OMICfpp: a fuzzy approach for paired RNA-Seq counts

Berral-Gonzalez, Alberto; Riffo-Campos, Angela L.; Ayala, Guillermo

doi:10.1186/s12864-019-5496-5

BMC Genomics

Table 2 The top 30 genes with differential expression reported by the OMICfpp method using an 0.37 and 0.93 orness value, respectively, with the complete distribution

From: OMICfpp: a fuzzy approach for paired RNA-Seq counts

ENSEMBL ID	Gene symbol	Synonyms	CRC status	Other cancer
Results using an orness value of 0.37
ENSG00000001497	LAS1L	FLJ12525, WTS, Las1-like, dJ475B7.2	New	Known [33]
ENSG00000002079	MYH16	MHC20, MYH16P, MYH5	New	New
ENSG00000003147	ICA1	ICA69, ICAp69	New	Known [34]
ENSG00000005844	ITGAL	CD11A; LFA-1; LFA1A	Known [40]	Known [41]
ENSG00000006071	ABCC8	HI, SUR, HHF1, MRP8, PHHI, SUR1, ABC36, HRINS, TNDM2, SUR1delta2	Known [42]	Known [43]
ENSG00000006327	TNFRSF12A	FN14, CD266, TWEAKR	New	Known [35]
ENSG00000006704	GTF2IRD1	BEN, WBS, GTF3, RBAP2, CREAM1, MUSTRD1, WBSCR11, WBSCR12, hMusTRD1alpha1	New	known [36]
ENSG00000010539	ZNF200	-	New	New
ENSG00000011201	ANOS1	HH1, HHA, KAL, KMS, KAL1, ADMLX, WFDC19, KALIG-1	Known [44]	Known [45]
ENSG00000013293	SLC7A14	PPP1R142	New	New
ENSG00000015285	WAS	THC, IMD2, SCNX, THC1, WASP, WASPA	Known [46]	Known [47]
ENSG00000015592	STMN4	RB3	Known [48]	Known [49]
ENSG00000018236	CNTN1	F3, GP135, MYPCN	Known [50]	Known [51]
ENSG00000018280	SLC11A1	LSH, NRAMP, NRAMP1	Known [30]	Known [52]
ENSG00000029559	IBSP	BSP, BNSP, SP-II, BSP-II	Known [53]	Known [53]
ENSG00000030304	MUSK	CMS9, FADS	Known [54]	Known [55]
ENSG00000033122	LRRC7	DENSIN	New	New
ENSG00000034971	MYOC	GPOA, JOAG, TIGR, GLC1A, JOAG1	New	Known [38]
ENSG00000036672	USP2	USP9, UBP41	Known [56]	Known [57]
ENSG00000040275	SPDL1	CCDC99, FLJ20364, hSpindly	New	Known [58]
ENSG00000040731	CDH10	-	New	Known [59]
ENSG00000043143	JADE2	PHF15, JADE-2	New	New
ENSG00000044012	GUCA2B	-	Known [60]	New
ENSG00000046774	MAGEC2	CT10, HCA587, MAGEE1	Known [31]	Known [31]
ENSG00000047617	ANO2	C12orf3, TMEM16B	New	New
ENSG00000048462	TNFRSF17	BCM, BCMA, CD269, TNFRSF13A	Known [61]	Known [62]
ENSG00000050030	NEXMIF	XPN, MRX98, KIDLIA, KIAA2022	New	New
ENSG00000053524	MCF2L2	ARHGEF22	New	New
ENSG00000058600	POLR3E	SIN; RPC5	New	New
ENSG00000060718	COL11A1	STL2, COLL6, CO11A1	Known [63]	Known [64]
Results using an orness value of 0.93
ENSG00000001460	STPG1	MAPO2, C1orf201	New	New
ENSG00000001497	LAS1L	FLJ12525, WTS, Las1-like, dJ475B7.2	New	Known [33]
ENSG00000002822	MAD1L1	MAD1, PIG9, TP53I9, TXBP181	Known [65]	Known [66]
ENSG00000003096	KLHL13	BKLHD2	New	New
ENSG00000003147	ICA1	ICA69, ICAp69	New	Known [34]
ENSG00000003249	DBNDD1	-	New	New
ENSG00000004487	KDM1A	AOF2, BHC110, KDM1, KIAA0601, LSD1	Known [67]	Known [68]
ENSG00000004848	ARX	SSX, PRTS, CT121, EIEE1, MRX29, MRX32, MRX33, MRX36, MRX38, MRX43, MRX54, MRX76, MRX87, MRXS1	New	Known [69]
ENSG00000005001	PRSS22	BSSP-4, SP001LA, hBSSP-4	Known [70]	Known [71]
ENSG00000005249	PRKAR2B	PRKAR2, RII-BETA	Known [72]	Known [73]
ENSG00000005448	WDR54	-	Known [74]	New
ENSG00000006194	ZNF263	FPM315, ZSCAN44, ZKSCAN12	New	New
ENSG00000006327	TNFRSF12A	FN14, CD266, TWEAKR	New	Known [35]
ENSG00000006704	GTF2IRD1	BEN, WBS, GTF3, RBAP2, CREAM1, MUSTRD1, WBSCR11, WBSCR12, hMusTRD1alpha1	New	known [36]
ENSG00000007392	LUC7L	Luc7, SR+89, LUC7B1, hLuc7B1	New	Known [75]
ENSG00000008300	CELSR3	FMI1, EGFL1, HFMI1, MEGF2, ADGRC3, CDHF11, RESDA1	New	Known [76]
ENSG00000010539	ZNF200	-	New	New
ENSG00000010610	CD4	CD4mut	Known [77]	Known [78]
ENSG00000011143	MKS1	BBS13, FLJ20345, MKS, POC12	New	New
ENSG00000011201	ANOS1	HH1, HHA, KAL, KMS, KAL1, ADMLX, WFDC19, KALIG-1	Known [44]	Known [45]
ENSG00000011243	AKAP8L	HAP95, NAKAP95	Known [79]	Known [79]
ENSG00000011260	UTP18	WDR50, CGI-48	New	Known [80]
ENSG00000012211	PRICKLE3	Pk3, LMO6	New	New
ENSG00000013523	ANGEL1	Ccr4e, KIAA0759	New	New
ENSG00000018236	CNTN1	F3, GP135, MYPCN	Known [50]	Known [51]
ENSG00000018280	SLC11A1	LSH, NRAMP, NRAMP1	Known [30]	Known [52]
ENSG00000018625	ATP1A2	FHM2, MHP2	New	Known [81]
ENSG00000023839	ABCC2	DJS, MRP2, cMRP, ABC30, CMOAT	Known [82]	Known [83]
ENSG00000025772	TOMM34	TOM34, URCC3, HTOM34P	Known [84]	Known [85]
ENSG00000029153	ARNTL2	CLIF, MOP9, BMAL2, PASD9, bHLHe6	Known [86]	Known [87]

The term “known” is assigned if the gene has been previously reported as differentially expressed in colorectal cancer (CRC) or in other types of cancer, otherwise “New” is used. The genes reported in common by OMICfpp with an orness value of 0.37 and 0.93, edgeR and DESeq2 are in bold entries

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ISSN: 1471-2164

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