Clean up notebook and add outputs

notebooks/beta_catenin_dou/analysis_output/go_results_discrete.csv

@@ -0,0 +1,21 @@
+,curie,name,p,mlp,q,mlq
+10407,go:0009987,cellular process,3.047003662099363e-08,7.516127023811921,0.00024042809778634176,3.619014779595691
+0,go:0005515,protein binding,8.67224819241658e-08,7.061868301486667,0.00024042809778634176,3.619014779595691
+3464,go:0044183,protein folding chaperone,8.67224819241658e-08,7.061868301486667,0.00024042809778634176,3.619014779595691
+11148,go:0140311,protein sequestering activity,8.67224819241658e-08,7.061868301486667,0.00024042809778634176,3.619014779595691
+4592,go:0006457,protein folding,8.838618402556495e-08,7.053615615873712,0.00024042809778634176,3.619014779595691
+628,go:0005509,calcium ion binding,3.293446323613209e-07,6.482349410269698,0.0007431276249053527,3.1289365940020484
+1622,go:0030178,negative regulation of Wnt signaling pathway,3.8246403752205497e-07,6.4174093946018305,0.0007431276249053527,3.1289365940020484
+812,go:0048306,calcium-dependent protein binding,4.941142351435279e-07,6.306172634159098,0.0008400559640233902,3.075691780537002
+1432,go:0012505,endomembrane system,2.164126459995871e-06,5.664717364973178,0.0032704759980448713,2.4853890337984637
+11907,go:0048731,system development,2.8126968196684943e-06,5.550877077874281,0.003825548944431119,2.417306237260242
+3290,go:0030111,regulation of Wnt signaling pathway,4.966888820533992e-06,5.303915561198453,0.005728784900281345,2.24193748397741
+365,go:0007275,multicellular organism development,5.0544385562367575e-06,5.296327078543825,0.005728784900281345,2.24193748397741
+760,go:0048856,anatomical structure development,1.6345213777411955e-05,4.786609394952488,0.017100865583583078,1.7669819066452852
+747,go:0090090,negative regulation of canonical Wnt signaling pathway,1.7853167640558282e-05,4.748284716987896,0.01734435236280237,1.7608419120520946
+436,go:0046872,metal ion binding,2.6677142597318348e-05,4.573860689773272,0.02418905443107512,1.6163811082149144
+4693,go:0032502,developmental process,3.586480656934232e-05,4.445331507114722,0.030487327134351556,1.5158806491566081
+12082,go:0043169,cation binding,4.465091624005425e-05,4.35016962492959,0.03397954432427526,1.4687824494451873
+68,go:0009966,regulation of signal transduction,4.707666895709805e-05,4.3271942744762475,0.03397954432427526,1.4687824494451873
+2226,go:0009968,negative regulation of signal transduction,4.7467931928625095e-05,4.3235996891063975,0.03397954432427526,1.4687824494451873
+3169,go:0046475,glycerophospholipid catabolic process,6.12329846806133e-05,4.213014571223601,0.041641491232051075,1.3804737262735427

notebooks/beta_catenin_dou/analysis_output/indra_downstream_results_discrete.csv

@@ -0,0 +1,15 @@
+,curie,name,p,mlp,q,mlq
+56,go:0030154,cell differentiation,3.9614915194701e-11,10.402141269448686,1.4088252290691515e-06,5.851142879678905
+430,go:0016477,cell migration,2.2628308483451025e-10,9.645347909313486,4.023652672984844e-06,5.3953795152076856
+58,go:0008283,cell population proliferation,1.0509538932877671e-07,6.978416336616793,0.001245835776899762,2.9045392015666742
+77,mesh:D009361,Neoplasm Invasiveness,7.91627912340161e-07,6.101478901224616,0.005957686240696306,2.224922372474168
+196,mesh:D009362,Neoplasm Metastasis,8.3762425002057e-07,6.07695075790793,0.005957686240696306,2.224922372474168
+11,go:0007165,signal transduction,2.01059468056165e-06,5.696675470794204,0.011917129770802325,1.923828331408067
+2052,hgnc:1071,BMP4,5.411398683341174e-06,5.2666904683596565,0.024865744178835004,1.6043985387271391
+20490,hgnc:11869,CEMIP2,5.593621275783259e-06,5.252306941504976,0.024865744178835004,1.6043985387271391
+435,go:0007155,cell adhesion,6.990844648323564e-06,5.155470348725729,0.026514908970620255,1.5765098595363738
+19410,hgnc:2411,CRYGD,7.4557570988443765e-06,5.127508249306155,0.026514908970620255,1.5765098595363738
+20474,hgnc:2510,CTNNA2,9.582882851926997e-06,5.018503820948346,0.03098146026027998,1.5088981163367896
+15298,hgnc:24709,VWA2,1.1974741701505678e-05,4.9217338456645985,0.035488144927553866,1.4499167019424422
+11145,hgnc:19185,FRAS1,1.4631076992057896e-05,4.834723704326327,0.04002499931296576,1.3976686668633829
+17393,hgnc:9935,RCN2,1.7551632245959666e-05,4.755682489314921,0.04458490696879026,1.3508121352233782

notebooks/beta_catenin_dou/analysis_output/indra_upstream_results_discrete.csv

@@ -0,0 +1,31 @@
+,curie,name,p,mlp,q,mlq
+48,chebi:33216,bisphenol A,2.1845369101489054e-11,10.660640613010456,9.794589690343633e-07,6.009013752517842
+90,chebi:39867,valproic acid,2.783293961653564e-09,8.55544092259805,6.239588403234959e-05,4.204844057769417
+55,chebi:28119,"2,3,7,8-tetrachlorodibenzodioxine",1.366192079007404e-08,7.864488236973215,0.00020418196018125322,3.6899826312002633
+102,chebi:16469,17beta-estradiol,2.8659822866229926e-08,7.542726498113714,0.0003212479545075712,3.4931596289490625
+822,chebi:27470,folic acid,5.739016623466938e-08,7.2411625172865834,0.0005146290986595272,3.2885056611299883
+16,hgnc:6551,LEF1,1.0920073869560679e-07,6.961774423807649,0.0008160207200260377,3.088298813698678
+182,mesh:C459179,"4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide",2.53943453534522e-07,6.595262978466331,0.0016265440975248326,2.788734157987974
+181,mesh:C516138,dorsomorphin,3.374867481306583e-07,6.471743275652872,0.0018914444798982745,2.723206402152202
+44,chebi:34372,"4,4'-sulfonyldiphenol",5.291834702050109e-07,6.276393730075749,0.0024207605994206473,2.6160481578905554
+829,chebi:15354,choline,5.399144882283539e-07,6.267675018383169,0.0024207605994206473,2.6160481578905554
+202,chebi:46024,trichostatin A,8.66247065453743e-07,6.0623582236175455,0.0035308230387894567,2.4521240482831566
+43,chebi:35549,perfluorooctanoic acid,1.7465946857187185e-06,5.757807865582874,0.006525859944073706,2.185362251137885
+45,chebi:34317,"3,3',4,4',5-pentachlorobiphenyl",2.328240558060765e-06,5.632972149605908,0.007880300218236958,2.103457236743944
+142,chebi:42588,4-hydroxyphenyl retinamide,2.5276169575811236e-06,5.59728873965114,0.007880300218236958,2.103457236743944
+350,chebi:15379,dioxygen,2.8592963070255958e-06,5.543740836653837,0.007880300218236958,2.103457236743944
+59,chebi:2504,aflatoxin B1,2.9597016933191695e-06,5.528752059033617,0.007880300218236958,2.103457236743944
+824,chebi:16643,L-methionine,2.9878915092788892e-06,5.524635175858284,0.007880300218236958,2.103457236743944
+430,mesh:C548651,2-(1'H-indole-3'-carbonyl)thiazole-4-carboxylic acid methyl ester,3.6849765016662974e-06,5.43356527720227,0.009178867023817228,2.0372109218129624
+157,chebi:28748,doxorubicin,4.816653958476761e-06,5.317254553461843,0.011366289309592844,1.944381293922058
+92,chebi:4031,cyclosporin A,5.959850151059682e-06,5.224764659619836,0.013360792068645596,1.874167794791203
+96,chebi:32506,"4,4'-diaminodiphenylmethane",6.854360490075392e-06,5.164033058538554,0.014634386044429537,1.8346254927798593
+866,chebi:17823,calcitriol,9.02194579483995e-06,5.044699786534763,0.01838672552988382,1.7354956068643559
+95,chebi:32509,pirinixic acid,9.586085740299261e-06,5.0183586908906195,0.018665557322779316,1.728959038226604
+63,chebi:15367,all-trans-retinoic acid,9.99137692360388e-06,5.000374657007612,0.018665557322779316,1.728959038226604
+88,chebi:45716,vorinostat,1.763227345275981e-05,4.7536916874549116,0.03162242450111755,1.5000048356343352
+98,chebi:28216,methylmercury chloride,2.056012055792545e-05,4.68697434310632,0.035455137128274826,1.450320830584525
+50,chebi:29865,benzo[a]pyrene,2.2084081848439373e-05,4.655920651938542,0.03667266273172695,1.4356575556049156
+84,chebi:50594,carbon nanotube,2.4568366769449033e-05,4.609623713141066,0.0393409747312506,1.405154883990672
+1,mesh:D001335,Vehicle Emissions,2.650738881758387e-05,4.5766330515188,0.040982251207765184,1.3874041889251425
+160,chebi:27385,tetrachloromethane,2.797865770766292e-05,4.553173124874161,0.04181503656602582,1.3786675191012097

notebooks/beta_catenin_dou/analysis_output/phenotype_results_discrete.csv

@@ -0,0 +1 @@
+,curie,name,p,mlp,q,mlq

notebooks/beta_catenin_dou/analysis_output/reactome_results_discrete.csv

@@ -0,0 +1,2 @@
+,curie,name,p,mlp,q,mlq
+184,reactome:R-HSA-1483115,Hydrolysis of LPC,9.582882851926997e-06,5.018503820948346,0.02396679001266942,1.6203901292178433

notebooks/beta_catenin_dou/analysis_output/shared_families.txt

@@ -0,0 +1 @@
+None

notebooks/beta_catenin_dou/analysis_output/shared_go_terms.csv

@@ -0,0 +1,15 @@
+"CURIE","Name","p-value","q-value"
+"go:0005509","calcium ion binding","9.59e-09","1.32e-04"
+"go:0005515","protein binding","3.18e-07","2.19e-03"
+"go:0030178","negative regulation of Wnt signaling pathway","4.87e-07","2.24e-03"
+"go:0048856","anatomical structure development","1.84e-06","5.74e-03"
+"go:0046872","metal ion binding","2.08e-06","5.74e-03"
+"go:0043169","cation binding","3.78e-06","8.62e-03"
+"go:0032502","developmental process","4.37e-06","8.62e-03"
+"go:0030111","regulation of Wnt signaling pathway","6.22e-06","1.07e-02"
+"go:0043167","ion binding","1.04e-05","1.60e-02"
+"go:0090090","negative regulation of canonical Wnt signaling pathway","2.09e-05","2.59e-02"
+"go:0036094","small molecule binding","2.13e-05","2.59e-02"
+"go:1990907","beta-catenin-TCF complex","2.25e-05","2.59e-02"
+"go:0009966","regulation of signal transduction","3.77e-05","4.01e-02"
+

notebooks/beta_catenin_dou/analysis_output/shared_pathways.txt

@@ -0,0 +1 @@
+[{'name': 'Pleural mesothelioma', 'id': 'WP5087'}, {'name': 'ncRNAs involved in Wnt signaling in hepatocellular carcinoma', 'id': 'WP4336'}, {'name': 'Wnt signaling', 'id': 'WP428'}, {'name': 'lncRNA in canonical Wnt signaling and colorectal cancer', 'id': 'WP4258'}, {'name': 'Signal Transduction', 'id': 'R-HSA-162582'}, {'name': 'Metabolism of proteins', 'id': 'R-HSA-392499'}, {'name': 'Alzheimer 39 s disease', 'id': 'WP5124'}, {'name': 'Pleural mesothelioma', 'id': 'WP5087'}, {'name': 'ncRNAs involved in Wnt signaling in hepatocellular carcinoma', 'id': 'WP4336'}, {'name': 'Wnt signaling', 'id': 'WP428'}, {'name': 'lncRNA in canonical Wnt signaling and colorectal cancer', 'id': 'WP4258'}, {'name': 'Extracellular vesicle mediated signaling in recipient cells', 'id': 'WP2870'}, {'name': 'Hair follicle development cytodifferentiation part 3 of 3', 'id': 'WP2840'}, {'name': 'Alzheimer 39 s disease and miRNA effects', 'id': 'WP2059'}, {'name': 'TCF dependent signaling in response to WNT', 'id': 'R-HSA-201681'}, {'name': 'Signaling by WNT', 'id': 'R-HSA-195721'}, {'name': 'Disease', 'id': 'R-HSA-1643685'}, {'name': 'Signal Transduction', 'id': 'R-HSA-162582'}, {'name': 'Diseases of signal transduction by growth factor receptors and second messengers', 'id': 'R-HSA-5663202'}, {'name': 'Signaling by WNT in cancer', 'id': 'R-HSA-4791275'}, {'name': 'Developmental Biology', 'id': 'R-HSA-1266738'}, {'name': 'Pleural mesothelioma', 'id': 'WP5087'}, {'name': 'Endometrial cancer', 'id': 'WP4155'}, {'name': 'Ectoderm differentiation', 'id': 'WP2858'}, {'name': 'Arrhythmogenic right ventricular cardiomyopathy', 'id': 'WP2118'}, {'name': 'Developmental Biology', 'id': 'R-HSA-1266738'}, {'name': 'Myogenesis', 'id': 'R-HSA-525793'}, {'name': 'TGF beta receptor signaling in skeletal dysplasias', 'id': 'WP4816'}, {'name': 'Disease', 'id': 'R-HSA-1643685'}, {'name': 'Metabolism of proteins', 'id': 'R-HSA-392499'}, {'name': 'Alzheimer 39 s disease', 'id': 'WP5124'}, {'name': 'Alzheimer 39 s disease and miRNA effects', 'id': 'WP2059'}, {'name': 'Pleural mesothelioma', 'id': 'WP5087'}, {'name': 'Hippo Merlin signaling dysregulation', 'id': 'WP4541'}, {'name': 'VEGFA VEGFR2 signaling', 'id': 'WP3888'}, {'name': 'Regulation of Expression and Function of Type II Classical Cadherins', 'id': 'R-HSA-9764260'}, {'name': 'Regulation of CDH11 function', 'id': 'R-HSA-9762292'}, {'name': 'Regulation of Homotypic Cell-Cell Adhesion', 'id': 'R-HSA-9759476'}, {'name': 'Regulation of CDH11 Expression and Function', 'id': 'R-HSA-9759475'}, {'name': 'Signal Transduction', 'id': 'R-HSA-162582'}, {'name': 'Cell-Cell communication', 'id': 'R-HSA-1500931'}, {'name': 'Cell junction organization', 'id': 'R-HSA-446728'}, {'name': 'Cell-cell junction organization', 'id': 'R-HSA-421270'}, {'name': 'Adherens junctions interactions', 'id': 'R-HSA-418990'}, {'name': 'VEGFA VEGFR2 signaling', 'id': 'WP3888'}, {'name': 'Signal Transduction', 'id': 'R-HSA-162582'}, {'name': 'Pleural mesothelioma', 'id': 'WP5087'}, {'name': 'Developmental Biology', 'id': 'R-HSA-1266738'}, {'name': 'DNA damage response only ATM dependent ', 'id': 'WP710'}, {'name': 'TGF beta receptor signaling', 'id': 'WP560'}, {'name': 'CKAP4 signaling pathway map', 'id': 'WP5322'}, {'name': 'Pleural mesothelioma', 'id': 'WP5087'}, {'name': 'Overlap between signal transduction pathways contributing to LMNA laminopathies', 'id': 'WP4879'}, {'name': 'Influence of laminopathies on Wnt signaling', 'id': 'WP4844'}, {'name': 'TGF beta receptor signaling in skeletal dysplasias', 'id': 'WP4816'}, {'name': 'Hippo signaling regulation pathways', 'id': 'WP4540'}, {'name': 'ncRNAs involved in Wnt signaling in hepatocellular carcinoma', 'id': 'WP4336'}, {'name': 'Wnt signaling', 'id': 'WP428'}, {'name': 'Breast cancer pathway', 'id': 'WP4262'}, {'name': 'lncRNA in canonical Wnt signaling and colorectal cancer', 'id': 'WP4258'}, {'name': 'Chromosomal and microsatellite instability in colorectal cancer ', 'id': 'WP4216'}, {'name': 'Endometrial cancer', 'id': 'WP4155'}, {'name': 'Wnt signaling pathway and pluripotency', 'id': 'WP399'}, {'name': 'Regulation of Wnt B catenin signaling by small molecule compounds', 'id': 'WP3664'}, {'name': 'Wnt beta catenin signaling pathway in leukemia', 'id': 'WP3658'}, {'name': 'Wnt signaling pathway', 'id': 'WP363'}, {'name': 'Endoderm differentiation', 'id': 'WP2853'}, {'name': 'Hair follicle development cytodifferentiation part 3 of 3', 'id': 'WP2840'}, {'name': 'Hair follicle development organogenesis part 2 of 3', 'id': 'WP2839'}, {'name': 'Arrhythmogenic right ventricular cardiomyopathy', 'id': 'WP2118'}, {'name': 'Generic Transcription Pathway', 'id': 'R-HSA-212436'}, {'name': 'Formation of the beta-catenin:TCF transactivating complex', 'id': 'R-HSA-201722'}, {'name': 'TCF dependent signaling in response to WNT', 'id': 'R-HSA-201681'}, {'name': 'Signaling by WNT', 'id': 'R-HSA-195721'}, {'name': 'Degradation of beta-catenin by the destruction complex', 'id': 'R-HSA-195253'}, {'name': 'RUNX3 regulates WNT signaling', 'id': 'R-HSA-8951430'}, {'name': 'Transcriptional regulation by RUNX3', 'id': 'R-HSA-8878159'}, {'name': 'Transcriptional Regulation by VENTX', 'id': 'R-HSA-8853884'}, {'name': 'Gene expression (Transcription)', 'id': 'R-HSA-74160'}, {'name': 'RNA Polymerase II Transcription', 'id': 'R-HSA-73857'}, {'name': 'Somitogenesis', 'id': 'R-HSA-9824272'}, {'name': 'Formation of axial mesoderm', 'id': 'R-HSA-9796292'}, {'name': 'Formation of paraxial mesoderm', 'id': 'R-HSA-9793380'}, {'name': 'Signal Transduction', 'id': 'R-HSA-162582'}, {'name': 'Gastrulation', 'id': 'R-HSA-9758941'}, {'name': 'Germ layer formation at gastrulation', 'id': 'R-HSA-9754189'}, {'name': 'Cardiogenesis', 'id': 'R-HSA-9733709'}, {'name': 'Developmental Biology', 'id': 'R-HSA-1266738'}, {'name': 'Binding of TCF/LEF:CTNNB1 to target gene promoters', 'id': 'R-HSA-4411364'}, {'name': 'Ca2+ pathway', 'id': 'R-HSA-4086398'}, {'name': 'Beta-catenin independent WNT signaling', 'id': 'R-HSA-3858494'}, {'name': 'Deactivation of the beta-catenin transactivating complex', 'id': 'R-HSA-3769402'}]

notebooks/beta_catenin_dou/analysis_output/shared_reactome.csv

@@ -0,0 +1,17 @@
+"CURIE","Name","p-value","q-value"
+"reactome:R-HSA-4411364","Binding of TCF/LEF:CTNNB1 to target gene promoters","8.10e-06","9.12e-03"
+"reactome:R-HSA-8951430","RUNX3 regulates WNT signaling","8.10e-06","9.12e-03"
+"reactome:R-HSA-1483115","Hydrolysis of LPC","1.04e-05","9.12e-03"
+"reactome:R-HSA-9762292","Regulation of CDH11 function","1.59e-05","1.04e-02"
+"reactome:R-HSA-9796292","Formation of axial mesoderm","2.63e-05","1.38e-02"
+"reactome:R-HSA-9754189","Germ layer formation at gastrulation","3.92e-05","1.72e-02"
+"reactome:R-HSA-9733709","Cardiogenesis","1.01e-04","3.19e-02"
+"reactome:R-HSA-9759475","Regulation of CDH11 Expression and Function","1.09e-04","3.19e-02"
+"reactome:R-HSA-525793","Myogenesis","1.17e-04","3.19e-02"
+"reactome:R-HSA-9764260","Regulation of Expression and Function of Type II Classical Cadherins","1.34e-04","3.19e-02"
+"reactome:R-HSA-9759476","Regulation of Homotypic Cell-Cell Adhesion","1.34e-04","3.19e-02"
+"reactome:R-HSA-4791275","Signaling by WNT in cancer","1.61e-04","3.52e-02"
+"reactome:R-HSA-201681","TCF dependent signaling in response to WNT","1.82e-04","3.68e-02"
+"reactome:R-HSA-8853884","Transcriptional Regulation by VENTX","2.12e-04","3.98e-02"
+"reactome:R-HSA-3769402","Deactivation of the beta-catenin transactivating complex","2.46e-04","4.31e-02"
+