduction
+hsa04072	Phospholipase D signaling pathway	Environmental Information Processing	Signal transduction
+hsa04071	Sphingolipid signaling pathway	Environmental Information Processing	Signal transduction
+hsa04024	cAMP signaling pathway	Environmental Information Processing	Signal transduction
+hsa04022	cGMP-PKG signaling pathway	Environmental Information Processing	Signal transduction
+hsa04151	PI3K-Akt signaling pathway	Environmental Information Processing	Signal transduction
+hsa04152	AMPK signaling pathway	Environmental Information Processing	Signal transduction
+hsa04150	mTOR signaling pathway	Environmental Information Processing	Signal transduction
+hsa04080	Neuroactive ligand-receptor interaction	Environmental Information Processing	Signaling molecules and interaction
+hsa04060	Cytokine-cytokine receptor interaction	Environmental Information Processing	Signaling molecules and interaction
+hsa04061	Viral protein interaction with cytokine and cytokine receptor	Environmental Information Processing	Signaling molecules and interaction
+hsa04512	ECM-receptor interaction	Environmental Information Processing	Signaling molecules and interaction
+hsa04514	Cell adhesion molecules (CAMs)	Environmental Information Processing	Signaling molecules and interaction
+hsa04144	Endocytosis	Cellular Processes	Transport and catabolism
+hsa04145	Phagosome	Cellular Processes	Transport and catabolism
+hsa04142	Lysosome	Cellular Processes	Transport and catabolism
+hsa04146	Peroxisome	Cellular Processes	Transport and catabolism
+hsa04140	Autophagy - animal	Cellular Processes	Transport and catabolism
+hsa04136	Autophagy - other	Cellular Processes	Transport and catabolism
+hsa04137	Mitophagy - animal	Cellular Processes	Transport and catabolism
+hsa04110	Cell cycle	Cellular Processes	Cell growth and death
+hsa04114	Oocyte meiosis	Cellular Processes	Cell growth and death
+hsa04210	Apoptosis	Cellular Processes	Cell growth and death
+hsa04215	Apoptosis - multiple species	Cellular Processes	Cell growth and death
+hsa04216	Ferroptosis	Cellular Processes	Cell growth and death
+hsa04217	Necroptosis	Cellular Processes	Cell growth and death
+hsa04115	p53 signaling pathway	Cellular Processes	Cell growth and death
+hsa04218	Cellular senescence	Cellular Processes	Cell growth and death
+hsa04510	Focal adhesion	Cellular Processes	Cellular community - eukaryotes
+hsa04520	Adherens junction	Cellular Processes	Cellular community - eukaryotes
+hsa04530	Tight junction	Cellular Processes	Cellular community - eukaryotes
+hsa04540	Gap junction	Cellular Processes	Cellular community - eukaryotes
+hsa04550	Signaling pathways regulating pluripotency of stem cells	Cellular Processes	Cellular community - eukaryotes
+hsa04810	Regulation of actin cytoskeleton	Cellular Processes	Cell motility
+hsa04640	Hematopoietic cell lineage	Organismal Systems	Immune system
+hsa04610	Complement and coagulation cascades	Organismal Systems	Immune system
+hsa04611	Platelet activation	Organismal Systems	Immune system
+hsa04620	Toll-like receptor signaling pathway	Organismal Systems	Immune system
+hsa04621	NOD-like receptor signaling pathway	Organismal Systems	Immune system
+hsa04622	RIG-I-like receptor signaling pathway	Organismal Systems	Immune system
+hsa04623	Cytosolic DNA-sensing pathway	Organismal Systems	Immune system
+hsa04625	C-type lectin receptor signaling pathway	Organismal Systems	Immune system
+hsa04650	Natural killer cell mediated cytotoxicity	Organismal Systems	Immune system
+hsa04612	Antigen processing and presentation	Organismal Systems	Immune system
+hsa04660	T cell receptor signaling pathway	Organismal Systems	Immune system
+hsa04658	Th1 and Th2 cell differentiation	Organismal Systems	Immune system
+hsa04659	Th17 cell differentiation	Organismal Systems	Immune system
+hsa04657	IL-17 signaling pathway	Organismal Systems	Immune system
+hsa04662	B cell receptor signaling pathway	Organismal Systems	Immune system
+hsa04664	Fc epsilon RI signaling pathway	Organismal Systems	Immune system
+hsa04666	Fc gamma R-mediated phagocytosis	Organismal Systems	Immune system
+hsa04670	Leukocyte transendothelial migration	Organismal Systems	Immune system
+hsa04672	Intestinal immune network for IgA production	Organismal Systems	Immune system
+hsa04062	Chemokine signaling pathway	Organismal Systems	Immune system
+hsa04911	Insulin secretion	Organismal Systems	Endocrine system
+hsa04910	Insulin signaling pathway	Organismal Systems	Endocrine system
+hsa04922	Glucagon signaling pathway	Organismal Systems	Endocrine system
+hsa04923	Regulation of lipolysis in adipocytes	Organismal Systems	Endocrine system
+hsa04920	Adipocytokine signaling pathway	Organismal Systems	Endocrine system
+hsa03320	PPAR signaling pathway	Organismal Systems	Endocrine system
+hsa04929	GnRH secretion	Organismal Systems	Endocrine system
+hsa04912	GnRH signaling pathway	Organismal Systems	Endocrine system
+hsa04913	Ovarian steroidogenesis	Organismal Systems	Endocrine system
+hsa04915	Estrogen signaling pathway	Organismal Systems	Endocrine system
+hsa04914	Progesterone-mediated oocyte maturation	Organismal Systems	Endocrine system
+hsa04917	Prolactin signaling pathway	Organismal Systems	Endocrine system
+hsa04921	Oxytocin signaling pathway	Organismal Systems	Endocrine system
+hsa04926	Relaxin signaling pathway	Organismal Systems	Endocrine system
+hsa04935	Growth hormone synthesis, secretion and action	Organismal Systems	Endocrine system
+hsa04918	Thyroid hormone synthesis	Organismal Systems	Endocrine system
+hsa04919	Thyroid hormone signaling pathway	Organismal Systems	Endocrine system
+hsa04928	Parathyroid hormone synthesis, secretion and action	Organismal Systems	Endocrine system
+hsa04916	Melanogenesis	Organismal Systems	Endocrine system
+hsa04924	Renin secretion	Organismal Systems	Endocrine system
+hsa04614	Renin-angiotensin system	Organismal Systems	Endocrine system
+hsa04925	Aldosterone synthesis and secretion	Organismal Systems	Endocrine system
+hsa04927	Cortisol synthesis and secretion	Organismal Systems	Endocrine system
+hsa04260	Cardiac muscle contraction	Organismal Systems	Circulatory system
+hsa04261	Adrenergic signaling in cardiomyocytes	Organismal Systems	Circulatory system
+hsa04270	Vascular smooth muscle contraction	Organismal Systems	Circulatory system
+hsa04970	Salivary secretion	Organismal Systems	Digestive system
+hsa04971	Gastric acid secretion	Organismal Systems	Digestive system
+hsa04972	Pancreatic secretion	Organismal Systems	Digestive system
+hsa04976	Bile secretion	Organismal Systems	Digestive system
+hsa04973	Carbohydrate digestion and absorption	Organismal Systems	Digestive system
+hsa04974	Protein digestion and absorption	Organismal Systems	Digestive system
+hsa04975	Fat digestion and absorption	Organismal Systems	Digestive system
+hsa04979	Cholesterol metabolism	Organismal Systems	Digestive system
+hsa04977	Vitamin digestion and absorption	Organismal Systems	Digestive system
+hsa04978	Mineral absorption	Organismal Systems	Digestive system
+hsa04962	Vasopressin-regulated water reabsorption	Organismal Systems	Excretory system
+hsa04960	Aldosterone-regulated sodium reabsorption	Organismal Systems	Excretory system
+hsa04961	Endocrine and other factor-regulated calcium reabsorption	Organismal Systems	Excretory system
+hsa04964	Proximal tubule bicarbonate reclamation	Organismal Systems	Excretory system
+hsa04966	Collecting duct acid secretion	Organismal Systems	Excretory system
+hsa04724	Glutamatergic synapse	Organismal Systems	Nervous system
+hsa04727	GABAergic synapse	Organismal Systems	Nervous system
+hsa04725	Cholinergic synapse	Organismal Systems	Nervous system
+hsa04728	Dopaminergic synapse	Organismal Systems	Nervous system
+hsa04726	Serotonergic synapse	Organismal Systems	Nervous system
+hsa04720	Long-term potentiation	Organismal Systems	Nervous system
+hsa04730	Long-term depression	Organismal Systems	Nervous system
+hsa04723	Retrograde endocannabinoid signaling	Organismal Systems	Nervous system
+hsa04721	Synaptic vesicle cycle	Organismal Systems	Nervous system
+hsa04722	Neurotrophin signaling pathway	Organismal Systems	Nervous system
+hsa04744	Phototransduction	Organismal Systems	Sensory system
+hsa04740	Olfactory transduction	Organismal Systems	Sensory system
+hsa04742	Taste transduction	Organismal Systems	Sensory system
+hsa04750	Inflammatory mediator regulation of TRP channels	Organismal Systems	Sensory system
+hsa04360	Axon guidance	Organismal Systems	Development and regeneration
+hsa04380	Osteoclast differentiation	Organismal Systems	Development and regeneration
+hsa04211	Longevity regulating pathway	Organismal Systems	Aging
+hsa04213	Longevity regulating pathway - multiple species	Organismal Systems	Aging
+hsa04710	Circadian rhythm	Organismal Systems	Environmental adaptation
+hsa04713	Circadian entrainment	Organismal Systems	Environmental adaptation
+hsa04714	Thermogenesis	Organismal Systems	Environmental adaptation
+hsa05200	Pathways in cancer	Human Diseases	Cancer: overview
+hsa05202	Transcriptional misregulation in cancer	Human Diseases	Cancer: overview
+hsa05206	MicroRNAs in cancer	Human Diseases	Cancer: overview
+hsa05205	Proteoglycans in cancer	Human Diseases	Cancer: overview
+hsa05204	Chemical carcinogenesis	Human Diseases	Cancer: overview
+hsa05203	Viral carcinogenesis	Human Diseases	Cancer: overview
+hsa05230	Central carbon metabolism in cancer	Human Diseases	Cancer: overview
+hsa05231	Choline metabolism in cancer	Human Diseases	Cancer: overview
+hsa05235	PD-L1 expression and PD-1 checkpoint pathway in cancer	Human Diseases	Cancer: overview
+hsa05210	Colorectal cancer	Human Diseases	Cancer: specific types
+hsa05212	Pancreatic cancer	Human Diseases	Cancer: specific types
+hsa05225	Hepatocellular carcinoma	Human Diseases	Cancer: specific types
+hsa05226	Gastric cancer	Human Diseases	Cancer: specific types
+hsa05214	Glioma	Human Diseases	Cancer: specific types
+hsa05216	Thyroid cancer	Human Diseases	Cancer: specific types
+hsa05221	Acute myeloid leukemia	Human Diseases	Cancer: specific types
+hsa05220	Chronic myeloid leukemia	Human Diseases	Cancer: specific types
+hsa05217	Basal cell carcinoma	Human Diseases	Cancer: specific types
+hsa05218	Melanoma	Human Diseases	Cancer: specific types
+hsa05211	Renal cell carcinoma	Human Diseases	Cancer: specific types
+hsa05219	Bladder cancer	Human Diseases	Cancer: specific types
+hsa05215	Prostate cancer	Human Diseases	Cancer: specific types
+hsa05213	Endometrial cancer	Human Diseases	Cancer: specific types
+hsa05224	Breast cancer	Human Diseases	Cancer: specific types
+hsa05222	Small cell lung cancer	Human Diseases	Cancer: specific types
+hsa05223	Non-small cell lung cancer	Human Diseases	Cancer: specific types
+hsa05310	Asthma	Human Diseases	Immune disease
+hsa05322	Systemic lupus erythematosus	Human Diseases	Immune disease
+hsa05323	Rheumatoid arthritis	Human Diseases	Immune disease
+hsa05320	Autoimmune thyroid disease	Human Diseases	Immune disease
+hsa05321	Inflammatory bowel disease (IBD)	Human Diseases	Immune disease
+hsa05330	Allograft rejection	Human Diseases	Immune disease
+hsa05332	Graft-versus-host disease	Human Diseases	Immune disease
+hsa05340	Primary immunodeficiency	Human Diseases	Immune disease
+hsa05010	Alzheimer disease	Human Diseases	Neurodegenerative disease
+hsa05012	Parkinson disease	Human Diseases	Neurodegenerative disease
+hsa05014	Amyotrophic lateral sclerosis (ALS)	Human Diseases	Neurodegenerative disease
+hsa05016	Huntington disease	Human Diseases	Neurodegenerative disease
+hsa05020	Prion diseases	Human Diseases	Neurodegenerative disease
+hsa05030	Cocaine addiction	Human Diseases	Substance dependence
+hsa05031	Amphetamine addiction	Human Diseases	Substance dependence
+hsa05032	Morphine addiction	Human Diseases	Substance dependence
+hsa05033	Nicotine addiction	Human Diseases	Substance dependence
+hsa05034	Alcoholism	Human Diseases	Substance dependence
+hsa05418	Fluid shear stress and atherosclerosis	Human Diseases	Cardiovascular disease
+hsa05410	Hypertrophic cardiomyopathy (HCM)	Human Diseases	Cardiovascular disease
+hsa05412	Arrhythmogenic right ventricular cardiomyopathy (ARVC)	Human Diseases	Cardiovascular disease
+hsa05414	Dilated cardiomyopathy (DCM)	Human Diseases	Cardiovascular disease
+hsa05416	Viral myocarditis	Human Diseases	Cardiovascular disease
+hsa04930	Type II diabetes mellitus	Human Diseases	Endocrine and metabolic disease
+hsa04940	Type I diabetes mellitus	Human Diseases	Endocrine and metabolic disease
+hsa04950	Maturity onset diabetes of the young	Human Diseases	Endocrine and metabolic disease
+hsa04932	Non-alcoholic fatty liver disease (NAFLD)	Human Diseases	Endocrine and metabolic disease
+hsa04931	Insulin resistance	Human Diseases	Endocrine and metabolic disease
+hsa04933	AGE-RAGE signaling pathway in diabetic complications	Human Diseases	Endocrine and metabolic disease
+hsa04934	Cushing syndrome	Human Diseases	Endocrine and metabolic disease
+hsa05110	Vibrio cholerae infection	Human Diseases	Infectious disease: bacterial
+hsa05120	Epithelial cell signaling in Helicobacter pylori infection	Human Diseases	Infectious disease: bacterial
+hsa05130	Pathogenic Escherichia coli infection	Human Diseases	Infectious disease: bacterial
+hsa05132	Salmonella infection	Human Diseases	Infectious disease: bacterial
+hsa05131	Shigellosis	Human Diseases	Infectious disease: bacterial
+hsa05135	Yersinia infection	Human Diseases	Infectious disease: bacterial
+hsa05133	Pertussis	Human Diseases	Infectious disease: bacterial
+hsa05134	Legionellosis	Human Diseases	Infectious disease: bacterial
+hsa05150	Staphylococcus aureus infection	Human Diseases	Infectious disease: bacterial
+hsa05152	Tuberculosis	Human Diseases	Infectious disease: bacterial
+hsa05100	Bacterial invasion of epithelial cells	Human Diseases	Infectious disease: bacterial
+hsa05166	Human T-cell leukemia virus 1 infection	Human Diseases	Infectious disease: viral
+hsa05170	Human immunodeficiency virus 1 infection	Human Diseases	Infectious disease: viral
+hsa05162	Measles	Human Diseases	Infectious disease: viral
+hsa05164	Influenza A	Human Diseases	Infectious disease: viral
+hsa05161	Hepatitis B	Human Diseases	Infectious disease: viral
+hsa05160	Hepatitis C	Human Diseases	Infectious disease: viral
+hsa05168	Herpes simplex virus 1 infection	Human Diseases	Infectious disease: viral
+hsa05163	Human cytomegalovirus infection	Human Diseases	Infectious disease: viral
+hsa05167	Kaposi sarcoma-associated herpesvirus infection	Human Diseases	Infectious disease: viral
+hsa05169	Epstein-Barr virus infection	Human Diseases	Infectious disease: viral
+hsa05165	Human papillomavirus infection	Human Diseases	Infectious disease: viral
+hsa05146	Amoebiasis	Human Diseases	Infectious disease: parasitic
+hsa05144	Malaria	Human Diseases	Infectious disease: parasitic
+hsa05145	Toxoplasmosis	Human Diseases	Infectious disease: parasitic
+hsa05140	Leishmaniasis	Human Diseases	Infectious disease: parasitic
+hsa05142	Chagas disease (American trypanosomiasis)	Human Diseases	Infectious disease: parasitic
+hsa05143	African trypanosomiasis	Human Diseases	Infectious disease: parasitic
+hsa01521	EGFR tyrosine kinase inhibitor resistance	Human Diseases	Drug resistance: antineoplastic
+hsa01524	Platinum drug resistance	Human Diseases	Drug resistance: antineoplastic
+hsa01523	Antifolate resistance	Human Diseases	Drug resistance: antineoplastic
+hsa01522	Endocrine resistance	Human Diseases	Drug resistance: antineoplastic