HNSCC clones corresponding to known genes.
| Functional Group | Clone ID | No. of Times Isolated | Identity | Unigene Cluster | Previously Identified by SEREX |
| DNA binding/ Transcription | AU-HN-2 | 1 | TREX1, 3' repair exonuclease | Hs.278408 | no |
| AU-HN-4 | 2 | BRAP (BRCA1 associated): Nuclear localization protein | Hs.122764 | yes | |
| AU-HN-5 | 1 | Trim 26 zinc finger domains | Hs.1287 | no | |
| AU-HN-10 | 1 | GTF21 transcription factor. Murine homolog TF11-1 | Hs.278589 | no | |
| AU-HN-11 | 6 | NSEP1 (YB-1) transcription factor | Hs.74497 | yes | |
| AU-HN-16 | 1 | MAZ transcription factor associated with c-myc | Hs.7647 | yes | |
| AU-HN-17 | 1 | SON (DBP-5; KIAA1019; NREBP DNA binding protein) | Hs.92909 | yes | |
| AU-HN-27 | 1 | NACA nascent polypeptide-associated complex | Hs.32916 | yes | |
| AU-HN-37 | 1 | NUBP2 nucleotide binding protein | Hs.256549 | no | |
| RNA processing/ Translation | AU-HN-3 | 1 | EEF2 Translation elongation factor 2 | Hs.75309 | no |
| AU-HN-13 | 2 | GU2 Putative RNA helicase | Hs.7392 | no | |
| AU-HN-30 | 1 | RPLI3A ribosomal protein | Hs.119122 | no | |
| AU-HN-31 | 1 | SFRS21P (CASP11; SIP1; SRRP1290 splicing factor) | Hs.51957 | no | |
| AU-HN-33 | 1 | RPS12 ribosomal protein | Hs.339696 | no | |
| AU-HN-34 | 1 | MGC2835 RNA helicase | Hs.70582 | no | |
| Regulatory | AU-HN-18 | 1 | TMF1, TATA modulatory factor | Hs.267632 | yes |
| AU-HN-23 | 1 | PRC1 regulator of cytokinesis | Hs.344037 | no | |
| Structural | AU-HN-22 | 2 | KRT14 keratin 14 | Hs.355214 | no |
| AU-HN-28 | 1 | Viniculin | Hs.75350 | yes | |
| AU-HN-32 | 1 | H2AFY histone family member | Hs.75258 | no | |
| Apoptosis repressor | AU-HN-14 | 2 | SLK (KIAA02304) Ste related kinase | Hs.105751 | no |
| AU-HN-20 | 2 | NOL3 (ARC) nuclear protein 3, apoptosis repressor | Hs.278439 | no | |
| Molecular chaperone | AU-HN-24 | 1 | DNAJA2 member of Hsp40 family | Hs.21189 | yes |
| AU-HN-35 | 1 | DNAJA1 member of HSP40 family | Hs.94 | yes | |
| Other | AU-HN-1 | 1 | LINE-1 retrotransposon | No | yes |
| AU-HN-6 | 1 | MOG (HSPC 165) Homolog of yeast protein | Hs.13605 | no | |
| AU-HN-12 | 4 | LIMS1 (PINCH): LIM and senescent antigen-like domain | Hs.112378, Hs.193700 | yes | |
| AU-HN-21 | 2 | COPB2 coatomer protein complex subunit protein | Hs.75724 | no | |
| AU-HN-25 | 1 | FLJ22548 hypothetical protein | Hs.103267 | no | |
| AU-HN-26 | 2 | C21orf97; FLJ21324; MGC15873 | Hs.4746 | yes | |
| AU-HN-29 | 3 | SSNA1 Sjogrens syndrome nuclear autoantigen 1 | Hs.18528 | no |