Interpret via gradient tracking

import scanpy as sc
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
import seaborn as sns
import random
import os
import sys

sys.path.append('/ix3/djishnu/alw399/SpaceTravLR/src')

%matplotlib inline

figure_params = {
    'dpi': 300, 
    'bbox_inches': 'tight', 
    'format': 'svg', 
    'transparent': True
}

plt.rcParams.update({
    "text.usetex": False,
    "svg.fonttype": 'none'
})

# there are cell-intrinsic networks, and cell-extrinsic 
# cell-extrinsic ligand expression is from other cells
# bottom up network or top down network? "sphere of influence"
# ligand --> TF/receptor 
# or TF/receptor --> ligand --> TF/receptor

training_dir = '/ix/djishnu/shared/djishnu_kor11/training_data_revision/mouse_lymph_slideseq_D5_1/chunk_0'
adata = sc.read_h5ad(os.path.join(training_dir, 'input_data/_adata.h5ad'))
adata

AnnData object with n_obs × n_vars = 12681 × 3354
    obs: 'celltype_label_tangram', 'cell_type', 'cell_type_int'
    uns: 'cell_thresholds', 'neighbors', 'received_ligands', 'received_ligands_tfl', 'umap'
    obsm: 'X_pca', 'X_spatial', 'X_umap', 'spatial', 'spatial_unscaled', 'tangram_ct_pred'
    varm: 'PCs'
    layers: 'imputed_count', 'normalized_count', 'raw_count'
    obsp: 'connectivities', 'distances'

gene = 'Nr3c1'
# gene = 'Bcl6'

gex_out, gradients = gf.perturb_track(
    target=gene,
    n_propagation=4,
    gene_expr=0,
)

save_dir = training_dir + '/genome_screens'

import pickle
with open(f'{save_dir}/{gene}_4n_0x_gradients.pkl', 'rb') as f:
    gradients = pickle.load(f)
gradients.keys()

dict_keys(['A2m', 'Adam15', 'Adam33', 'Adamts15', 'Adamts16', 'Adamts8', 'Adamts9', 'Adat3', 'Adcy4', 'Adcy5', 'Adcy9', 'Adgrd1', 'Adgre5', 'Adgrf3', 'Adgrf5', 'Adgrl2', 'Adgrv1', 'Adh1', 'Adh6-ps1', 'Adhfe1', 'Adig', 'Adipoq', 'Adipor1', 'Adora1', 'Adora3', 'Adpgk', 'Adprhl1', 'Adra1b', 'Adra2a', 'Adrb1', 'Adrb3', 'Adssl1', 'Adtrp', 'Afap1l1', 'Afap1l2', 'Aga', 'Ager', 'Agfg2', 'Agpat2', 'Agtr1a', 'Ahcyl2', 'Ahdc1', 'Ahi1', 'Ahnak', 'Ahr', 'Aicda', 'Aifm2', 'Aig1', 'Ajap1', 'Ak1', 'Akap12', 'Akap9', 'Akr1b8', 'Akr1c14', 'Akr1cl', 'Akr1e1', 'Alas2', 'Aldh1a7', 'Aldh2', 'Aldh3a1', 'Aldh3a2', 'Aldh3b2', 'Aldh6a1', 'Aldh7a1', 'Alg11', 'Alg14', 'Alkbh2', 'Alkbh8', 'Alox15', 'Alox5ap', 'Als2', 'Als2cr12', 'Amdhd1', 'Amotl1', 'Amotl2', 'Amph', 'Amy1', 'Anapc10', 'Anapc4', 'Ang', 'Angpt1', 'Angptl4', 'Ankdd1b', 'Ankfn1', 'Ankhd1', 'Ankrd1', 'Ankrd13b', 'Ankrd2', 'Ankrd26', 'Ankrd45', 'Ankrd46', 'Anks1b', 'Anks6', 'Ano1', 'Anxa1', 'Anxa2', 'Anxa4', 'Anxa8', 'Aoc2', 'Aoc3', 'Aox1', 'Aox4', 'Ap5b1', 'Apbb1', 'Apex1', 'Aph1b', 'Apln', 'Apoa4', 'Apoc1', 'Apoc3', 'Apod', 'Apoe', 'Apol10b', 'Apol6', 'Apold1', 'App', 'Aqp11', 'Aqp7', 'Aqp9', 'Arap3', 'Arfip2', 'Arhgap20os', 'Arhgap25', 'Arhgap28', 'Arhgap29', 'Arhgap42', 'Arhgap5', 'Arhgef10', 'Arhgef15', 'Arhgef25', 'Arhgef39', 'Arhgef9', 'Arid4b', 'Arid5b', 'Arl15', 'Arl4a', 'Arl4d', 'Armc8', 'Armc9', 'Armcx4', 'Arpp21', 'Arrdc4', 'Arsg', 'Arxes1', 'Arxes2', 'Asb14', 'Ascl3', 'Asic1', 'Asns', 'Aspa', 'Aspg', 'Asph', 'Asphd2', 'Aspn', 'Aste1', 'Astn1', 'Atad2b', 'Atad5', 'Atf3', 'Atf4', 'Atf5', 'Atf6b', 'Atg10', 'Atg4c', 'Atg9b', 'Atp13a2', 'Atp1a2', 'Atp1b2', 'Atp5s', 'Atp6v0b', 'Atp6v0e2', 'Atp8a1', 'Atp9a', 'Atpaf2', 'Atrn', 'Atrnl1', 'Auts2', 'Avpr1a', 'B3galt2', 'B3gnt3', 'B3gnt8', 'B4gat1', 'Bace1', 'Bace2', 'Bach2', 'Bahcc1', 'Bambi', 'Batf', 'Bbs12', 'Bbs5', 'Bbs7', 'Bcar1', 'Bche', 'Bckdha', 'Bckdhb', 'Bcl11a', 'Bcl2l2', 'Bcl6', 'Bcl6b', 'Bcl7c', 'Bco2', 'Bean1', 'Begain', 'Bend5', 'Bex6', 'Bik', 'Birc5', 'Blm', 'Bloc1s6', 'Bmp2', 'Bok', 'Bola1', 'Bola3', 'Bpgm', 'Bpifa1', 'Brca1', 'Brinp1', 'Bspry', 'Bst1', 'Bst2', 'Btbd19', 'Btbd3', 'Btc', 'Btg3', 'Btla', 'Btnl9', 'Btrc', 'Bvht', 'C1qc', 'C1qtnf6', 'C1qtnf7', 'C1ra', 'C1rl', 'C2cd5', 'C3', 'C4b', 'C5ar1', 'C5ar2', 'C6', 'C77080', 'Cables1', 'Cabp1', 'Cabp4', 'Cabyr', 'Cacna2d1', 'Cacnb2', 'Cadm1', 'Cadps2', 'Cage1', 'Calml4', 'Calr4', 'Camk1', 'Camk2n1', 'Camk2n2', 'Camsap2', 'Camta1', 'Cap1', 'Capn5', 'Capn6', 'Capn9', 'Car14', 'Car2', 'Car3', 'Car5b', 'Car8', 'Car9', 'Card9', 'Carhsp1', 'Caskin1', 'Casp1', 'Casp3', 'Cass4', 'Catsper3', 'Cav2', 'Cbr2', 'Cbr4', 'Cbs', 'Ccar1', 'Ccbe1', 'Ccdc102a', 'Ccdc112', 'Ccdc114', 'Ccdc122', 'Ccdc125', 'Ccdc126', 'Ccdc160', 'Ccdc18', 'Ccdc57', 'Ccdc59', 'Ccdc62', 'Ccdc66', 'Ccdc80', 'Ccdc86', 'Ccdc88a', 'Ccl17', 'Ccl19', 'Ccl20', 'Ccl22', 'Ccl24', 'Ccl27a', 'Ccl5', 'Ccl6', 'Ccl7', 'Ccl8', 'Ccl9', 'Ccnd1', 'Ccnjl', 'Ccnt1', 'Ccnyl1', 'Ccr1', 'Ccr2', 'Ccr3', 'Ccr4', 'Ccr5', 'Ccr6', 'Ccr7', 'Ccr9', 'Ccser1', 'Cd109', 'Cd163', 'Cd180', 'Cd1d1', 'Cd200', 'Cd209a', 'Cd209b', 'Cd209f', 'Cd22', 'Cd244', 'Cd27', 'Cd274', 'Cd28', 'Cd300e', 'Cd300ld', 'Cd300lg', 'Cd302', 'Cd34', 'Cd36', 'Cd4', 'Cd40', 'Cd44', 'Cd48', 'Cd52', 'Cd59a', 'Cd5l', 'Cd6', 'Cd63', 'Cd69', 'Cd72', 'Cd74', 'Cd79b', 'Cd80', 'Cd86', 'Cd8a', 'Cd8b1', 'Cd9', 'Cd93', 'Cd96', 'Cdc14a', 'Cdc27', 'Cdc42bpa', 'Cdc42ep2', 'Cdh2', 'Cdh26', 'Cdh4', 'Cdh5', 'Cdkn1c', 'Cdkn2a', 'Cdnf', 'Cdo1', 'Cdyl', 'Ceacam16', 'Cebpb', 'Cebpe', 'Celf4', 'Celf6', 'Celsr2', 'Celsr3', 'Cenpe', 'Cenpk', 'Cenpm', 'Cenpn', 'Cenpo', 'Cenpp', 'Cenpq', 'Cenpt', 'Cenpw', 'Cep19', 'Cep57', 'Ces1d', 'Ces1f', 'Cfap36', 'Cfap97', 'Cfd', 'Cfh', 'Cfp', 'Cftr', 'Cgnl1', 'Cgref1', 'Ch25h', 'Chaf1b', 'Chchd10', 'Chd3os', 'Chdh', 'Chpt1', 'Chrna2', 'Chrna9', 'Chrnb1', 'Chst1', 'Chst12', 'Chst7', 'Cib2', 'Cib3', 'Cidea', 'Cidec', 'Ciita', 'Cit', 'Ciz1', 'Ckap4', 'Ckb', 'Clasp2', 'Clcf1', 'Clcn3', 'Clcn6', 'Cldn10', 'Cldn13', 'Cldn15', 'Clec10a', 'Clec12a', 'Clec2d', 'Clec2i', 'Clec3b', 'Clec4a2', 'Clec4b1', 'Clec4d', 'Clec4g', 'Clec4n', 'Clec5a', 'Clic5', 'Clip4', 'Cln8', 'Clp1', 'Clstn3', 'Clybl', 'Cma1', 'Cmbl', 'Cmklr1', 'Cmtm3', 'Cmtr2', 'Cngb1', 'Cnr1', 'Coa4', 'Coch', 'Cog3', 'Col15a1', 'Col16a1', 'Col18a1', 'Col1a1', 'Col1a2', 'Col20a1', 'Col23a1', 'Col3a1', 'Col4a1', 'Col4a2', 'Col5a1', 'Col5a2', 'Col6a1', 'Col6a5', 'Col6a6', 'Col9a3', 'Colec11', 'Colgalt1', 'Colq', 'Commd1', 'Comtd1', 'Coq10b', 'Coro2a', 'Cox4i1', 'Cox4i2', 'Cox6b2', 'Cox7a1', 'Cox8b', 'Cp', 'Cpa3', 'Cpd', 'Cpe', 'Cplx2', 'Cpn2', 'Cpne5', 'Cpne7', 'Cpq', 'Cpxm1', 'Cr2', 'Crabp1', 'Crabp2', 'Crat', 'Crb3', 'Creb1', 'Creb3l3', 'Creg1', 'Creg2', 'Crem', 'Crim1', 'Crip2', 'Crlf1', 'Crlf2', 'Crls1', 'Crmp1', 'Crnde', 'Crybb3', 'Cs', 'Csad', 'Csf1', 'Csf1r', 'Csf2ra', 'Csf2rb', 'Csf3r', 'Csl', 'Cspg4', 'Cspg5', 'Cst3', 'Ctc1', 'Ctcf', 'Ctdspl', 'Ctf2', 'Ctgf', 'Cthrc1', 'Ctif', 'Ctla2a', 'Ctla4', 'Ctnnal1', 'Ctrc', 'Ctsd', 'Ctsk', 'Ctsl', 'Cttn', 'Cuedc1', 'Cul5', 'Cul9', 'Cux1', 'Cx3cr1', 'Cxadr', 'Cxcl1', 'Cxcl10', 'Cxcl12', 'Cxcl13', 'Cxcl14', 'Cxcl16', 'Cxcl9', 'Cxcr2', 'Cxcr3', 'Cxcr4', 'Cxcr5', 'Cxcr6', 'Cxxc4', 'Cyb5d1', 'Cyb5rl', 'Cybb', 'Cycs', 'Cyp1b1', 'Cyp21a1', 'Cyp27b1', 'Cyp2d22', 'Cyp2e1', 'Cyp2f2', 'Cyp2j6', 'Cyp4b1', 'Cyp4f16', 'Cyp4f17', 'Cyr61', 'Cys1', 'Dab2', 'Dach1', 'Dact1', 'Dact2', 'Dag1', 'Dapk1', 'Dbi', 'Dbil5', 'Dbndd2', 'Dbt', 'Dcaf12l1', 'Dclre1c', 'Dcn', 'Dcst1', 'Dcun1d4', 'Ddc', 'Ddo', 'Ddr1', 'Ddx43', 'Ddx50', 'Ddx60', 'Decr1', 'Defb42', 'Dennd2a', 'Dennd5a', 'Deptor', 'Dgat1', 'Dgat2', 'Dgki', 'Dhh', 'Dhrs2', 'Dhrs3', 'Dhtkd1', 'Dhx57', 'Dio2', 'Dip2c', 'Dixdc1', 'Dkc1', 'Dkk2', 'Dkk3', 'Dkkl1', 'Dlat', 'Dlc1', 'Dleu7', 'Dlg5', 'Dlgap3', 'Dlst', 'Dmpk', 'Dmrt1', 'Dmxl2', 'Dnah1', 'Dnah6', 'Dnah7b', 'Dnaic1', 'Dnajb14', 'Dnajb3', 'Dnajc12', 'Dnajc21', 'Dnajc25', 'Dnase1l3', 'Dnm1', 'Dnm3os', 'Dnmt1', 'Doc2b', 'Dock5', 'Dock7', 'Dpf3', 'Dph1', 'Dpp7', 'Dpt', 'Dpy19l1', 'Draxin', 'Drd4', 'Dsc2', 'Dsc3', 'Dstn', 'Dstyk', 'Dtx4', 'Dusp18', 'Dusp19', 'Dusp28', 'Dusp6', 'Dusp8', 'Dvl1', 'Dydc2', 'Dync1i2', 'Dync1li2', 'Dynlrb2', 'Dynlt1f', 'Dyrk2', 'E2f3', 'E2f4', 'Eaf2', 'Ear2', 'Ebf1', 'Ebf2', 'Ebf3', 'Ebpl', 'Ece2', 'Ech1', 'Echdc2', 'Echs1', 'Eci1', 'Eci3', 'Ecm1', 'Ecscr', 'Ect2l', 'Efcab11', 'Efcab2', 'Efcab7', 'Efcc1', 'Efemp1', 'Efemp2', 'Efhd1', 'Efnb1', 'Efnb2', 'Efnb3', 'Efr3b', 'Efs', 'Egfl7', 'Egr1', 'Egr2', 'Ehbp1', 'Ehd4', 'Ehhadh', 'Eif2b4', 'Eif4e3', 'Elane', 'Elf1', 'Elf2', 'Elf4', 'Elk1', 'Elk3', 'Elk4', 'Elmod3', 'Eln', 'Elovl3', 'Elp6', 'Emc1', 'Emilin1', 'Emilin2', 'Emp1', 'Emp2', 'Enox1', 'Enpp4', 'Entpd2', 'Epdr1', 'Epha2', 'Epha5', 'Epha7', 'Ephx1', 'Ephx2', 'Epn2', 'Eps8l1', 'Epyc', 'Erbb3', 'Ercc4', 'Erg', 'Erlin1', 'Ermp1', 'Erp27', 'Erv3', 'Espl1', 'Etfa', 'Etfb', 'Etfdh', 'Etl4', 'Ets1', 'Etv1', 'Etv4', 'Etv6', 'Evi5', 'Exo1', 'Exoc2', 'Exoc3l', 'Exoc7', 'F11r', 'F12', 'F13a1', 'F2r', 'F3', 'F5', 'F7', 'F8', 'F8a', 'Fabp1', 'Fabp3', 'Fabp4', 'Fads6', 'Fah', 'Fahd1', 'Fam109a', 'Fam110c', 'Fam120aos', 'Fam122b', 'Fam124a', 'Fam13a', 'Fam160a1', 'Fam162b', 'Fam167b', 'Fam174a', 'Fam174b', 'Fam184a', 'Fam189a2', 'Fam199x', 'Fam20c', 'Fam210b', 'Fam213a', 'Fam217a', 'Fam217b', 'Fam222b', 'Fam26f', 'Fam71f2', 'Fam78b', 'Fam83c', 'Fam84a', 'Fam84b', 'Fance', 'Fancm', 'Fas', 'Fbln2', 'Fbln5', 'Fbln7', 'Fbn1', 'Fbn2', 'Fbp2', 'Fbxl12os', 'Fbxl13', 'Fbxo21', 'Fbxo47', 'Fbxo48', 'Fbxo5', 'Fbxw10', 'Fbxw18', 'Fcer2a', 'Fcgr3', 'Fcgrt', 'Fcna', 'Fcnb', 'Fcor', 'Fcrl5', 'Fcrl6', 'Fcrla', 'Fcrls', 'Fermt2', 'Fes', 'Ffar1', 'Ffar2', 'Ffar4', 'Fgd2', 'Fgd4', 'Fgd5', 'Fgf16', 'Fgf18', 'Fgf2', 'Fgfr1', 'Fgfrl1', 'Fggy', 'Fgl1', 'Fhdc1', 'Fhit', 'Fhl1', 'Fhl2', 'Fhod1', 'Fibcd1', 'Fibin', 'Fitm2', 'Fkbp14', 'Fkbp1b', 'Fkbp3', 'Fkbp7', 'Fkbp9', 'Fli1', 'Flnc', 'Flrt3', 'Flt1', 'Flt3', 'Flt3l', 'Flt4', 'Fmn1', 'Fmo1', 'Fmo2', 'Fmo4', 'Fn1', 'Fndc4', 'Fnip2', 'Fnta', 'Folr2', 'Fos', 'Fosb', 'Fosl2', 'Foxa3', 'Foxj2', 'Foxj3', 'Foxk1', 'Foxn3', 'Foxo1', 'Foxo3', 'Foxo4', 'Foxp1', 'Foxp3', 'Foxq1', 'Foxs1', 'Fsbp', 'Fst', 'Fstl1', 'Fuom', 'Fut8', 'Fv1', 'Fxn', 'Fxyd1', 'Fxyd2', 'Fxyd6', 'Fzd1', 'Fzd5', 'Fzd7', 'G0s2', 'G2e3', 'G6pdx', 'Gabarapl1', 'Gabpa', 'Gadd45a', 'Gadd45g', 'Gal3st3', 'Galc', 'Galnt15', 'Galnt16', 'Galnt18', 'Galt', 'Gamt', 'Gas6', 'Gata2', 'Gata3', 'Gatm', 'Gbe1', 'Gbp2b', 'Gbp4', 'Gbp5', 'Gbx2', 'Gck', 'Gcnt1', 'Gcnt4', 'Gda', 'Gde1', 'Gemin4', 'Gfer', 'Gfpt2', 'Ggact', 'Ggct', 'Ggnbp1', 'Ggps1', 'Gh', 'Ghitm', 'Ghr', 'Ginm1', 'Gins3', 'Gipr', 'Gja1', 'Gja4', 'Gjc2', 'Gkap1', 'Gla', 'Glb1l', 'Glb1l2', 'Glg1', 'Glis3', 'Glrx5', 'Glycam1', 'Gm10037', 'Gm10364', 'Gm10516', 'Gm10548', 'Gm10785', 'Gm1141', 'Gm11423', 'Gm12128', 'Gm12185', 'Gm12532', 'Gm12709', 'Gm128', 'Gm13056', 'Gm13199', 'Gm14295', 'Gm14326', 'Gm14634', 'Gm15056', 'Gm15133', 'Gm15326', 'Gm15706', 'Gm15735', 'Gm15910', 'Gm16287', 'Gm16576', 'Gm16617', 'Gm16630', 'Gm16675', 'Gm16845', 'Gm16894', 'Gm17455', 'Gm17634', 'Gm1966', 'Gm1976', 'Gm20878', 'Gm21814', 'Gm26641', 'Gm3086', 'Gm32200', 'Gm4285', 'Gm4750', 'Gm4759', 'Gm4876', 'Gm4951', 'Gm5127', 'Gm5177', 'Gm6787', 'Gm7694', 'Gm826', 'Gm9159', 'Gm9530', 'Gm9828', 'Gm9949', 'Gmpr', 'Gnb3', 'Gng11', 'Gngt1', 'Gnpda2', 'Gpatch3', 'Gpc3', 'Gpd1', 'Gpd2', 'Gpnmb', 'Gpr137c', 'Gpr150', 'Gpr152', 'Gpr19', 'Gpr33', 'Gpr55', 'Gpr75', 'Gpt', 'Gpt2', 'Gpx3', 'Gpx7', 'Gpx8', 'Gramd2', 'Gramd4', 'Grb10', 'Grb14', 'Grin2d', 'Grk4', 'Grk5', 'Grk6', 'Grm8', 'Grn', 'Grrp1', 'Gsn', 'Gsr', 'Gsta4', 'Gstk1', 'Gstm6', 'Gstm7', 'Gsto2', 'Gstt1', 'Gtf2b', 'Gtf2i', 'Gtsf1', 'Guca1a', 'Gypa', 'Gys1', 'Gys2', 'Gzma', 'H1f0', 'H2afy2', 'H6pd', 'Hacd2', 'Hadh', 'Hadhb', 'Hagh', 'Haglr', 'Hapln3', 'Havcr2', 'Hcar1', 'Hcar2', 'Hcst', 'Hddc2', 'Hddc3', 'Heatr3', 'Hells', 'Herpud1', 'Hexa', 'Hhla1', 'Hibch', 'Hif1a', 'Hif3a', 'Higd1b', 'Hist1h1c', 'Hist1h1d', 'Hist1h2ab', 'Hist1h2ak', 'Hist1h2bc', 'Hist1h2bj', 'Hist1h3a', 'Hist1h4a', 'Hist1h4k', 'Hist2h3c2', 'Hist3h2ba', 'Hlf', 'Hmgcll1', 'Hmgcs2', 'Hnmt', 'Hnrnph2', 'Hormad2', 'Hoxa4', 'Hoxb3', 'Hoxb4', 'Hoxb5', 'Hoxb7', 'Hoxc4', 'Hoxd8', 'Hoxd9', 'Hr', 'Hrct1', 'Hs3st3a1', 'Hs3st6', 'Hs6st2', 'Hsbp1l1', 'Hsd17b13', 'Hsdl2', 'Hsf1', 'Hsp90aa1', 'Hspa1b', 'Hspa2', 'Hspb1', 'Hspb2', 'Hspb8', 'Hspb9', 'Hspg2', 'Htra1', 'Htra3', 'Hyal1', 'Hyal2', 'Hyi', 'Hykk', 'Hyls1', 'Ica1', 'Icam1', 'Icam2', 'Icos', 'Icosl', 'Id1', 'Id4', 'Idh1', 'Idh3a', 'Idh3b', 'Ier3', 'Ier5l', 'Ifi204', 'Ifi27', 'Ifi30', 'Ifi44', 'Ifit1', 'Ifit3', 'Ifit3b', 'Ifitm3', 'Ifnar1', 'Ifnar2', 'Ifngr1', 'Ifngr2', 'Ifnlr1', 'Ifrd1', 'Ift74', 'Igf1', 'Igf1r', 'Igf2bp1', 'Igf2r', 'Igfbp6', 'Igfbp7', 'Igsf3', 'Iigp1', 'Ikbip', 'Ikzf1', 'Ikzf3', 'Ikzf4', 'Il10', 'Il10ra', 'Il10rb', 'Il11ra1', 'Il12b', 'Il12rb1', 'Il13', 'Il13ra1', 'Il13ra2', 'Il15ra', 'Il16', 'Il17ra', 'Il17rc', 'Il18', 'Il18r1', 'Il1a', 'Il1rap', 'Il1rl1', 'Il2', 'Il21', 'Il21r', 'Il22ra2', 'Il27ra', 'Il2ra', 'Il2rb', 'Il2rg', 'Il33', 'Il34', 'Il4', 'Il4ra', 'Il5ra', 'Il6ra', 'Il6st', 'Il7', 'Il7r', 'Il9r', 'Ildr2', 'Inca1', 'Ing4', 'Inhba', 'Inmt', 'Inpp5a', 'Insl6', 'Insrr', 'Intu', 'Ipp', 'Iqcg', 'Iqgap2', 'Irf1', 'Irf2', 'Irf3', 'Irf4', 'Irf7', 'Irf8', 'Irf9', 'Irs2', 'Isg15', 'Islr', 'Ispd', 'Itga1', 'Itga2b', 'Itga4', 'Itga5', 'Itga6', 'Itga7', 'Itga9', 'Itgae', 'Itgal', 'Itgam', 'Itgax', 'Itgb1', 'Itgb1bp1', 'Itgb1bp2', 'Itgb2', 'Itgb3', 'Itgb7', 'Itgbl1', 'Itih4', 'Itpr2', 'Jag1', 'Jag2', 'Jam3', 'Jazf1', 'Jchain', 'Jmy', 'Jpx', 'Jrk', 'Jun', 'Junb', 'Jund', 'Jup', 'Kank1', 'Kank2', 'Kank3', 'Kank4', 'Katnal2', 'Kbtbd8', 'Kcna5', 'Kcnd2', 'Kcne2', 'Kcng1', 'Kcnip3', 'Kcnj1', 'Kcnj10', 'Kcnj14', 'Kcnj15', 'Kcnj16', 'Kcnk13', 'Kcnk3', 'Kcnk5', 'Kcnk6', 'Kcnn2', 'Kcnn3', 'Kcnq1ot1', 'Kcnq4', 'Kcns3', 'Kctd10', 'Kctd15', 'Kctd6', 'Kdelc1', 'Kdelc2', 'Kdelr3', 'Kdr', 'Khdc1b', 'Khdc3', 'Khdrbs3', 'Kif18a', 'Kif1c', 'Kif26a', 'Kif26b', 'Kif5b', 'Kirrel3', 'Kitl', 'Kl', 'Klf10', 'Klf13', 'Klf2', 'Klf3', 'Klf4', 'Klf6', 'Klf7', 'Klf9', 'Klhl2', 'Klhl32', 'Klhl38', 'Klhl5', 'Klhl8', 'Klk1', 'Klra1', 'Klra3', 'Klrb1b', 'Klrb1c', 'Klrb1f', 'Klrc2', 'Klrd1', 'Klrk1', 'Kng2', 'Krt12', 'Krt19', 'Krt7', 'Kxd1', 'Kynu', 'L3hypdh', 'Lacc1', 'Lag3', 'Lair1', 'Lama3', 'Lama4', 'Lamb1', 'Lamb2', 'Lamb3', 'Larp6', 'Layn', 'Lcat', 'Lck', 'Lcn4', 'Lcor', 'Ldb2', 'Ldb3', 'Ldhb', 'Ldhd', 'Ldlr', 'Ldlrad4', 'Ldlrap1', 'Lef1', 'Lepr', 'Lgals12', 'Lgals3', 'Lgals4', 'Lgals7', 'Lgals9', 'Lhfpl2', 'Lhfpl4', 'Lhpp', 'Lhx6', 'Lhx8', 'Lif', 'Lifr', 'Lilra5', 'Lilra6', 'Limch1', 'Limk2', 'Lin28a', 'Lipe', 'Liph', 'Litaf', 'Lix1', 'Llgl2', 'Lmbrd2', 'Lmcd1', 'Lmna', 'Lmntd1', 'Lmo1', 'Lmo4', 'Lmod1', 'Lonrf2', 'Loxl4', 'Lpgat1', 'Lpin3', 'Lpl', 'Lrch2', 'Lrg1', 'Lrp1', 'Lrp2', 'Lrp5', 'Lrrc17', 'Lrrc18', 'Lrrc20', 'Lrrc25', 'Lrrc3', 'Lrrc39', 'Lrrc4', 'Lrrc71', 'Lrrn1', 'Lsm3', 'Lta', 'Ltb', 'Ltbp4', 'Ltbr', 'Ltc4s', 'Ltf', 'Lurap1l', 'Luzp1', 'Ly6d', 'Ly6g5b', 'Ly6g6c', 'Ly6g6f', 'Ly6k', 'Lypd1', 'Lypd2', 'Lyrm1', 'Lyrm4', 'Lyst', 'Lyve1', 'Lyz1', 'Lyz2', 'Lztfl1', 'Lzts1', 'Lzts3', 'Mab21l2', 'Macrod2', 'Mad2l1', 'Maf', 'Maff', 'Magee2', 'Mageh1', 'Magohb', 'Mal', 'Mal2', 'Malat1', 'Mamld1', 'Man2b2', 'Man2c1os', 'Manbal', 'Maneal', 'Maoa', 'Maob', 'Map10', 'Map1lc3a', 'Map2', 'Map3k15', 'Map3k9', 'Map6', 'Map7d2', 'Mapkapk2', 'Mapt', 'March7', 'March9', 'Marco', 'Mark1', 'Matn1', 'Maz', 'Mb21d2', 'Mcam', 'Mcee', 'Mcemp1', 'Mcf2l', 'Mcfd2', 'Mcoln2', 'Mcpt4', 'Mctp1', 'Mcts2', 'Mdh1b', 'Mdk', 'Me1', 'Me3', 'Med16', 'Mef2a', 'Mef2c', 'Mef2d', 'Meg3', 'Megf9', 'Meiob', 'Meis1', 'Meis2', 'Meox1', 'Meox2', 'Met', 'Metrnl', 'Mettl13', 'Mettl15', 'Mettl21c', 'Mettl24', 'Mettl7a1', 'Mettl7a2', 'Mfap3l', 'Mfap5', 'Mfge8', 'Mfsd2b', 'Mfsd6l', 'Mgat3', 'Mgl2', 'Mgll', 'Mgp', 'Mgst1', 'Miat', 'Micall2', 'Mid2', 'Mier3', 'Mif', 'Miip', 'Milr1', 'Minos1', 'Mks1', 'Mlph', 'Mlxipl', 'Mmd', 'Mme', 'Mmp11', 'Mmp13', 'Mmp15', 'Mmp28', 'Mn1', 'Mob3c', 'Mocos', 'Mogat1', 'Mon1b', 'Morn1', 'Morn3', 'Mpc2', 'Mpo', 'Mpp3', 'Mpz', 'Mpzl1', 'Mr1', 'Mrap', 'Mrc1', 'Mrc2', 'Mrgpra6', 'Mroh7', 'Mroh8', 'Mrpl20', 'Mrpl53', 'Mrpl55', 'Mrps18c', 'Ms4a1', 'Msc', 'Msl3l2', 'Msr1', 'Msrb3', 'Mss51', 'Msx2', 'Mta3', 'Mtf2', 'Mtfr1', 'Mtg1', 'Mtm1', 'Mtrf1', 'Mtss1', 'Mtus1', 'Mtx1', 'Mustn1', 'Mx1', 'Mxd1', 'Mxi1', 'Mxra8', 'Mycl', 'Myct1', 'Myh3', 'Myl10', 'Myl12b', 'Mylk3', 'Myo1d', 'Myo7a', 'Myom1', 'Myzap', 'Mzf1', 'Mzt2', 'Naaa', 'Naalad2', 'Nacc2', 'Nagpa', 'Naip5', 'Naip6', 'Nampt', 'Nanp', 'Nap1l3', 'Naprt', 'Nat14', 'Nat6', 'Nat8l', 'Nbl1', 'Ncald', 'Ncoa1', 'Ncoa4', 'Nde1', 'Ndn', 'Ndrg2', 'Ndufa2', 'Ndufa4', 'Ndufa5', 'Ndufab1', 'Ndufb10', 'Ndufb3', 'Ndufb6', 'Ndufb7', 'Ndufb9', 'Ndufc2', 'Ndufs2', 'Ndufs4', 'Ndufs7', 'Ndufv1', 'Ndufv2', 'Neat1', 'Necab3', 'Nedd4', 'Negr1', 'Nek2', 'Nenf', 'Neo1', 'Nepn', 'Nes', 'Neurl1b', 'Nexn', 'Nfam1', 'Nfat5', 'Nfatc1', 'Nfatc2', 'Nfatc3', 'Nfib', 'Nfxl1', 'Nfya', 'Nfyb', 'Nfyc', 'Ngef', 'Nhlrc1', 'Nhsl2', 'Nid1', 'Ninj1', 'Ninj2', 'Nipal4', 'Nkain4', 'Nkapl', 'Nkpd1', 'Nln', 'Nlrp3', 'Nmnat1', 'Nnat', 'Nnmt', 'Nol8', 'Nos2', 'Nos3', 'Notch2', 'Nox4', 'Noxa1', 'Noxo1', 'Nphp1', 'Npr2', 'Nptn', 'Npy4r', 'Nqo2', 'Nr1h3', 'Nr2f6', 'Nr3c1', 'Nr3c2', 'Nr4a1', 'Nr4a2', 'Nrbp2', 'Nrf1', 'Nrg4', 'Nrip2', 'Nrp1', 'Nrp2', 'Nsdhl', 'Nsg1', 'Ntm', 'Ntn4', 'Ntrk1', 'Ntrk2', 'Ntrk3', 'Nts', 'Nuak2', 'Nudt12', 'Nudt4', 'Nudt7', 'Nudt9', 'Nup210l', 'Nup43', 'Nxn', 'Oas1c', 'Oasl2', 'Ociad2', 'Odf2', 'Odf3', 'Odf3l1', 'Ogn', 'Oip5', 'Olfm1', 'Olfml1', 'Olfml2b', 'Olfr1155', 'Olfr78', 'Olig2', 'Ophn1', 'Optn', 'Orai3', 'Orc1', 'Orm1', 'Ormdl3', 'Osbpl10', 'Osbpl1a', 'Osbpl5', 'Osbpl6', 'Osmr', 'Osr1', 'Otof', 'Otop1', 'Otub2', 'Ovgp1', 'Ovol1', 'Ovol2', 'P2rx1', 'P2rx4', 'P3h1', 'P4ha2', 'Pacsin3', 'Pafah1b2', 'Pag1', 'Pald1', 'Palmd', 'Pank1', 'Panx1', 'Paqr8', 'Pard3', 'Parm1', 'Parp11', 'Parp3', 'Parp8', 'Parp9', 'Parvb', 'Pate2', 'Pawr', 'Pax5', 'Pbx3', 'Pcbd1', 'Pcca', 'Pccb', 'Pcdh12', 'Pcdh18', 'Pcdhb13', 'Pcdhb17', 'Pcdhb18', 'Pcdhb7', 'Pcdhga8', 'Pcdhgc5', 'Pck1', 'Pck2', 'Pcolce', 'Pcolce2', 'Pcsk5', 'Pdcd1', 'Pdcd1lg2', 'Pde3a', 'Pde4a', 'Pdgfc', 'Pdha1', 'Pdhb', 'Pdhx', 'Pdia5', 'Pdk4', 'Pdlim1', 'Pdlim3', 'Pdlim4', 'Pdpn', 'Pebp4', 'Pecam1', 'Peg10', 'Peg3', 'Peli2', 'Pemt', 'Penk', 'Pepd', 'Pex11a', 'Pex11g', 'Pex12', 'Pex26', 'Pex5', 'Pf4', 'Pfdn4', 'Pfkm', 'Pgam2', 'Pgf', 'Pggt1b', 'Pgls', 'Pgm2', 'Pgm2l1', 'Pgm5', 'Phactr1', 'Phf11d', 'Phkg1', 'Phlda3', 'Phldb1', 'Phldb2', 'Phtf1', 'Phyh', 'Pi16', 'Pid1', 'Pigb', 'Pigk', 'Pim1', 'Pim3', 'Pip5k1b', 'Pirb', 'Pja1', 'Pkhd1', 'Pla2g16', 'Pla2g3', 'Pla2r1', 'Plat', 'Plau', 'Plbd1', 'Plcb4', 'Plce1', 'Plcl1', 'Plcxd3', 'Pld1', 'Pld2', 'Plekhg1', 'Plekhg3', 'Plekhg4', 'Plekhg5', 'Plekhh2', 'Plet1os', 'Plin1', 'Plin2', 'Plin5', 'Plk2', 'Pls1', 'Plxdc2', 'Plxna2', 'Plxna4', 'Plxna4os1', 'Plxnc1', 'Pmch', 'Pmepa1', 'Pmp22', 'Pms2', 'Pnisr', 'Pnldc1', 'Pnn', 'Pnpla2', 'Pnpla3', 'Podn', 'Podnl1', 'Polh', 'Poli', 'Polk', 'Poln', 'Polr2l', 'Polr3g', 'Pomc', 'Pon1', 'Pon3', 'Postn', 'Pou2f1', 'Pou2f2', 'Pou5f2', 'Ppa1', 'Ppara', 'Ppard', 'Pparg', 'Ppargc1a', 'Ppargc1b', 'Ppbp', 'Ppfibp1', 'Ppic', 'Ppil6', 'Ppl', 'Ppm1e', 'Ppp1r12a', 'Ppp1r16b', 'Ppp1r1a', 'Ppp1r3b', 'Ppp1r3c', 'Ppp1r3d', 'Ppp2r2c', 'Ppp4r4', 'Ppy', 'Pqlc1', 'Prdm1', 'Prdm16', 'Prelp', 'Prf1', 'Prg2', 'Prg3', 'Prg4', 'Prickle1', 'Prickle2', 'Prkaca', 'Prkar2b', 'Prkce', 'Prkcz', 'Prkd1', 'Prkg1', 'Prmt3', 'Proca1', 'Procr', 'Pros1', 'Prpf38b', 'Prpf40b', 'Prr36', 'Prrg4', 'Prrx1', 'Prrx2', 'Prss23', 'Prtg', 'Psap', 'Psca', 'Psd4', 'Psen2', 'Psma8', 'Psors1c2', 'Ptafr', 'Ptch1', 'Ptch2', 'Ptchd1', 'Pter', 'Ptger3', 'Ptges', 'Ptges2', 'Ptges3l', 'Ptgfrn', 'Ptgis', 'Ptgr1', 'Ptgr2', 'Ptgs1', 'Pth1r', 'Ptk7', 'Ptn', 'Ptp4a1', 'Ptpmt1', 'Ptpn11', 'Ptpn12', 'Ptpn21', 'Ptpn3', 'Ptprc', 'Ptprd', 'Ptprf', 'Ptprk', 'Ptprr', 'Pxmp2', 'Pycr1', 'Pygl', 'Pygo1', 'Pyroxd1', 'Pyroxd2', 'Pzp', 'Qrfp', 'Qsox1', 'R74862', 'Rab11fip3', 'Rab12', 'Rab13', 'Rab20', 'Rab23', 'Rab27b', 'Rab31', 'Rab39', 'Rab3il1', 'Rab44', 'Rab7b', 'Rabl2', 'Raet1d', 'Rag1', 'Rai2', 'Ralb', 'Ralgapa1', 'Ralgds', 'Ranbp17', 'Rap1gap', 'Rapgef3', 'Raph1', 'Rara', 'Rarb', 'Rasal1', 'Rasal2', 'Rasip1', 'Rasl10a', 'Rasl2-9', 'Rassf1', 'Rassf8', 'Rax', 'Rbak', 'Rbbp8', 'Rbl1', 'Rbl2', 'Rbm20', 'Rbm46', 'Rbms3', 'Rbp1', 'Rbp4', 'Rbp7', 'Rbpms2', 'Rcan2', 'Rccd1', 'Rd3', 'Rdh10', 'Rdh5', 'Rec114', 'Reep1', 'Reep2', 'Reg3g', 'Rel', 'Rela', 'Rell1', 'Reln', 'Rem1', 'Rergl', 'Rest', 'Retn', 'Retnla', 'Retnlg', 'Retsat', 'Rev1', 'Rexo1', 'Rfx3', 'Rfx5', 'Rgcc', 'Rgmb', 'Rgs17', 'Rgs18', 'Rgs2', 'Rgs4', 'Rgs5', 'Rgs7', 'Rgs9', 'Rgs9bp', 'Rhbdd3', 'Rhbdf1', 'Rhbdf2', 'Rhobtb3', 'Rhoc', 'Rhoj', 'Rhou', 'Ric8b', 'Rilp', 'Rimkla', 'Rims3', 'Rin1', 'Rnase2a', 'Rnase4', 'Rnase6', 'Rnd1', 'Rnf122', 'Rnf125', 'Rnf130', 'Rnf144b', 'Rnf151', 'Rnf152', 'Rnf180', 'Rnf24', 'Rnls', 'Robo2', 'Ropn1l', 'Ror2', 'Rora', 'Rras2', 'Rreb1', 'Rrp15', 'Rsad2', 'Rsbn1l', 'Rtn4ip1', 'Rtn4r', 'Rtp4', 'Rufy4', 'Rundc3a', 'Runx1', 'Rwdd2a', 'Rxra', 'Rxrg', 'S100a1', 'S100a16', 'S100a6', 'S100a9', 'S100b', 'S1pr5', 'Saa1', 'Saa3', 'Samd3', 'Samhd1', 'Sapcd1', 'Satb1', 'Sc5d', 'Scamp1', 'Scarb2', 'Scarf1', 'Scarna17', 'Scarna2', 'Scd1', 'Scfd2', 'Scg2', 'Scg3', 'Scg5', 'Scgb3a1', 'Sclt1', 'Scml2', 'Scn7a', 'Scnn1g', 'Scrn3', 'Sctr', 'Scube3', 'Sdc2', 'Sdc3', 'Sdc4', 'Sdf2l1', 'Sdha', 'Sdhaf1', 'Sdhb', 'Sdhc', 'Sdsl', 'Sec61g', 'Selenbp1', 'Sell', 'Selplg', 'Sema3a', 'Sema3b', 'Sema3c', 'Sema3d', 'Sema3g', 'Sema4a', 'Sema4d', 'Sema6a', 'Sema6b', 'Sema7a', 'Sephs2', 'Sepsecs', 'Sept3', 'Sept7', 'Serf1', 'Serpina10', 'Serpina1b', 'Serpina3c', 'Serpinb6a', 'Serpinb7', 'Serpinb8', 'Serpine2', 'Serpinh1', 'Sertad4', 'Sesn2', 'Sez6l', 'Sfrp1', 'Sfrp2', 'Sfxn3', 'Sfxn5', 'Sgca', 'Sgcd', 'Sgce', 'Sgk2', 'Sh3bgrl2', 'Sh3d19', 'Sh3rf2', 'Sh3tc2', 'Shc4', 'Shisa3', 'Shox2', 'Shroom2', 'Shroom4', 'Siglec1', 'Siglece', 'Siglecg', 'Siglech', 'Sik2', 'Sirpa', 'Sirpb1b', 'Sirt3', 'Sirt4', 'Siva1', 'Six3os1', 'Skor1', 'Skp2', 'Slamf7', 'Slc10a1', 'Slc10a7', 'Slc11a1', 'Slc12a9', 'Slc13a3', 'Slc15a4', 'Slc16a4', 'Slc16a9', 'Slc17a8', 'Slc22a13b-ps', 'Slc22a17', 'Slc22a27', 'Slc22a3', 'Slc22a4', 'Slc24a3', 'Slc25a10', 'Slc25a23', 'Slc25a26', 'Slc25a27', 'Slc25a30', 'Slc25a33', 'Slc25a34', 'Slc25a39', 'Slc25a42', 'Slc25a48', 'Slc26a11', 'Slc26a6', 'Slc26a8', 'Slc27a1', 'Slc27a2', 'Slc27a3', 'Slc28a1', 'Slc29a2', 'Slc2a1', 'Slc2a13', 'Slc2a2', 'Slc2a4', 'Slc30a6', 'Slc31a2', 'Slc35f5', 'Slc35g2', 'Slc36a2', 'Slc37a1', 'Slc39a10', 'Slc39a7', 'Slc40a1', 'Slc48a1', 'Slc4a10', 'Slc4a2', 'Slc4a4', 'Slc5a9', 'Slc6a15', 'Slc6a2', 'Slc7a2', 'Slc7a3', 'Slc8a2', 'Slc8b1', 'Slc9b2', 'Slco4a1', 'Slfn10-ps', 'Slfn14', 'Slfn9', 'Slit3', 'Slpi', 'Slx', 'Slx4ip', 'Smarca1', 'Smarca5-ps', 'Smc2', 'Smim22', 'Smoc2', 'Smpd1', 'Smtn', 'Smtnl2', 'Snai1', 'Snai2', 'Snca', 'Snhg11', 'Snhg18', 'Snhg20', 'Snhg4', 'Snora41', 'Snord104', 'Snord14a', 'Snord17', 'Snord22', 'Snord49a', 'Snord55', 'Snord73a', 'Snrk', 'Sntb2', 'Snx24', 'Snx29', 'Snx31', 'Snx7', 'Socs5', 'Sod2', 'Sorbs1', 'Sorbs2', 'Sostdc1', 'Sox13', 'Sox18', 'Sox4', 'Sox6', 'Sp1', 'Sp2', 'Sp3', 'Sp4', 'Spa17', 'Sparc', 'Spata17', 'Spata21', 'Spata31d1b', 'Spata7', 'Spatc1l', 'Spc24', 'Spc25', 'Speer1', 'Speg', 'Spib', 'Spn', 'Sprtn', 'Spry2', 'Spry4', 'Spsb1', 'Sptb', 'Sqle', 'Srebf2', 'Srxn1', 'Ssb', 'Sspn', 'St14', 'St18', 'St3gal4', 'Stab1', 'Stambp', 'Stap2', 'Star', 'Stard13', 'Stard6', 'Stard8', 'Stat1', 'Stat2', 'Stat3', 'Stat4', 'Stat6', 'Stau2', 'Steap4', 'Stfa2l1', 'Stk19', 'Stmn3', 'Stox1', 'Stra8', 'Stx3', 'Styk1', 'Sucla2', 'Suclg1', 'Sucnr1', 'Sufu', 'Sugct', 'Sult1a1', 'Sv2c', 'Svopl', 'Sycp2', 'Syn1', 'Syne2', 'Syngap1', 'Syt3', 'Syt4', 'Sytl4', 'Tac4', 'Tacstd2', 'Taf13', 'Taf1a', 'Taf7', 'Tas1r1', 'Tas2r122', 'Tatdn3', 'Tbc1d32', 'Tbc1d7', 'Tbc1d8b', 'Tbx18', 'Tbx2', 'Tbxas1', 'Tcaf1', 'Tcaf2', 'Tcea3', 'Tceal1', 'Tceal8', 'Tcf12', 'Tcf3', 'Tcf7', 'Tcn2', 'Tcp11l1', 'Tcta', 'Tcte2', 'Tdrkh', 'Tead2', 'Tecrl', 'Tenm3', 'Tex11', 'Tfap4', 'Tff2', 'Tfpi', 'Tfpi2', 'Tfr2', 'Tfrc', 'Tgfa', 'Tgfb1', 'Tgfb1i1', 'Tgfb3', 'Tgfbi', 'Tgfbr1', 'Tgfbr2', 'Tgif1', 'Tgm2', 'Thada', 'Thap11', 'Thbs3', 'Thbs4', 'Them4', 'Thnsl2', 'Thoc2', 'Thrsp', 'Thsd1', 'Thsd4', 'Thy1', 'Tifab', 'Timd4', 'Timm10', 'Timm8a1', 'Timp1', 'Timp4', 'Tinagl1', 'Tjp2', 'Tjp3', 'Tlcd1', 'Tlcd2', 'Tlr3', 'Tlr4', 'Tlx2', 'Tm2d1', 'Tm2d2', 'Tm4sf1', 'Tm6sf1', 'Tm9sf1', 'Tmbim1', 'Tmcc2', 'Tmcc3', 'Tmco3', 'Tmed5', 'Tmed6', 'Tmeff1', 'Tmeff2', 'Tmem100', 'Tmem120a', 'Tmem132cos', 'Tmem141', 'Tmem150a', 'Tmem161b', 'Tmem171', 'Tmem181b-ps', 'Tmem202', 'Tmem204', 'Tmem205', 'Tmem221', 'Tmem236', 'Tmem237', 'Tmem243', 'Tmem246', 'Tmem30b', 'Tmem37', 'Tmem38b', 'Tmem39b', 'Tmem45a', 'Tmem45b', 'Tmem47', 'Tmem50b', 'Tmem53', 'Tmem79', 'Tmem86a', 'Tmem88b', 'Tmem8b', 'Tmem97', 'Tmprss11d', 'Tmsb4x', 'Tmub1', 'Tnc', 'Tnfaip1', 'Tnfaip6', 'Tnfrsf10b', 'Tnfrsf11a', 'Tnfrsf13b', 'Tnfrsf13c', 'Tnfrsf18', 'Tnfrsf1a', 'Tnfrsf1b', 'Tnfrsf25', 'Tnfrsf4', 'Tnfrsf9', 'Tnfsf10', 'Tnfsf4', 'Tnfsf9', 'Tnni3', 'Tnr', 'Tns2', 'Tob1', 'Tob2', 'Tomm20', 'Top3b', 'Tor4a', 'Tpd52l1', 'Tpm2', 'Tpmt', 'Tppp', 'Tppp3', 'Tpsb2', 'Tpx2', 'Trabd2b', 'Traf3ip1', 'Trappc11', 'Trappc2', 'Trat1', 'Trem2', 'Treml2', 'Trex1', 'Trf', 'Trib1', 'Trim10', 'Trim13', 'Trim14', 'Trim16', 'Trim30b', 'Trim62', 'Trip6', 'Trmt2a', 'Trove2', 'Trp53inp2', 'Trp63', 'Trpm4', 'Trpv2', 'Trpv3', 'Trub2', 'Tsacc', 'Tsga10', 'Tsku', 'Tslp', 'Tsnaxip1', 'Tspan15', 'Tspan17', 'Tspan6', 'Tspan7', 'Tssk1', 'Tstd1', 'Ttc25', 'Ttc30b', 'Tti1', 'Ttk', 'Ttll13', 'Ttll7', 'Tub', 'Tuba8', 'Tubb1', 'Tuft1', 'Tulp3', 'Tusc5', 'Txlng', 'Txndc8', 'Txnip', 'Txnrd1', 'Tyrobp', 'Uaca', 'Ubd', 'Ube2f', 'Ube2ql1', 'Ublcp1', 'Ubtd2', 'Uchl1', 'Uckl1os', 'Ucn2', 'Ucp1', 'Ucp3', 'Unc13b', 'Unc45b', 'Unc5b', 'Upf2', 'Uqcr10', 'Uqcr11', 'Uqcrb', 'Uqcrfs1', 'Uros', 'Ush1g', 'Ushbp1', 'Usp2', 'Usp21', 'Usp33', 'Usp53', 'Usp6nl', 'Uspl1', 'Uty', 'Uxs1', 'Vamp3', 'Vars2', 'Vasn', 'Vat1l', 'Vax2', 'Vax2os', 'Vcam1', 'Vcan', 'Vegfa', 'Vezf1', 'Vgll3', 'Vgll4', 'Vipr1', 'Vit', 'Vma21', 'Vmo1', 'Vopp1', 'Vpreb2', 'Vps13a', 'Vrk2', 'Vtn', 'Vwa8', 'Vwce', 'Vwf', 'Wasf1', 'Wbp1', 'Wdfy2', 'Wdhd1', 'Wdpcp', 'Wdr38', 'Wdr4', 'Wdr60', 'Wdr62', 'Wdr78', 'Wee1', 'Wipi1', 'Wnt11', 'Wnt2', 'Wnt9a', 'Wt1', 'Wwc1', 'Wwc2', 'Xcl1', 'Xkr8', 'Xlr5b', 'Xlr5c', 'Xndc1', 'Xpo4', 'Xylb', 'Xylt2', 'Yap1', 'Ybx1', 'Ybx2', 'Yy1', 'Zbed5', 'Zbp1', 'Zbtb17', 'Zbtb20', 'Zbtb33', 'Zbtb39', 'Zcchc14', 'Zcchc2', 'Zcchc6', 'Zcrb1', 'Zcwpw1', 'Zdhhc1', 'Zdhhc15', 'Zdhhc2', 'Zeb1', 'Zeb2', 'Zeb2os', 'Zfhx4', 'Zfp110', 'Zfp111', 'Zfp112', 'Zfp13', 'Zfp143', 'Zfp148', 'Zfp169', 'Zfp180', 'Zfp182', 'Zfp185', 'Zfp189', 'Zfp248', 'Zfp281', 'Zfp287', 'Zfp300', 'Zfp322a', 'Zfp341', 'Zfp354a', 'Zfp354c', 'Zfp358', 'Zfp365', 'Zfp384', 'Zfp422', 'Zfp423', 'Zfp433', 'Zfp442', 'Zfp459', 'Zfp462', 'Zfp467', 'Zfp521', 'Zfp523', 'Zfp532', 'Zfp560', 'Zfp563', 'Zfp566', 'Zfp57', 'Zfp583', 'Zfp612', 'Zfp637', 'Zfp651', 'Zfp768', 'Zfp770', 'Zfp771', 'Zfp811', 'Zfp82', 'Zfp839', 'Zfp85os', 'Zfp870', 'Zfp874a', 'Zfp93', 'Zfp944', 'Zfp946', 'Zfp947', 'Zfp955a', 'Zfx', 'Zfyve16', 'Zfyve9', 'Zkscan14', 'Znhit1', 'Znrd1as', 'Zscan20', 'Zscan22', 'Zswim7', 'Zufsp'])

cois = adata.obs[adata.obs.cell_type == 'Tfh'].index
# delta_df = delta_df.loc[cois]
# end_nodes = delta_df.mean().sort_values(ascending=False, key=abs).head(10)
# end_nodes

end_node = 'Il21'

# think of gradient accumulation from the perturbation of interest to CXCR4 
# IL21 --> CXCR4 

ligands = list(adata.uns['received_ligands'].columns)
len(ligands)

138

ccc = adata.uns['cell_thresholds'].columns[adata.uns['cell_thresholds'].sum() != 0]
receptors = set(ccc) - set(ligands)
len(receptors)

96

import networkx as nx 
from tqdm import tqdm

G = nx.DiGraph()

target_gene = end_node
n_top = 5
next_layer = [target_gene]
edges = []

for i in tqdm(range(5)):  # n hops
    
    curr_layer = next_layer.copy()

    for node in curr_layer:
        if node in G.nodes():
            continue

        upstream_df = gradients[node].loc[cois]
        upstream_df.columns = [x.split('_')[1] for x in upstream_df.columns]
        tmp = upstream_df.mean(axis=0).sort_values(ascending=False, key=abs)
        tmp = tmp[tmp.abs() > 1e-6]
        top_nodes = tmp.head(n_top)

        edges.extend([(top_node, node, weight) for top_node, weight in top_nodes.items()])
        next_layer.extend(top_nodes.index)
        G.add_node(node, layer=4-i+1)

100%|██████████| 5/5 [00:00<00:00, 78.53it/s]

G.add_weighted_edges_from(edges)

distances = nx.single_source_shortest_path_length(G, gene, cutoff=5)
# for node, dist in distances.items():
#     G.nodes[node]['layer'] = dist

G.remove_nodes_from(set(G.nodes()) - set(distances.keys()))

# source perturbation node
G.nodes[gene]['layer'] = 0
# target node
G.nodes[end_node]['layer'] = 5
G.nodes(data=True)

NodeDataView({'Il21': {'layer': 5}, 'Nr3c1': {'layer': 0}, 'Gata3': {'layer': 4}, 'Tcf7': {'layer': 4}, 'Mxi1': {'layer': 4}, 'Nfatc1': {'layer': 4}, 'Nfatc3': {'layer': 3}, 'Sp1': {'layer': 3}, 'Foxp1': {'layer': 3}, 'Stat3': {'layer': 3}, 'Gabpa': {'layer': 3}, 'Klf2': {'layer': 3}, 'Stat2': {'layer': 3}, 'Stat1': {'layer': 3}, 'Irf4': {'layer': 3}, 'Klf3': {'layer': 3}, 'Rxra': {'layer': 3}, 'Lef1': {'layer': 3}, 'Ctcf': {'layer': 3}, 'Sp3': {'layer': 3}, 'Stat6': {'layer': 3}, 'Rest': {'layer': 3}, 'Maf': {'layer': 2}, 'Fli1': {'layer': 2}, 'Fosl2': {'layer': 2}, 'Nfyb': {'layer': 2}, 'E2f4': {'layer': 2}, 'Vezf1': {'layer': 2}, 'Jund': {'layer': 2}, 'Gtf2i': {'layer': 2}, 'Klf9': {'layer': 2}, 'Erg': {'layer': 1}, 'Pax5': {'layer': 1}, 'Cebpb': {'layer': 1}, 'Junb': {'layer': 1}})

from collections import Counter
nodes_per_layer = Counter(d['layer'] for n, d in G.nodes(data=True))
nodes_per_layer

Counter({3: 16, 2: 9, 4: 4, 1: 4, 5: 1, 0: 1})

from collections import defaultdict

pos = {}
nodes_by_layer = defaultdict(list)
for node, data in G.nodes(data=True):
    nodes_by_layer[data['layer']].append(node)

for layer, nodes in nodes_by_layer.items():
    n = len(nodes)
    # Spread nodes evenly from y = -0.5 to y = +0.5 for each layer (can tweak spread)
    y_positions = np.linspace(-0.5, 0.5, n) if n > 1 else [0.0]
    for node, y in zip(nodes, y_positions):
        pos[node] = (layer, y)

network_genes = np.loadtxt('/ix3/djishnu/alw399/SpaceTravLR/notebooks/mouse_lymph_visiumHD_Tfh/network_genes.txt', dtype=str)
len(network_genes)

291

scenic_genes = np.loadtxt('/ix3/djishnu/alw399/SpaceTravLR/notebooks/mouse_lymph_visiumHD_Tfh/scenic_genes.txt', dtype=str)
len(scenic_genes)

1971

plt.figure(figsize=(8, 8))

node_colors = []
for node in G.nodes():
    if node in network_genes and node in scenic_genes:
        node_colors.append('green')
    elif node in network_genes:
        node_colors.append('royalblue')
    elif node in scenic_genes:
        node_colors.append('orange')
    else: 
        node_colors.append('skyblue')

nx.draw_networkx_nodes(
    G, pos, 
    node_size=900, 
    node_color=node_colors, 
    edgecolors='black', 
    linewidths=0.4,
    alpha=0.6,
)

edges_data = list(G.edges(data=True))
edges_weights = []
edges_colors = []
for _, _, d in edges_data:
    w = d['weight'] if isinstance(d, dict) and 'weight' in d else 1.0
    edges_weights.append(w)
    edges_colors.append("gray")
    # if w < 0:
    #     edges_colors.append("skyblue")
    # else:
    #     edges_colors.append("salmon")

max_w = max(abs(float(w)) for w in edges_weights) if edges_weights else 1.0
widths = [abs(float(w))/(max_w+1e-10)*5+0.5 for w in edges_weights]

import itertools
connectionstyles = []
for idx, (u, v, d) in enumerate(edges_data):
    arc_rad = 0.2 if idx % 2 == 0 else -0.2
    connectionstyles.append(f"arc3,rad={arc_rad}")

for i, ((u, v, d), color, width, connstyle) in enumerate(zip(edges_data, edges_colors, widths, connectionstyles)):
    nx.draw_networkx_edges(
        G, pos,
        edgelist=[(u, v)],
        width=width,
        edge_color=color,
        arrowstyle='-|>',
        arrowsize=15,
        alpha=0.7,
        connectionstyle=connstyle,
        min_source_margin=10,
        min_target_margin=16
    )

labels = {node: f"$\mathit{{{node.capitalize()}}}$" for node in G.nodes()}
nx.draw_networkx_labels(G, pos, labels=labels, font_size=14)

import matplotlib.patches as mpatches
from matplotlib.lines import Line2D
import matplotlib

node_patches = [
    mpatches.Patch(facecolor='green', edgecolor='black', label='CoreNET & SCENIC'),
    mpatches.Patch(facecolor='royalblue', edgecolor='black', label='CoreNET only'),
    mpatches.Patch(facecolor='orange', edgecolor='black', label='SCENIC only'),
    mpatches.Patch(facecolor='skyblue', edgecolor='black', label='Other gene')
]

plt.legend(handles=node_patches,  #+ edge_patches, 
           loc='center left', 
           bbox_to_anchor=(1.02, 0.5),
           frameon=True, fontsize=9, ncol=1, title="Legend", title_fontsize=10)


plt.title(f"$\mathit{{{gene.capitalize()}}}$ KO → $\mathit{{{target_gene.capitalize()}}}$ expression")
plt.axis('off')
plt.show()