DEGnext: classification of differentially expressed genes from RNA-seq data using a convolutional neural network with transfer learning

Table 6 Number of genes and samples from preprocessed and filtered gene expression data used in labeling, training, fine-tuning, and testing

Dataset	Filtered genes (FG)\(\#\)gene\(\times\) \(\#\)normal samples \(\#\) tumor samples	Significant labeled DEGs (SDEGs)	Bio genes(Q)	Non-bio train data(T1)	Non-bio test(T2)	Fine-tune(F1)	Bio-test(T3)
BRCA	6514\(\times\) 113 1102	4939	2327	3349	838	1861	466
BLCA	6514\(\times\) 19 414	2496	254	5008	1252	203	51
CHOL	6514\(\times\) 9 36	2811	552	4768	1193	441	111
COAD	6514\(\times\) 41 478	4213	1399	4092	1023	1119	280
ESCA	6514\(\times\) 11 161	1420	193	5056	1265	154	39
HNSC	6514\(\times\) 44 500	3860	734	4624	1156	587	147
KICH	6514\(\times\) 24 65	3422	306	4966	1242	244	62
KIRC	6514\(\times\) 72 538	4822	455	4847	1212	364	91
KIRP	6514\(\times\) 32 288	3535	337	4941	1236	269	68
LIHC	6514\(\times\) 32 288	4372	1498	4012	1004	1198	300
LUAD	6514\(\times\) 59 533	4387	566	4758	1190	452	114
LUSC	6514\(\times\) 49 502	4833	839	4540	1135	671	168
PRAD	6514\(\times\) 52 498	3803	1080	4347	1087	864	216
READ	6514\(\times\) 10 166	2678	121	5114	1279	96	25
STAD	6514\(\times\) 32 375	3379	388	4900	1226	310	78
THCA	6514\(\times\) 58 502	4292	3031	2786	697	2424	607
UCEC	6514\(\times\) 35 551	3992	999	4412	1103	799	200

Q: bio data; T1: non-bio train data; T2: non-bio test data; F1: fine tune data; T3: bio test data

ISSN: 1471-2105