MicroRNA Expression Profiling by Bead Array Technology in Human Tumor Cell Lines Treated with Interf
364
−32.16***
13,112
358
−35.64***
12,201
315
−37.74***
12,355
355
−33.83***
Hybdridization controls
array_hyb_con4
6,404
7,110
0.11
7,724
6,684
−0.16
7,031
6,739
−0.04
6,964
6,746
−0.03
array_hyb_con3
6,923
7,681
0.11
7,833
7,368
−0.06
7,422
7,054
−0.05
6,906
7,365
0.07
array_hyb_con1
10,779
11,868
0.10
11,812
11,728
−0.0.01
11,436
11,382
0.00
11,059
11,522
0.04
array_hyb_con2
10,258
11,145
0.09
11,382
10,829
−0.05
11,075
10,650
−0.04
9,997
10,283
0.03
List of calculated relative fluorescent levels (without background correction) and calculated differences (CHF) between hepatoma (HuH7) and melanoma (ME-15) cells. A linear model with ME-15 and HuH7 as separate factors was used to estimate cell line differences in microRNA expression. The genes with the highest significance (and log factor change >0.5) are listed in the upper section and the bottom shows data for the hybridization controls as reference. Change factors show the cell line differences of the retransformed mean to the linear scale. p values (limma t test) were adjusted by false discovery rate correction. Significance codes are defined by the intervals: ‘***’ < 0.001 ≤ ‘**’ < 0.01 ≤ ‘*’ < 0.05 Table 2 Modulation of microRNA expression by IFNα―4 and 24 h after stimulation
Control | Interferon-alpha treated | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
4 h | 24 h | 4 h | 24 h | |||||||||
a | ME-15 | HuH7 | CHF | ME-15 | HuH7 | CHF | ME-15 | HuH7 | CHF | ME-15 | HuH7 | CHF |
Validated microRNAs | ||||||||||||
hsa-miR-19a | 13,617 | 6,726 | −1.02 | 18,318 | 17,178 | −0.07 | 19,226 | 17,409 | −0.10 | 14,425 | 14,079 | −0.02 |
hsa-miR-19b | 13,365 | 9,406 | −0.42 | 25,463 | 22,438 | −0.13 | 21,532 | 20,625 | −0.04 | 18,039 | 17,440 | −0.03 |
hsa-miR-30e-5p | 9,497 | 6,838 | −0.39 | 13,045 | 11,321 | −0.15 | 12,643 | 10,887 | −0.16 | 13,230 | 11,809 | −0.12 |
hsa-let-7a | 15,244 | 4,335 | −2.52. | 28,304 | 6,181 | −3.58 *** | 22,226 | 6,386 | −2.48*** | 30,449 | 5,612 | −4.43*** |
hsa-let-7b | 8,236 | 539 | −14.28*** | 12,563 | 475 | −25.44*** | 12,150 | 500 | −23.30 *** | 12,309 | 452 | −26.24*** |
hsa-miR-203 | 907 | 325 | −1.79** | 1,155 | 348 | 2.32*** | 1,302 | 359 | −2.63*** | 1,186 | 5,757 | −1.07** |
hsa-miR-130b | 5,700 | 8,316 | −0.46 | 13,023 | 13,880 | 0.07 | 9,994 | 14,055 | 0.41 | 12,053 | 12,432 | 0.03 |
hsa-miR-455 | 2,677 | 2,604 | −0.03 | 3,944 | 5,285 | 0.34* | 3,437 | 5,927 | 0.72** | 3,262 | 5,342 | 0.64* |
b | ME-15 | HuH7 | ||||||||||
4 h | 24 h | 4 h | 24 h | |||||||||
−IFNa | +IFNa | CHF | −IFNa | +IFNa | CHF | −IFNa | +IFNa | CHF | −IFNa | +IFNa | CHF | |
Interferon-regulated microRNAs | ||||||||||||
hsa-miR-33b | 1,226 | 3,484 | 1.84** | 2,888 | 2,318 | −0.25 | 476 | 1,113 | 1.34** | 1,306 | 1,851 | 0.42*** |
hsa-miR-33 | 2,631 | 7,352 | 1.79 | 9,774 | 5,764 | −0.70* | 1,887 | 6,645 | 2.52. | 8,893 | 2,726 | −2.26 |
hsa-miR-126* | 2,221 | 5,409 | 1.44* | 5,578 | 6,111 | 0.10 | 4,749 | 6,410 | 0.35. | 5,687 | 5,803 | 0.02*** |
hsa-miR-10b | 1,695 | 3,564 | 1.10* | 2,929 | 4,297 | 0.47** | 378 | 411 | 0.09 | 371 | 382 | 0.03 |
hsa-miR-551b | 2,085 | 4,169 | 1.00* | 4,423 | 3,419 | −0.29 | 1,804 | 4,979 | 1.76* | 5,221 | 4,865 | −0.07 |
hsa-miR-137 | 1,037 | 1,966 | 0.90 | 2,523 | 2,872 | 0.14 | 1,613 | 3,155 | 0.96** | 3,429 | 3,598 | 0.05 |
hsa-miR-138 | 2,158 | 4,074 | 0.89* | 4,709 | 3,701 | −0.27 | 725 | 828 | 0.14 | 903 | 859 | −0.05 |
hsa-miR-130b | 5,700 | 9,994 | 0.75 | 13,023 | 12,053 | −0.08 | 8,316 | 14,055 | 0.69** | 13,880 | 12,432 | −0.12 |
hsa-miR-101 | 6,701 | 11,387 | 0.70 | 13,088 | 11,688 | −0.12 | 3,569 | 10,871 | 2.05** | 10,445 | 10,796 | 0.03 |
hsa-miR-140 | 7,339 | 12,236 | 0.67 | 15,512 | 15,931 | 0.03 | 3,058 | 5,976 | 0.95* | 6,135 | 7,221 | 0.18 |
HS_92 | 829 | 1,356 | 0.64. | 1,246 | 1,179 | −0.06 | 407 | 587 | 0.44 | 492 | 478 | −0.03 |
hsa-miR-362 | 1,382 | 2,234 | 0.62* | 2,144 | 2,276 | 0.06 | 1,907 | 2,737 | 0.43* | 2,456 | 2,519 | 0.03 |
hsa-miR-19b | 13,365 | 21,532 | 0.61** | 25,463 | 18,039 | −0.41 | 9,406 | 20,625 | 1.19* | 22,438 | 17,440 | −0.29 |
hsa-miR-130a | 13,031 | 20,878 | 0.60. | 27,571 | 23,048 | −0.20 | 17,884 | 31,012 | 0.73* | 33,801 | 28,875 | −0.17 |
hsa-miR-579 | 552 | 816 | 0.48. | 992 | 1,053 | 0.06 | 729 | 1,362 | 0.87* | 1,250 | 1,308 | 0.05 |
hsa-miR-29b | 23,138 | 34,148 | 0.48. | 32,691 | 29,710 | −0.10 | 8,737 | 17,989 | 1.06* | 20,599 | 17,405 | −0.18. |
hsa-miR-19a | 13,617 | 19,226 | 0.41* | 18,318 | 14,425 | −0.27 | 6,726 | 17,409 | 1.59. | 17,178 | 14,079 | −0.22. |
hsa-miR-338 | 1,298 | 1,813 | 0.40. | 1,870 | 1,603 | −0.17 | 2,363 | 4,603 | 0.95. | 5,109 | 4,088 | -0.25 |
hsa-miR-590 | 1,403 | 1,949 | 0.39. | 1,545 | 1,367 | −0.13 | 669 | 1,068 | 0.60. |
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