A Prevalence of Imprinted Genes within the Total Transcriptomes of Human Tissues and Cells

Table 3

The SAGE libraries with 10% most and 10% least cumulative and average expression of established and candidate imprinted genes subsets.

ID^a	Primary ID^b	SAGE library	Sample	Cluster^c	Sum^d	Average^e	Max^f
Top 10% libraries
76	301	GSM125353	Bronchial brushings, former smoker	N	43,563.92	251.81	40,054.67
4	6	GSM574	Central retina (macula)	N	33,159.24	191.67	26,692.01
142	427	GSM383793	Mammary gland, ductal carcinoma in situ	C	29,781.50	172.15	25,275.20
29	104	GSM1730	Breast, ductal carcinoma in situ	C	29,575.98	170.96	25,125.63
75	300	GSM125352	Bronchial brushings, former smoker	N	29,184.64	168.70	24,955.09
145	430	GSM383797	Mammary gland, ductal carcinoma	C	27,222.30	157.35	22,422.27
99	346	GSM194651	Oral biopsy	N	27,066.16	156.45	21,312.29
90	273	GSM112808	Neuroblastoma, primary tumor, stage 4S	C	25,944.14	149.97	17,365.83
55	155	GSM14753	Breast carcinoma metastasis to lung	C	23,941.22	138.39	20,247.08
143	428	GSM383794	Mammary gland, ductal carcinoma in situ	C	23,570.83	136.25	18,977.90
30	105	GSM1731	Breast, ductal carcinoma in situ	C	23,346.84	134.95	18,746.14
167	507	GSM383893	Gallbladder tubular adenocarcinoma	C	23,262.07	134.46	20,154.48
27	561	GSM384016	Vascular endothelium, hemangioma, benign hyperplasia	D	22,688.19	131.15	12,514.88
91	274	GSM112809	Neuroblastoma, primary tumor, stage 4S	C	22,633.99	130.83	11,595.94
28	101	GSM1516	Hemangioma tumor	C	22,622.41	130.77	12,500.82
100	347	GSM194652	Oral biopsy	N	21,279.52	123.00	11,932.33
146	440	GSM383807	Mammary gland, ductal carcinoma in situ	C	20,570.15	118.90	16,071.37
62	433	GSM383800	Breast carcinoma cell line	IV	20,467.40	118.31	12,710.80
140	425	GSM383790	Mammary gland, ductal carcinoma	C	20,417.00	118.02	15,536.62
144	537	GSM383946	Whole body, fetal	N	20,274.33	117.19	9,698.99
149	443	GSM383812	Mammary gland, ductal carcinoma	C	20,036.49	115.82	13,377.93
5	21	GSM688	Breast, ductal carcinoma in situ	C	19,968.16	115.42	15,538.48
118	416	GSM383775	Cortex, pooled sample	N	19,926.52	115.18	13,701.49
54	263	GSM85616	Bronchial epithelium	N	19,665.60	113.67	15,918.74
53	262	GSM85611	Bronchial epithelium	N	19,653.98	113.61	15,655.95
17	340	GSM194386	Metaplastic bronchial epithelium	D	19,376.31	112.00	14,577.13
81	306	GSM125358	Bronchial brushings, never smoker	N	19,369.05	111.96	14,172.30
137	509	GSM383895	Gallbladder	N	19,320.00	111.68	15,346.14
66	437	GSM383804	Breast carcinoma cell line	IV	19,247.28	111.26	9,389.55
31	106	GSM1733	Mammary gland, ductal invasive in situ carcinoma	C	19,126.03	110.56	14,594.68
92	276	GSM112812	Neuroblastoma, primary tumor, stage 4	C	18,914.78	109.33	12,349.04
3	5	GSM573	Peripheral retina	N	18,817.72	108.77	12,293.99
2	4	GSM572	Peripheral retina	N	18,781.47	108.56	8,727.76
96	331	GSM194377	Nonsmall cell lung cancer: squamous cell carcinoma in situ	C	18,122.08	104.75	14,601.68
71	181	GSM14781	Brain desmoplastic medulloblastoma	C	18,106.48	104.66	11,244.70
68	439	GSM383806	Breast carcinoma cell line	IV	17,991.89	104.00	8,886.81
66	291	GSM125343	Bronchial brushings, former smoker	N	17,662.13	102.09	12,756.35
60	285	GSM125337	Bronchial brushings, current smoker	N	17,598.56	101.73	12,699.28
121	387	GSM383710	Ependymoma	C	17,524.27	101.30	10,222.49
51	260	GSM82458	Hippocampus	N	17,289.52	99.94	8,268.90
72	297	GSM125349	Bronchial brushings, former smoker	N	17,225.16	99.57	13,193.26
109	361	GSM296391	Lung biopsy	N	17,223.67	99.56	13,839.55
62	287	GSM125339	Bronchial brushings, current smoker	N	16,871.13	97.52	10,737.09
98	333	GSM194379	Nonsmall cell lung cancer: squamous cell carcinoma in situ	C	16,572.81	95.80	12,713.33
74	299	GSM125351	Bronchial brushings, former smoker	N	16,456.57	95.12	11,137.34
70	295	GSM125347	Bronchial brushings, former smoker	N	16,306.85	94.26	11,835.62
7	216	GSM37212	Adrenal cortex affected by primary pigmented nodular adrenocortical disease	D	16,221.46	93.77	4,205.56
59	284	GSM125336	Bronchial brushings, current smoker	N	16,090.33	93.01	11,242.21
94	329	GSM194375	Nonsmall cell lung cancer: squamous cell carcinoma in situ	C	15,715.04	90.84	11,679.51
Bottom 10% libraries
83	488	GSM383868	Colon carcinoma, cell line	IV	4,179.31	24.16	422.91
38	180	GSM14780	Gastric epithelial tissue from the antrum	N	4,169.95	24.10	1,615.39
84	204	GSM14807	Lung, poorly differentiated adenocarcinoma with lymphoplasmacytic infiltration	C	4,146.18	23.97	460.69
181	553	GSM383998	Gastroesophageal junction adenocarcinoma	C	4,141.08	23.94	1,351.60
1	7	GSM668	Kidney, embryonic cell line 293, uninduced cells	IV	4,119.01	23.81	920.45
4	120	GSM3244	AIDS-KS lesion	D	4,107.85	23.74	1,245.47
25	522	GSM383914	Lung, tumor associated (focal fibrosis and chronic inflammation)	D	4,103.62	23.72	606.45
30	121	GSM3245	CD4+ T cells	N	4,088.74	23.63	978.17
44	137	GSM14734	Medulloblastoma, cerebellum	C	4,081.98	23.60	804.90
56	162	GSM14760	Stomach, poorly differentiated carcinoma	C	4,081.16	23.59	1,340.95
54	153	GSM14751	Skin, melanoma	C	4,072.22	23.54	2,497.12
80	485	GSM383865	Colon carcinoma, cell line	IV	4,048.02	23.40	404.80
130	404	GSM383753	Medulloblastoma	C	3,987.16	23.05	1,069.73
82	487	GSM383867	Colon carcinoma, cell line	IV	3,961.32	22.90	506.24
12	71	GSM747	Colon, cancer cell line	IV	3,945.42	22.81	673.61
166	506	GSM383892	Gallbladder adenocarcinoma	C	3,909.95	22.60	651.66
115	372	GSM311354	CD15+ myeloid progenitor cells	N	3,859.27	22.31	1,108.11
52	261	GSM82459	Spermatozoa	N	3,814.90	22.05	1,288.15
50	259	GSM82243	Spermatozoa, pooled sample	N	3,811.16	22.03	1,429.18
94	328	GSM180670	Lymphocytes from children 1–4 years old (pooled samples)	N	3,794.27	21.93	843.17
81	486	GSM383866	Colon carcinoma, cell line	IV	3,746.12	21.65	378.40
39	183	GSM14784	Bone marrow	N	3,740.58	21.62	962.65
88	318	GSM136195	Cord blood-derived activated Th1 cells	N	3,668.81	21.21	777.29
20	423	GSM383787	Breast stroma, ductal carcinoma in situ associated	D	3,663.78	21.18	334.67
38	234	GSM66698	HL-60 cells	IV	3,661.81	21.17	920.25
168	508	GSM383894	Gallbladder tubular adenocarcinoma	C	3,643.40	21.06	624.22
28	217	GSM37337	Primary bronchial epithelial cells	IV	3,604.30	20.83	804.84
177	546	GSM383970	Retinoblastoma	C	3,561.82	20.59	384.45
71	475	GSM383852	Cartilage chondrosarcoma cell line	IV	3,502.94	20.25	515.14
38	127	GSM7800	Primary gastric cancer, poorly differentiated (scirrhous type)	C	3,413.27	19.73	636.37
130	466	GSM383840	Mammary myoepithelium, CD10+ cells	N	3,364.85	19.45	291.33
39	235	GSM66712	HL-60 cells exposed to 2.45 GHz radiofrequency for 2 h	IV	3,293.77	19.04	982.36
97	344	GSM194649	Oral brushing	N	3,290.72	19.02	996.85
173	523	GSM383915	Lymph node, B-cell lymphoma	C	3,166.97	18.31	555.61
140	514	GSM383902	Leukocytes	N	2,991.69	17.29	439.34
65	436	GSM383803	Breast carcinoma cell line	IV	2,988.12	17.27	597.62
63	434	GSM383801	Breast carcinoma cell line	IV	2,977.71	17.21	297.77
21	84	GSM784	Gastric epithelial tissues	N	2,970.06	17.17	673.21
151	554	GSM384002	Stomach	N	2,813.83	16.26	654.38
170	515	GSM383903	Liver cholangiocarcinoma metastasis	C	2,736.32	15.82	1,575.46
29	578	GSM389908	Total blood after EPO treatment, pooled sample	D	2,684.90	15.52	747.69
68	175	GSM14775	Skin, primary malignant melanoma	C	2,612.99	15.10	653.25
40	236	GSM66714	HL-60 cells exposed to 2.45 GHz radiofrequency for 6 h	IV	1,879.82	10.87	639.52
143	533	GSM383937	Pancreas	N	1,813.11	10.48	278.94
83	308	GSM135389	Skeletal muscle, 5 days training young men	N	1,673.61	9.67	435.14
86	311	GSM135392	Skeletal muscle, detraining young men	N	1,670.43	9.66	510.41
165	576	GSM389906	Total blood, pooled sample	N	1,511.12	8.73	436.55
82	307	GSM135388	Skeletal muscle, pretraining young men	N	1,091.72	6.31	327.52
28	577	GSM389907	Total blood during EPO treatment, pooled sample	D	811.75	4.69	162.35

Indexes (GSM numbers) represent GEO database accession numbers for SAGE libraries (one accession number selected for redundant entries).
^aID: listing within each cluster (see Supplementary Table 2).
^bPrimary ID: listing within a full dataset (see Supplementary Table 1).
^cClusters: C: cancer tissue; N: normal tissue and cells; IV: cells cultured in vitro; D: nontumorous disease tissue and cells.
^dSum: cumulative (total) tag per million (tpm) value for SAGE tags matching established and candidate imprinted genes within the SAGE library.
^eAverage: tpm value for SAGE tags matching established and candidate imprinted genes within the SAGE library.
^fMax: maximum tpm value for SAGE tags matching established and candidate imprinted genes within the SAGE library.
Particular sum: average and maximum values could be recalculated to the fraction of the total gene expression by dividing tpm value to 1,000,000.
Entries are sorted according to the cumulative (total) tpm value.