Just Add Data: Automated Predictive Modeling for Knowledge Discovery and Feature Selection

Nature – npj Precision Oncology: https://www.nature.com/articles/s41698-022-00274-8

Authors: Ioannis Tsamardinos, Paulos Charonyktakis, Giorgos Papoutsoglou, Giorgos Borboudakis, Kleanthi Lakiotaki,
Jean Claude Zenklusen, Hartmut Juhl, Ekaterini Chatzaki, Vincenzo Lagani

Abstract:
Fully automated machine learning (AutoML) for predictive modeling is becoming a reality, giving rise to a whole new field. We present the basic ideas and principles of Just Add Data Bio (JADBio), an AutoML platform applicable to the low-sample, high-dimensional omics data that arise in translational medicine and bioinformatics applications. In addition to predictive and diagnostic models ready for clinical use, JADBio focuses on knowledge discovery by performing feature selection and identifying the corresponding biosignatures, i.e., minimal-size subsets of biomarkers that are jointly predictive of the outcome or phenotype of interest. It also returns a palette of useful information for interpretation, clinical use of the models, and decision making. JADBio is qualitatively and quantitatively compared against Hyper-Parameter Optimization Machine Learning libraries. Results show that in typical omics dataset analysis, JADBio manages to identify signatures comprising of just a handful of features while maintaining competitive predictive performance and accurate out-of-sample performance estimation.

JADBio is qualitatively and quantitatively compared against Hyper-Parameter Optimization li-braries, namely auto sklearn, TPOT, TPOT-MDR, GAMA, and AutoPrognosis. It is shown that in typical omics dataset analysis, JADBio manages to identify signatures comprising of just a handful of features without a statistically significant drop in predictive performance.

Here at JADBio, we support a scientific approach to the quality control of our products, methods, models, and results. The paper above is a testament to this claim. In addition, we support the reproducibility of published scientific results. This page contains the resources to investigate in detail the results and claims of the paper and compare them against novel methods or approaches. Specifically, you can find and download:

– The results from all tested tools in a tidy, tabular format [link]

– All JADBio raw results in text format [link]

– Codes for reproducing the figures [link]

– Script used for running the AutoML tools that were contrasted against JADBio [link]

– Example of plain English (natural language) report produced by JADBio [link]

– The datasets included in the study. These are presented in the searchable table below and are available for download. They can also be found at biodataome.

Dataset identifier	Omics type	No. samples	No. features	Repository	Disease	Disease group	Link
GSE10006	microarray	87	54675	Biodataome	chronic obstructive pulmonary disease	disease of anatomical entity	GSE10006.csv
GSE10041	microarray	72	54675	Biodataome	relaxation response		GSE10041.csv
GSE10063	microarray	60	54675	Biodataome	lung cancer	disease of cellular proliferation	GSE10063.csv
GSE10135	microarray	59	54675	Biodataome	cancer	disease of cellular proliferation	GSE10135.csv
GSE10334	microarray	247	54675	Biodataome	aggressive periodontitis	disease of anatomical entity	GSE10334.csv
GSE10780	microarray	185	54675	Biodataome	breast cancer	disease of cellular proliferation	GSE10780.csv
GSE10810	microarray	58	54675	Biodataome	breast cancer	disease of cellular proliferation	GSE10810.csv
GSE10890	microarray	112	54675	Biodataome	breast carcinoma	disease of cellular proliferation	GSE10890.csv
GSE10927	microarray	65	54675	Biodataome	adrenocortical carcinoma	disease of cellular proliferation	GSE10927.csv
GSE11083	microarray	83	54675	Biodataome	atherosclerosis	disease of anatomical entity	GSE11083.csv
GSE11135	microarray	204	54675	Biodataome	leukemia	disease of cellular proliferation	GSE11135.csv
GSE11190	microarray	78	54675	Biodataome	hepatitis c	disease by infectious agent	GSE11190.csv
GSE11348	microarray	93	54675	Biodataome	viral infectious disease	disease by infectious agent	GSE11348.csv
GSE11755	microarray	41	54675	Biodataome	sepsis	disease by infectious agent	GSE11755.csv
GSE11784	microarray	171	54675	Biodataome	chronic obstructive pulmonary disease	disease of anatomical entity	GSE11784.csv
GSE11869	microarray	75	54675	Biodataome	endometrial cancer	disease of cellular proliferation	GSE11869.csv
GSE11906	microarray	217	54675	Biodataome	pulmonary emphysema	disease of anatomical entity	GSE11906.csv
GSE11952	microarray	83	54675	Biodataome	chronic obstructive pulmonary disease	disease of anatomical entity	GSE11952.csv
GSE12452	microarray	41	54675	Biodataome	nasopharyngeal carcinoma	disease of cellular proliferation	GSE12452.csv
GSE12453	microarray	67	54675	Biodataome	non-hodgkin lymphoma	disease of cellular proliferation	GSE12453.csv
GSE12460	microarray	64	54675	Biodataome	neuroblastoma	disease of cellular proliferation	GSE12460.csv
GSE12662	microarray	106	54675	Biodataome	acute promyelocytic leukemia	disease of cellular proliferation	GSE12662.csv
GSE12711	microarray	47	54675	Biodataome			GSE12711.csv
GSE12790	microarray	98	54675	Biodataome	breast cancer	disease of cellular proliferation	GSE12790.csv
GSE13139	microarray	54	54675	Biodataome	atherosclerosis	disease of anatomical entity	GSE13139.csv
GSE13355	microarray	180	54675	Biodataome	psoriasis	disease of anatomical entity	GSE13355.csv
GSE13367	microarray	56	54675	Biodataome	ulcerative colitis	disease of anatomical entity	GSE13367.csv
GSE13548	microarray	42	54675	Biodataome	cancer	disease of cellular proliferation	GSE13548.csv
GSE13732	microarray	113	54675	Biodataome	multiple sclerosis	disease of anatomical entity	GSE13732.csv
GSE13896	microarray	70	54675	Biodataome	chronic obstructive pulmonary disease	disease of anatomical entity	GSE13896.csv
GSE13911	microarray	69	54675	Biodataome	gastric cancer	disease of cellular proliferation	GSE13911.csv
GSE13931	microarray	98	54675	Biodataome	chronic obstructive pulmonary disease	disease of anatomical entity	GSE13931.csv
GSE13933	microarray	87	54675	Biodataome	lung disease	disease of anatomical entity	GSE13933.csv
GSE14671	microarray	59	54675	Biodataome	chronic myeloid leukemia	disease of cellular proliferation	GSE14671.csv
GSE14905	microarray	82	54675	Biodataome	psoriasis	disease of anatomical entity	GSE14905.csv
GSE14924	microarray	41	54675	Biodataome	acute myeloid leukemia	disease of cellular proliferation	GSE14924.csv
GSE15061	microarray	870	54675	Biodataome	myelodysplastic syndrome	disease of cellular proliferation	GSE15061.csv
GSE15396	microarray	156	54675	Biodataome			GSE15396.csv
GSE15490	microarray	50	54675	Biodataome	chronic lymphocytic leukemia	disease of cellular proliferation	GSE15490.csv
GSE15605	microarray	74	54675	Biodataome	melanoma	disease of cellular proliferation	GSE15605.csv
GSE15645	microarray	42	54675	Biodataome	arthropathy	disease of anatomical entity	GSE15645.csv
GSE15913	microarray	40	54675	Biodataome	chronic lymphocytic leukemia	disease of cellular proliferation	GSE15913.csv
GSE16059	microarray	88	54675	Biodataome	chronic fatigue syndrome	syndrome	GSE16059.csv
GSE16134	microarray	310	54675	Biodataome	periodontitis	disease of anatomical entity	GSE16134.csv
GSE16214	microarray	240	54675	Biodataome	multiple sclerosis	disease of anatomical entity	GSE16214.csv
GSE16387	microarray	46	54675	Biodataome			GSE16387.csv
GSE16395	microarray	48	54675	Biodataome	langerhans-cell histiocytosis	disease of anatomical entity	GSE16395.csv
GSE16515	microarray	52	54675	Biodataome	pancreatic cancer	disease of cellular proliferation	GSE16515.csv
GSE16696	microarray	45	54675	Biodataome	lung disease	disease of anatomical entity	GSE16696.csv
GSE16837	microarray	113	54675	Biodataome	bacterial infection		GSE16837.csv
GSE16879	microarray	133	54675	Biodataome	crohn's disease	disease of anatomical entity	GSE16879.csv
GSE17612	microarray	51	54675	Biodataome	schizophrenia	disease of mental health	GSE17612.csv
GSE17624	microarray	60	54675	Biodataome		disease of cellular proliferation	GSE17624.csv
GSE17674	microarray	62	54675	Biodataome	neuroectodermal tumor	disease of cellular proliferation	GSE17674.csv
GSE17679	microarray	117	54675	Biodataome	neuroectodermal tumor	disease of cellular proliferation	GSE17679.csv
GSE17905	microarray	157	54675	Biodataome	chronic obstructive pulmonary disease	disease of anatomical entity	GSE17905.csv
GSE18105	microarray	111	54675	Biodataome	colorectal cancer	disease of cellular proliferation	GSE18105.csv
GSE18123	microarray	99	54675	Biodataome	autism spectrum disorder	disease of anatomical entity	GSE18123.csv
GSE18206	microarray	48	54675	Biodataome	irritant dermatitis	disease of anatomical entity	GSE18206.csv
GSE18520	microarray	63	54675	Biodataome	spindle cell carcinoma	disease of cellular proliferation	GSE18520.csv
GSE18521	microarray	75	54675	Biodataome	spindle cell carcinoma	disease of cellular proliferation	GSE18521.csv
GSE18781	microarray	55	54675	Biodataome		disease of anatomical entity	GSE18781.csv
GSE18791	microarray	57	54675	Biodataome	viral infectious disease	disease by infectious agent	GSE18791.csv
GSE18842	microarray	91	54675	Biodataome	lung cancer	disease of cellular proliferation	GSE18842.csv
GSE19069	microarray	147	54675	Biodataome	adult t-cell leukemia	disease of cellular proliferation	GSE19069.csv
GSE19123	microarray	44	54675	Biodataome	breast cancer	disease of cellular proliferation	GSE19123.csv
GSE19188	microarray	156	54675	Biodataome	lung cancer	disease of cellular proliferation	GSE19188.csv
GSE19407	microarray	127	54675	Biodataome	chronic obstructive pulmonary disease	disease of anatomical entity	GSE19407.csv
GSE19667	microarray	121	54675	Biodataome	lung disease	disease of anatomical entity	GSE19667.csv
GSE19722	microarray	58	54675	Biodataome	lung adenocarcinoma	disease of cellular proliferation	GSE19722.csv
GSE19743	microarray	177	54675	Biodataome			GSE19743.csv
GSE19804	microarray	120	54675	Biodataome	non-small cell lung carcinoma	disease of cellular proliferation	GSE19804.csv
GSE20257	microarray	135	54675	Biodataome	chronic obstructive pulmonary disease	disease of anatomical entity	GSE20257.csv
GSE20489	microarray	54	54675	Biodataome			GSE20489.csv
GSE20713	microarray	108	54675	Biodataome	breast cancer	disease of cellular proliferation	GSE20713.csv
GSE20916	microarray	145	54675	Biodataome	colorectal cancer	disease of cellular proliferation	GSE20916.csv
GSE21094	microarray	49	54675	Biodataome	acute lymphoblastic leukemia	genetic disease	GSE21094.csv
GSE21138	microarray	59	54675	Biodataome	schizophrenia	disease of mental health	GSE21138.csv
GSE2125	microarray	45	54675	Biodataome	cigarette smoke exposure	disease of anatomical entity	GSE2125.csv
GSE21510	microarray	104	54675	Biodataome	colorectal cancer	disease of cellular proliferation	GSE21510.csv
GSE21545	microarray	223	54675	Biodataome	atherosclerosis	disease of anatomical entity	GSE21545.csv
GSE21912	microarray	42	54675	Biodataome	multiple myeloma	disease of cellular proliferation	GSE21912.csv
GSE22047	microarray	230	54675	Biodataome	chronic obstructive pulmonary disease	disease of anatomical entity	GSE22047.csv
GSE22229	microarray	58	54675	Biodataome	kidney transplantation		GSE22229.csv
GSE22459	microarray	65	54675	Biodataome	kidney transplantation		GSE22459.csv
GSE23293	microarray	41	54675	Biodataome	chronic lymphocytic leukemia	disease of cellular proliferation	GSE23293.csv
GSE23394	microarray	96	54675	Biodataome	non-hodgkin lymphoma	disease of cellular proliferation	GSE23394.csv
GSE23878	microarray	59	54675	Biodataome	colorectal cancer	disease of cellular proliferation	GSE23878.csv
GSE24147	microarray	42	54675	Biodataome	leukemia	disease of cellular proliferation	GSE24147.csv
GSE24223	microarray	179	54675	Biodataome			GSE24223.csv
GSE25902	microarray	120	54675	Biodataome			GSE25902.csv
GSE26049	microarray	181	54675	Biodataome	essential thrombocythemia	disease of cellular proliferation	GSE26049.csv
GSE26378	microarray	103	54675	Biodataome	toxic shock syndrome	disease by infectious agent	GSE26378.csv
GSE26440	microarray	130	54675	Biodataome	toxic shock syndrome	disease by infectious agent	GSE26440.csv
GSE27202	microarray	48	54675	Biodataome			GSE27202.csv
GSE27210	microarray	114	54675	Biodataome			GSE27210.csv
GSE27211	microarray	438	54675	Biodataome			GSE27211.csv
GSE27536	microarray	54	54675	Biodataome		disease of anatomical entity	GSE27536.csv
GSE27562	microarray	162	54675	Biodataome	breast cancer	disease of cellular proliferation	GSE27562.csv
GSE27716	microarray	40	54675	Biodataome	lung adenocarcinoma	disease of cellular proliferation	GSE27716.csv
GSE27830	microarray	155	54675	Biodataome	breast cancer	disease of cellular proliferation	GSE27830.csv
GSE27854	microarray	115	54675	Biodataome	colorectal cancer	disease of cellular proliferation	GSE27854.csv
GSE27858	microarray	56	54675	Biodataome	chronic lymphocytic leukemia	disease of cellular proliferation	GSE27858.csv
GSE28492	microarray	80	54675	Biodataome			GSE28492.csv
GSE28702	microarray	54	54675	Biodataome	colorectal cancer	disease of cellular proliferation	GSE28702.csv
GSE28750	microarray	41	54675	Biodataome	sepsis		GSE28750.csv
GSE29265	microarray	49	54675	Biodataome	thyroid cancer	disease of cellular proliferation	GSE29265.csv
GSE29431	microarray	66	54675	Biodataome	breast cancer	disease of cellular proliferation	GSE29431.csv
GSE30219	microarray	307	54675	Biodataome	lung cancer	disease of cellular proliferation	GSE30219.csv
GSE30240	microarray	75	54675	Biodataome	cancer	disease of cellular proliferation	GSE30240.csv
GSE30674	microarray	56	54675	Biodataome	common cold	disease of anatomical entity	GSE30674.csv
GSE30784	microarray	229	54675	Biodataome	squamous cell carcinoma	disease of cellular proliferation	GSE30784.csv
GSE31048	microarray	221	54675	Biodataome	chronic lymphocytic leukemia	disease of cellular proliferation	GSE31048.csv
GSE31189	microarray	92	54675	Biodataome	bladder cancer	disease of anatomical entity	GSE31189.csv
GSE31210	microarray	246	54675	Biodataome	lung cancer	disease of cellular proliferation	GSE31210.csv
GSE32448	microarray	80	54675	Biodataome	prostate cancer	disease of cellular proliferation	GSE32448.csv
GSE32474	microarray	174	54675	Biodataome	cancer	disease of cellular proliferation	GSE32474.csv
GSE33630	microarray	105	54675	Biodataome	thyroid cancer	disease of cellular proliferation	GSE33630.csv
GSE33943	microarray	58	54675	Biodataome	inflammatory bowel disease	disease of anatomical entity	GSE33943.csv
GSE34437	microarray	66	54675	Biodataome			GSE34437.csv
GSE34450	microarray	132	54675	Biodataome	chronic obstructive pulmonary disease	disease of anatomical entity	GSE34450.csv
GSE34748	microarray	56	54675	Biodataome	kidney transplantation		GSE34748.csv
GSE35570	microarray	116	54675	Biodataome	thyroid cancer	disease of cellular proliferation	GSE35570.csv
GSE35711	microarray	49	54675	Biodataome	bacterial pneumonia	disease of anatomical entity	GSE35711.csv
GSE35713	microarray	203	54675	Biodataome	bacterial pneumonia	disease of anatomical entity	GSE35713.csv
GSE35725	microarray	114	54675	Biodataome	bacterial pneumonia	disease of anatomical entity	GSE35725.csv
GSE35864	microarray	72	54675	Biodataome	acquired immunodeficiency syndrome	disease by infectious agent	GSE35864.csv
GSE36059	microarray	410	54675	Biodataome	vasculitis	disease of anatomical entity	GSE36059.csv
GSE36769	microarray	60	54675	Biodataome	breast cancer	disease of cellular proliferation	GSE36769.csv
GSE36809	microarray	857	54675	Biodataome			GSE36809.csv
GSE36895	microarray	76	54675	Biodataome	renal cell carcinoma	disease of cellular proliferation	GSE36895.csv
GSE36907	microarray	46	54675	Biodataome	chronic lymphocytic leukemia	disease of cellular proliferation	GSE36907.csv
GSE37069	microarray	590	54675	Biodataome			GSE37069.csv
GSE37168	microarray	40	54675	Biodataome	chronic lymphocytic leukemia	disease of cellular proliferation	GSE37168.csv
GSE37364	microarray	94	54675	Biodataome	colorectal cancer	disease of cellular proliferation	GSE37364.csv
GSE37416	microarray	48	54675	Biodataome	bacterial infection		GSE37416.csv
GSE37964	microarray	44	54675	Biodataome	colorectal cancer	disease of cellular proliferation	GSE37964.csv
GSE38663	microarray	52	54675	Biodataome	hepatitis c	disease by infectious agent	GSE38663.csv
GSE38666	microarray	45	54675	Biodataome	ovarian cancer	disease of cellular proliferation	GSE38666.csv
GSE39088	microarray	142	54675	Biodataome	systemic lupus erythematosus	disease of anatomical entity	GSE39088.csv
GSE39156	microarray	64	54675	Biodataome	thyroid cancer	disease of cellular proliferation	GSE39156.csv
GSE39411	microarray	152	54675	Biodataome	chronic lymphocytic leukemia	disease of cellular proliferation	GSE39411.csv
GSE39582	microarray	585	54675	Biodataome	colon cancer	disease of cellular proliferation	GSE39582.csv
GSE39612	microarray	138	54675	Biodataome	merkel cell carcinoma	disease of cellular proliferation	GSE39612.csv
GSE40611	microarray	49	54675	Biodataome	sjogren's syndrome	disease of anatomical entity	GSE40611.csv
GSE40791	microarray	194	54675	Biodataome	lung cancer	disease of cellular proliferation	GSE40791.csv
GSE40967	microarray	585	54675	Biodataome	colon cancer	disease of cellular proliferation	GSE40967.csv
GSE41296	microarray	120	54675	Biodataome	cancer	disease of cellular proliferation	GSE41296.csv
GSE41662	microarray	48	54675	Biodataome	psoriasis	disease of anatomical entity	GSE41662.csv
GSE41663	microarray	81	54675	Biodataome	psoriasis	disease of anatomical entity	GSE41663.csv
GSE41664	microarray	157	54675	Biodataome	psoriasis	disease of anatomical entity	GSE41664.csv
GSE41804	microarray	40	54675	Biodataome	hepatocellular carcinoma	disease of cellular proliferation	GSE41804.csv
GSE41828	microarray	50	54675	Biodataome	spindle cell sarcoma	disease of cellular proliferation	GSE41828.csv
GSE41831	microarray	78	54675	Biodataome	arthropathy	disease of anatomical entity	GSE41831.csv
GSE41861	microarray	138	54675	Biodataome	asthma	disease of anatomical entity	GSE41861.csv
GSE41862	microarray	116	54675	Biodataome	asthma	disease of anatomical entity	GSE41862.csv
GSE42045	microarray	50	54675	Biodataome	spindle cell carcinoma	disease of cellular proliferation	GSE42045.csv
GSE42048	microarray	62	54675	Biodataome	nonpapillary renal cell carcinoma	disease of cellular proliferation	GSE42048.csv
GSE42050	microarray	194	54675	Biodataome	nonpapillary renal cell carcinoma	disease of cellular proliferation	GSE42050.csv
GSE42057	microarray	136	54675	Biodataome		disease of anatomical entity	GSE42057.csv
GSE42204	microarray	65	54675	Biodataome	b-cell lymphoma	disease of cellular proliferation	GSE42204.csv
GSE42568	microarray	121	54675	Biodataome	breast cancer	disease of cellular proliferation	GSE42568.csv
GSE42743	microarray	103	54675	Biodataome	oral cavity cancer	disease of cellular proliferation	GSE42743.csv
GSE4290	microarray	180	54675	Biodataome	neuroectodermal tumor	disease of cellular proliferation	GSE4290.csv
GSE43010	microarray	42	54675	Biodataome	cancer	disease of cellular proliferation	GSE43010.csv
GSE4302	microarray	118	54675	Biodataome	asthma	disease of anatomical entity	GSE4302.csv
GSE43081	microarray	97	54675	Biodataome	melanoma	disease of cellular proliferation	GSE43081.csv
GSE43346	microarray	68	54675	Biodataome	lung cancer	disease of cellular proliferation	GSE43346.csv
GSE43939	microarray	149	54675	Biodataome	chronic obstructive pulmonary disease	disease of anatomical entity	GSE43939.csv
GSE44927	microarray	40	54675	Biodataome	prostate cancer	disease of cellular proliferation	GSE44927.csv
GSE45267	microarray	87	54675	Biodataome	spindle cell carcinoma	disease of cellular proliferation	GSE45267.csv
GSE45404	microarray	42	54675	Biodataome	colorectal cancer	disease of cellular proliferation	GSE45404.csv
GSE45426	microarray	45	54675	Biodataome	response to exercise		GSE45426.csv
GSE45436	microarray	134	54675	Biodataome	spindle cell carcinoma	disease of cellular proliferation	GSE45436.csv
GSE45536	microarray	123	54675	Biodataome	rheumatoid arthritis	disease of anatomical entity	GSE45536.csv
GSE45537	microarray	135	54675	Biodataome	rheumatoid arthritis	disease of anatomical entity	GSE45537.csv
GSE45827	microarray	155	54675	Biodataome	cancer	disease of cellular proliferation	GSE45827.csv
GSE45867	microarray	40	54675	Biodataome	rheumatoid arthritis	disease of anatomical entity	GSE45867.csv
GSE4607	microarray	123	54675	Biodataome	appendicitis	disease of anatomical entity	GSE4607.csv
GSE46474	microarray	40	54675	Biodataome	kidney transplantation		GSE46474.csv
GSE46699	microarray	130	54675	Biodataome	renal cell carcinoma	disease of metabolism	GSE46699.csv
GSE47908	microarray	60	54675	Biodataome	ulcerative colitis	disease of anatomical entity	GSE47908.csv
GSE48311	microarray	56	54675	Biodataome	endotoxinic challenge		GSE48311.csv
GSE48472	methylation	56	485512	Biodataome	various tissues		GSE48472.csv
GSE49695	microarray	64	54675	Biodataome	chronic lymphocytic leukemia	disease of cellular proliferation	GSE49695.csv
GSE50006	microarray	220	54675	Biodataome	chronic lymphocytic leukemia	disease of cellular proliferation	GSE50006.csv
GSE50161	microarray	130	54675	Biodataome	medulloblastoma	disease of cellular proliferation	GSE50161.csv
GSE50705	microarray	351	54675	Biodataome	breast cancer	disease of cellular proliferation	GSE50705.csv
GSE50772	microarray	81	54675	Biodataome	systemic lupus erythematosus	disease of anatomical entity	GSE50772.csv
GSE50811	microarray	241	54675	Biodataome	endometrial cancer	disease of cellular proliferation	GSE50811.csv
GSE50830	microarray	168	54675	Biodataome	endometrial cancer	disease of cellular proliferation	GSE50830.csv
GSE50831	microarray	189	54675	Biodataome	endometrial cancer	disease of cellular proliferation	GSE50831.csv
GSE50832	microarray	598	54675	Biodataome	endometrial cancer	disease of cellular proliferation	GSE50832.csv
GSE51024	microarray	96	54675	Biodataome	lung cancer	disease of cellular proliferation	GSE51024.csv
GSE51401	microarray	64	54675	Biodataome	hepatocellular carcinoma	disease of cellular proliferation	GSE51401.csv
GSE51981	microarray	148	54675	Biodataome	endometriosis	disease of anatomical entity	GSE51981.csv
GSE52237	microarray	58	54675	Biodataome	lung disease	disease of anatomical entity	GSE52237.csv
GSE52553	microarray	84	54675	Biodataome	alcohol dependence	disease of mental health	GSE52553.csv
GSE52724	microarray	286	54675	Biodataome	diabetes insipidus	disease of anatomical entity	GSE52724.csv
GSE5281	microarray	161	54675	Biodataome	alzheimer's disease	disease of anatomical entity	GSE5281.csv
GSE53091	microarray	125	54675	Biodataome	colorectal cancer	disease of cellular proliferation	GSE53091.csv
GSE5350	microarray	140	54675	Biodataome	spindle cell carcinoma	disease of cellular proliferation	GSE5350.csv
GSE53552	microarray	99	54675	Biodataome	psoriasis	disease of anatomical entity	GSE53552.csv
GSE53757	microarray	144	54675	Biodataome	renal cell carcinoma	disease of cellular proliferation	GSE53757.csv
GSE53987	microarray	205	54675	Biodataome	schizophrenia	disease of mental health	GSE53987.csv
GSE54129	microarray	132	54675	Biodataome		disease of cellular proliferation	GSE54129.csv
GSE54169	microarray	75	54675	Biodataome	mantle cell lymphoma	disease of cellular proliferation	GSE54169.csv
GSE55092	microarray	140	54675	Biodataome	virus associated cancer	disease by infectious agent	GSE55092.csv
GSE55201	microarray	81	54675	Biodataome	psoriasis	disease of anatomical entity	GSE55201.csv
GSE55849	microarray	64	54675	Biodataome	chronic granulomatous disease	disease of anatomical entity	GSE55849.csv
GSE56315	microarray	122	54675	Biodataome	b-cell lymphoma	disease of cellular proliferation	GSE56315.csv
GSE57051	microarray	40	54675	Biodataome	arsenic exposure		GSE57051.csv
GSE5816	microarray	42	54675	Biodataome	colon cancer	disease of cellular proliferation	GSE5816.csv
GSE58294	microarray	92	54675	Biodataome	cardioembolic stroke	disease of anatomical entity	GSE58294.csv
GSE58331	microarray	175	54675	Biodataome	orbital inflammatory diseases	disease of anatomical entity	GSE58331.csv
GSE5900	microarray	78	54675	Biodataome	multiple myeloma	disease of cellular proliferation	GSE5900.csv
GSE59294	microarray	40	54675	Biodataome	atopic dermatitis	disease of anatomical entity	GSE59294.csv
GSE59312	microarray	79	54675	Biodataome	hepatitis c		GSE59312.csv
GSE60185	methylation	285	485512	Biodataome	breast cancer	disease of cellular proliferation	GSE60185.csv
GSE60542	microarray	92	54675	Biodataome	thyroid cancer	disease of anatomical entity	GSE60542.csv
GSE61441	methylation	92	485512	Biodataome	renal cell carcinoma	disease of cellular proliferation	GSE61441.csv
GSE61629	microarray	54	54675	Biodataome	cancer	disease of cellular proliferation	GSE61629.csv
GSE61804	microarray	325	54675	Biodataome	acute myeloid leukemia	disease of cellular proliferation	GSE61804.csv
GSE62232	microarray	91	54675	Biodataome	hepatocellular carcinoma	disease by infectious agent	GSE62232.csv
GSE6338	microarray	60	54675	Biodataome	anaplastic large cell lymphoma	disease of cellular proliferation	GSE6338.csv
GSE63409	methylation	74	485512	Biodataome	acute myeloid leukemia	disease of cellular proliferation	GSE63409.csv
GSE63514	microarray	128	54675	Biodataome	cervical cancer	disease of cellular proliferation	GSE63514.csv
GSE63695	methylation	97	485512	Biodataome	osteoarthritis	disease of anatomical entity	GSE63695.csv
GSE64256	microarray	125	54675	Biodataome	colorectal cancer	disease of cellular proliferation	GSE64256.csv
GSE64300	microarray	42	54675	Biodataome			GSE64300.csv
GSE64738	microarray	45	54675	Biodataome	mithramycin treatment	disease of cellular proliferation	GSE64738.csv
GSE64857	microarray	81	54675	Biodataome	colorectal cancer	disease of cellular proliferation	GSE64857.csv
GSE64913	microarray	59	54675	Biodataome	asthma	disease of anatomical entity	GSE64913.csv
GSE64951	microarray	94	54675	Biodataome	gastric cancer	disease of cellular proliferation	GSE64951.csv
GSE65010	microarray	48	54675	Biodataome	rheumatoid arthritis	disease of anatomical entity	GSE65010.csv
GSE65127	microarray	40	54675	Biodataome	vitiligo	disease of anatomical entity	GSE65127.csv
GSE65194	microarray	178	54675	Biodataome	breast cancer	disease of cellular proliferation	GSE65194.csv
GSE65914	microarray	58	54675	Biodataome	rosacea	disease of anatomical entity	GSE65914.csv
GSE66210	methylation	60	485512	Biodataome	patau and down syndrome	genetic disease	GSE66210.csv
GSE66272	microarray	54	54675	Biodataome	cancer	disease of cellular proliferation	GSE66272.csv
GSE66313	methylation	55	485512	Biodataome	breast cancer	disease of cellular proliferation	GSE66313.csv
GSE66354	microarray	149	54675	Biodataome	neuroectodermal tumor	disease of cellular proliferation	GSE66354.csv
GSE66360	microarray	99	54675	Biodataome	acute myocardial infarction	disease of anatomical entity	GSE66360.csv
GSE66552	methylation	45	485512	Biodataome	deletion or duplication of 7q11.23	disease of mental health	GSE66552.csv
GSE66836	methylation	183	485512	Biodataome	lung cancer	disease of cellular proliferation	GSE66836.csv
GSE67596	microarray	72	54675	Biodataome	arthropathy	disease of anatomical entity	GSE67596.csv
GSE6764	microarray	75	54675	Biodataome	cancer	disease of cellular proliferation	GSE6764.csv
GSE6791	microarray	84	54675	Biodataome	virus associated cancer	disease of cellular proliferation	GSE6791.csv
GSE68015	microarray	112	54675	Biodataome	cancer	disease of cellular proliferation	GSE68015.csv
GSE68060	methylation	120	485512	Biodataome		disease of cellular proliferation	GSE68060.csv
GSE68801	microarray	122	54675	Biodataome	alopecia areata	disease of anatomical entity	GSE68801.csv
GSE68825	methylation	144	485512	Biodataome	lung cancer	disease of cellular proliferation	GSE68825.csv
GSE68848	microarray	580	54675	Biodataome	cancer	disease of cellular proliferation	GSE68848.csv
GSE71065	microarray	80	54675	Biodataome	acquired immunodeficiency syndrome	disease by infectious agent	GSE71065.csv
GSE71222	microarray	152	54675	Biodataome	colorectal cancer	disease of cellular proliferation	GSE71222.csv
GSE71717	microarray	60	54675	Biodataome	ishikawa cells treated with genistein	disease of cellular proliferation	GSE71717.csv
GSE71730	microarray	47	54675	Biodataome	ulcerative colitis	disease of anatomical entity	GSE71730.csv
GSE71955	methylation	135	485512	Biodataome	graves' disease	disease of anatomical entity	GSE71955.csv
GSE71996	microarray	65	54675	Biodataome			GSE71996.csv
GSE72140	microarray	48	54675	Biodataome	melasma	disease of anatomical entity	GSE72140.csv
GSE72754	microarray	52	54675	Biodataome	systemic lupus erythematosus	disease of anatomical entity	GSE72754.csv
GSE72798	microarray	82	54675	Biodataome	lupus nephritis	disease of anatomical entity	GSE72798.csv
GSE72867	methylation	69	485512	Biodataome	viral infectious disease		GSE72867.csv
GSE72925	microarray	168	54675	Biodataome	kidney disease	disease of anatomical entity	GSE72925.csv
GSE74167	methylation	42	485512	Biodataome	obesity	disease of metabolism	GSE74167.csv
GSE74432	methylation	122	485512	Biodataome	sotos syndrome	genetic disease	GSE74432.csv
GSE74738	methylation	79	485512	Biodataome	imprinted methylation in placenta	disease of anatomical entity	GSE74738.csv
GSE75132	microarray	41	54675	Biodataome	cervical cancer	disease of cellular proliferation	GSE75132.csv
GSE77269	methylation	60	485512	Biodataome	hepatocellular carcinoma	disease of cellular proliferation	GSE77269.csv
GSE77348	methylation	85	485512	Biodataome	breast cancer	disease of cellular proliferation	GSE77348.csv
GSE7753	microarray	47	54675	Biodataome	arthropathy	disease of anatomical entity	GSE7753.csv
GSE77658	microarray	184	54675	Biodataome			GSE77658.csv
GSE77954	methylation	48	485512	Biodataome	colorectal adenocarcinoma	disease of cellular proliferation	GSE77954.csv
GSE7904	microarray	62	54675	Biodataome	breast carcinoma	disease of cellular proliferation	GSE7904.csv
GSE79695	methylation	44	485512	Biodataome	acute myeloid leukemia	disease of cellular proliferation	GSE79695.csv
GSE80060	microarray	206	54675	Biodataome		disease of anatomical entity	GSE80060.csv
GSE80468	methylation	60	485512	Biodataome		disease of anatomical entity	GSE80468.csv
GSE8157	microarray	43	54675	Biodataome	polycystic ovary syndrome	syndrome	GSE8157.csv
GSE83556	microarray	40	54675	Biodataome	fmr1 expansion		GSE83556.csv
GSE8507	microarray	141	54675	Biodataome	job's syndrome	disease of anatomical entity	GSE8507.csv
GSE85210	methylation	253	485512	Biodataome	cigarette smoke exposure		GSE85210.csv
GSE8545	microarray	54	54675	Biodataome	chronic obstructive pulmonary disease	disease of anatomical entity	GSE8545.csv
GSE8581	microarray	58	54675	Biodataome		disease of anatomical entity	GSE8581.csv
GSE85828	methylation	114	485512	Biodataome	induced pluripotency		GSE85828.csv
GSE86574	microarray	110	54675	Biodataome	neuroectodermal tumor	disease of cellular proliferation	GSE86574.csv
GSE8671	microarray	64	54675	Biodataome	colorectal cancer	disease of cellular proliferation	GSE8671.csv
GSE9196	microarray	53	54675	Biodataome			GSE9196.csv
GSE9348	microarray	82	54675	Biodataome	colorectal cancer	disease of cellular proliferation	GSE9348.csv
GSE94349	microarray	168	54675	Biodataome	spinal meningioma	disease of cellular proliferation	GSE94349.csv
GSE94521	microarray	60	54675	Biodataome	developmental toxicity	disease of anatomical entity	GSE94521.csv
GSE9489	microarray	60	54675	Biodataome	kidney disease	disease of anatomical entity	GSE9489.csv
GSE9493	microarray	82	54675	Biodataome	kidney disease	disease of anatomical entity	GSE9493.csv
GSE9692	microarray	45	54675	Biodataome	toxic shock syndrome	disease by infectious agent	GSE9692.csv
GSE9826	microarray	45	54675	Biodataome	ovarian cancer	disease of cellular proliferation	GSE9826.csv
SRP007825	rnaseq	66	58037	Biodataome	psoriasis	disease of anatomical entity	SRP007825.csv
SRP010038	rnaseq	40	58037	Biodataome	pterygium	disease of anatomical entity	SRP010038.csv
SRP022043	rnaseq	70	58037	Biodataome	alzheimer's disease	disease of anatomical entity	SRP022043.csv
SRP023262	rnaseq	72	58037	Biodataome	breast cancer	disease of cellular proliferation	SRP023262.csv
SRP026042	rnaseq	84	58037	Biodataome	psoriasis	disease of anatomical entity	SRP026042.csv
SRP029880	rnaseq	54	58037	Biodataome	colorectal cancer	disease of cellular proliferation	SRP029880.csv
SRP035988	rnaseq	173	58037	Biodataome	psoriasis	disease of anatomical entity	SRP035988.csv
SRP041036	rnaseq	60	58037	Biodataome	multiple myeloma	disease of cellular proliferation	SRP041036.csv
SRP041538	rnaseq	187	58037	Biodataome	chronic obstructive pulmonary disease	disease of anatomical entity	SRP041538.csv
SRP043162	rnaseq	53	58037	Biodataome	asthma	disease of anatomical entity	SRP043162.csv
SRP044668	rnaseq	91	58037	Biodataome	glioma	disease of cellular proliferation	SRP044668.csv
SRP047194	rnaseq	45	58037	Biodataome	autism spectrum disorder	disease of mental health	SRP047194.csv
SRP049097	rnaseq	54	58037	Biodataome	leiomyosarcoma	disease of cellular proliferation	SRP049097.csv
SRP049593	rnaseq	57	58037	Biodataome	williams-beuren syndrome	genetic disease	SRP049593.csv
SRP050892	rnaseq	302	58037	Biodataome	toxic encephalopathy	disease of anatomical entity	SRP050892.csv
SRP051848	rnaseq	187	58037	Biodataome	post-traumatic stress disorder	disease of mental health	SRP051848.csv
SRP053794	rnaseq	40	58037	Biodataome	atopic dermatitis	disease of anatomical entity	SRP053794.csv
SRP056733	rnaseq	152	58037	Biodataome	bacterial infection	disease by infectious agent	SRP056733.csv
SRP059057	rnaseq	73	58037	Biodataome	coeliac disease	disease of anatomical entity	SRP059057.csv
SRP062025	rnaseq	73	58037	Biodataome	myelodysplastic syndrome	disease of cellular proliferation	SRP062025.csv
SRP062966	rnaseq	117	58037	Biodataome	systemic lupus erythematosus	disease of anatomical entity	SRP062966.csv
SRP063867	rnaseq	63	58037	Biodataome	induced pluripotency	disease of anatomical entity	SRP063867.csv
SRP065812	rnaseq	52	58037	Biodataome	psoriasis	disease of anatomical entity	SRP065812.csv
ST000005	metabolomics	87	41	Metabolomics Workbench			ST000005.csv
ST000009	metabolomics	114	417	Metabolomics Workbench	obesity	disease of metabolism	ST000009.csv
ST000011	metabolomics	40	238	Metabolomics Workbench			ST000011.csv
ST000014	metabolomics	72	67	Metabolomics Workbench			ST000014.csv
ST000015	metabolomics	125	55	Metabolomics Workbench			ST000015.csv
ST000016	metabolomics	110	643	Metabolomics Workbench	lymphoma	disease of cellular proliferation	ST000016.csv
ST000017	metabolomics	42	537	Metabolomics Workbench			ST000017.csv
ST000062	metabolomics	97	158	Metabolomics Workbench	major depressive disorder	disease of mental health	ST000062.csv
ST000063	metabolomics	94	172	Metabolomics Workbench	major depressive disorder	disease of mental health	ST000063.csv
ST000105	metabolomics	111	447	Metabolomics Workbench	polycystic ovary syndrome	syndrome	ST000105.csv
ST000106	metabolomics	64	589	Metabolomics Workbench	obesity	disease of metabolism	ST000106.csv
ST000135	metabolomics	58	18	Metabolomics Workbench			ST000135.csv
ST000163	metabolomics	100	17762	Metabolomics Workbench			ST000163.csv
ST000168	metabolomics	200	37	Metabolomics Workbench	obesity	disease of metabolism	ST000168.csv
ST000195	metabolomics	51	26	Metabolomics Workbench			ST000195.csv
ST000196	metabolomics	135	28	Metabolomics Workbench			ST000196.csv
ST000209	metabolomics	48	20	Metabolomics Workbench			ST000209.csv
ST000212	metabolomics	60	20	Metabolomics Workbench			ST000212.csv
ST000244	metabolomics	51	47	Metabolomics Workbench			ST000244.csv
ST000252	metabolomics	40	79	Metabolomics Workbench			ST000252.csv
ST000286	metabolomics	40	436	Metabolomics Workbench			ST000286.csv
ST000336	metabolomics	58	23	Metabolomics Workbench	duchenne muscular dystrophy	disease of anatomical entity	ST000336.csv
ST000353	metabolomics	42	96	Metabolomics Workbench			ST000353.csv
ST000355	metabolomics	214	149	Metabolomics Workbench	breast cancer	disease of cellular proliferation	ST000355.csv
ST000356	metabolomics	134	119	Metabolomics Workbench	breast cancer	disease of cellular proliferation	ST000356.csv
ST000393	metabolomics	68	70	Metabolomics Workbench			ST000393.csv
ST000396	metabolomics	299	137	Metabolomics Workbench	lung cancer	disease of cellular proliferation	ST000396.csv
ST000401	metabolomics	40	168	Metabolomics Workbench			ST000401.csv
ST000402	metabolomics	71	119	Metabolomics Workbench			ST000402.csv
ST000421	metabolomics	56	20387	Metabolomics Workbench	diabetes	disease of metabolism	ST000421.csv
ST000422	metabolomics	60	19348	Metabolomics Workbench	diabetes	disease of metabolism	ST000422.csv
ST000450	metabolomics	84	232	Metabolomics Workbench	chronic fatigue syndrome	syndrome	ST000450.csv
ST000477	metabolomics	113	148	Metabolomics Workbench			ST000477.csv
ST000483	metabolomics	40	40	Metabolomics Workbench	obesity	disease of metabolism	ST000483.csv
ST000484	metabolomics	40	40	Metabolomics Workbench	obesity	disease of metabolism	ST000484.csv
ST000496	metabolomics	100	70	Metabolomics Workbench	periodontitis	disease of anatomical entity	ST000496.csv
ST000608	metabolomics	60	264	Metabolomics Workbench			ST000608.csv
ST000659	metabolomics	138	15	Metabolomics Workbench			ST000659.csv
ST000805	metabolomics	60	15	Metabolomics Workbench			ST000805.csv
ST000808	metabolomics	60	46	Metabolomics Workbench			ST000808.csv
ST000843	metabolomics	67	56	Metabolomics Workbench	asthma	disease of anatomical entity	ST000843.csv
ST000872	metabolomics	66	54	Metabolomics Workbench			ST000872.csv
ST000884	metabolomics	183	716	Metabolomics Workbench			ST000884.csv

This research has been co‐financed by the European Regional Development Fund of the European Union and Greek national funds through the Operational Program Competitiveness, Entrepreneurship and Innovation, under the call RESEARCH–CREATE–INNOVATE (project code:T1EDK-00905).

The research leading to these results has been co-funded by the European Commission under the H2020 Research Infrastructures contract no. 675121 (project VI-SEEM).

This work was supported by computational time granted from the National Infrastructures for Research and Technology S.A. (GRNET S.A.) in the National HPC facility – ARIS – under project ID vspr003006

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