Lung Cancer Signature Biomarkers: tissue specific semantic similarity based clustering of Digital Differential Display (DDD) data

Srivastava, Mousami; Khurana, Pankaj; Sugadev, Ragumani

doi:10.1186/1756-0500-5-617

Table 2 Lung cancer signature biomarker clusters

From: Lung Cancer Signature Biomarkers: tissue specific semantic similarity based clustering of Digital Differential Display (DDD) data

Clustering of lung tissue specific cancer Biomarkers			DDD1			DDD2
Panel / Cluster of Biomarker	Type / class of Biomarker	GeneSymbol	Transcript frequency		Foldchange	Transcript frequency		Foldchange
			Pool A (normallung tissues)	Pool B (Normalbody tissuesexcluding lung)		Pool A (normallung tissues)	Pool B (lungtissue specificcancers)
Panel 1 / Cluster 4	Lung cancer metastasisdiagnostic markers	UCHL1	0	0.0002	-	0	0.0011	+
		LTF	0.0224	0.0018	+12.44	0.0224	0.0002	-112
Panel 2 / Cluster 5	Chemotherapy/ drugresistance related lungcancer biomarkers	TUBA1B	0	0.0002	-	0	0.0013	+
		RPSA	0.0001	0.0004	-4	0.0001	0.0027	+27
		RPL9	0.0002	0.0006	-3	0.0002	0.002	+10
		TMSB4X	0.0004	0.001	-2.5	0.0004	0.0016	+4
		COPB1	0.0007	0.0002	+3.5	0.0007	0	-
		API5	0.0007	0.0003	+2.3	0.0007	0	-
		NT5C2	0.0008	0.0003	+2.6	0.0008	0	-
		CPN	0.0009	0.0001	+9	0.0009	0	-
		PRKAR1A	0.0017	0.0006	+2.83	0.0017	0	-
Panel 3 / Cluster 6	Hypoxia related lungcancer biomarkers	FTL	0.0001	0.0011	-11	0.0001	0.0065	+65
		COL1A2	0.0001	0.0006	-6	0.0001	0.0023	+23
		GAPDH	0.0001	0.001	-10	0.0001	0.0011	+11
		IGKC	0.0002	0.0009	-4.5	0.0002	0.0016	+8
		ALDOA	0.0002	0.0006	-3	0.0002	0.0014	+7
		COL1A1	0.0001	0.0004	-4	0.0001	0.0009	+9
		FN1	0.0025	0.0012	+2.08	0.0025	0.0007	-3.57
		TGM2	0.0026	0.0008	+3.25	0.0026	0.0007	-3.71
		FOS	0.0015	0.0007	+2.14	0.0015	0.0002	-7.5
		CTNNA1	0.0034	0.0008	+4.25	0.0034	0.0003	-11.33
		FOSB	0.0024	0.0003	+8	0.0024	0.0002	-12
		APLP2	0.0109	0.0044	+2.47	0.0109	0.0008	-13.63
		NCOA4	0.0016	0.0005	+3.2	0.0016	0.0001	-16
		HIF1A	0.0011	0.0004	+2.75	0.0011	0	-
		AZIN1	0.001	0.0005	+2	0.001	0	-
		EHF	0.001	0.0001	+10	0.001	0	-
		TICAM2	0.001	0.0003	+3.33	0.001	0	-
		NAMPT	0.0008	0.0002	+4	0.0008	0	-
		TNFRSF1A	0.0008	0.0004	+2	0.0008	0	-
		DMBT1	0.0008	0.0001	+8	0.0008	0	-
		CSNK1A1	0.0007	0.0003	+2.33	0.0007	0	-
Panel 4 / Cluster 7	Lung cancer specificextra cellular matrixbiomarkers	TFPI2	0	0.0004	-	0	0.002	+
		RPL10	0.0001	0.0007	-7	0.0001	0.0014	+14
		SFTPA1	0.0004	0	+	0.0001	0.0011	+11
		KIAA1324	0.0013	0.0002	+6.5	0.0013	0	-
		CRISP3	0.0009	0.0001	+9	0.0009	0	-
		NET1	0.0007	0.0002	+3.5	0.0007	0	-

Note: (−) represents down regulation and (+) represents up regulation. Except SFTPA1, remaining all the up regulated genes in normal condition observed to be down regulated in cancerous condition and vice versa.

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ISSN: 1756-0500

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