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Table 2 List of 32 UniGene clusters and corresponding TCs selected for qRT-PCR analysis of their expression.

From: Identification and validation of reference genes for quantitative RT-PCR normalization in wheat

Unigene Cluster Gene annotation CV TPM NS UniGene Rank UniGene TIGR contig TIGR freq. Rank TIGR
1) Ta54963 GABARAP (GABA-receptor-associated protein) 9.85 356 1 TC304353, TC304722, TC295997 66/197 29
2) Ta54171 Superoxide dismutase [Cu-Zn] 11.95 1316 2 TC317053, TC294760, TC297148 110/197 8
3) Ta50503 Ubiquitin 12.79 1088 3 TC278495, TC296829, TC280981 72/197 22
4) Ta2776 Similar to RNase L inhibitor-like protein 13.17 158 4 TC278756, TC314244 38/197 91
5) Ta54733 Protein of unknown function (DUF 866) 15.47 167 5 TC335842, TC286574 40/197 86
6) Ta54948 Rab GTPase homolog (Rab7 subfamily) 16.22 366 6 TC278352, TC303984 33/197 110
7) Ta30797 Similar to phosphogluconate dehydrogenase 17.27 138 9 TC279294, TC284282 25/197 143
8) Ta35284 Protein transport protein Sec23A 17.95 101 10 TC278525 31/197 116
9) Ta54447 Acetyl-CoA acyltransferase 18.47 365 13 TC279279, TC283613 65/197 32
10) Ta54448 Protein of unknown function (DUF52 family) 19.24 99 15 TC279558 36/197 96
11) Ta 22845 ATP-depend. 26S proteasome regulatory sub. 20.48 186 24 TC353778 64/197 33
12) Ta659 Translation elongation factor 1 alpha-subunit 29.67 3026 94 TC288390 139/197 1
13) Ta30768 GAPDH (Glyceraldehyde-3-phosph. dehydrog.) 22.68 1807 32 TC304401, TC348958, TC310664, TC326825 137/197 2
14) Ta53919 S-adenosylmethionine decarboxylase 24.73 2533 47 TC320440, TC279487 135/197 3
15) Ta35497 Peptidyl-prolyl cis-trans isomerase (Cyclophilin) 30.81 2131 107 TC348130, TC348051, TC352472 135/197 4
16) Ta53937 Cytosolic malate dehydrogenase 24.58 1368 45 TC300803, TC279938 127/197 5
17) Ta53891 Zn-finger, A20-like domain containing protein 25.19 1291 50 TC293469 126/197 6
18) Ta45379 ADP-ribosylation factor 24.90 1180 48 TC337136 118/197 7
19) Ta1698 NADP-isocitrate dehydrogenase 24.39 761 42 TC283369, TC282416 95/197 10
20) Ta27771 60S ribosomal protein L18a-1 31.94 580 120 TC363506, TC298941 94/197 11
21) Ta53964 Translation elongation factor EF-1alpha (GTPase) 26.88 1074 68 TC279148 89/197 12
22) Ta54227 Cell div. control prot. (AAA-superfam. ATPases) 24.65 670 46 TC308517, TC281050 87/197 13
23) Ta54280 Translation initiation factor SuI1 family protein 23.53 609 36 TC297312, TC338691 82/197 15
24) Ta54512 Cytochrome b5 family protein 21.70 695 29 TC284040, TC283036, TC284818 77/197 17
25) Ta4045 Ubiquinol-cytochrome C reduct. iron-sulfur sub. 23.76 384 37 TC350975, TC327386 77/197 18
26) Ta53889 Hypothetical protein 29.95 603 97 TC317382, TC333515 74/197 19
27) Ta53967 Vacuolar ATP synthase 16 kDa proteolipid sub. 25.00 719 49 TC292895, TC344391 71/197 23
28) Ta44405 Beta-tubulin 4 (Tubb4) 22.94 114 33 TC278209 20/197 167
29) Ta54238 Ubiquitin-conjugating enzyme E2 28.67 165 86 TC295800, TC289972, TC289612 57/197 47
30) Ta38797 Similar to histone H3 (Arabidopsis) 33.94 1066 137 TC290356, TC280404, TC313660 68/197 27
31) Ta55512 Cathepsin B-like cysteine protease 24.55 171 43 TC311052, TC278654 52/197 53
32) Ta2291 ADP-ribosylation factor 38.31 377 162 TC278558, TC278370 66/197 31
  1. Italics = novel reference genes; normal = traditional reference genes.
  2. CV/TPM = Coefficient of Variation calculated on the expression values (TPMs) in six tissues (flower, inflorescence, leaf, root, seed and stem), UniGene Profile Viewer.
  3. NS UniGene = Number of EST sequences included in each UniGene cluster.
  4. Rank UniGene = Ranking of the UniGene clusters on the basis of the CV of their expression values (TPMs) in six wheat tissues.
  5. TIGR frequency = Number of hosting libraries/total number of cDNA libraries, calculated for each TC or group of TCs linked to the selected UniGene clusters.
  6. Rank TIGR = Ranking of the TCs or group of TCs linked to the selected UniGene clusters on the basis of their frequency.