Table 4 Top 30 differentially regulated genes in KS sample A.
Gene symbol / Accession no. / Fold change / Gene description1 / XP_497569.1 / XM_497569 / 59.61 / similar to immunoglobulin lambda-like polypeptide 1 precursor
2 / SBDS / NR_001588 / 50.31 / Shwachman-Bodian-Diamond syndrome protein
3 / NP_000583.1 / NM_007293 / 22.39 / complement component 4B preproprotein
4 / OSR2 / NM_053001 / 21.72 / odd-skipped related 2
5 / CALD1 / NM_033139 / 17.79 / Caldesmon
6 / MCL1 / NM_021960 / 17.24 / Induced myeloid leukemia cell differentiation protein Mcl-1.
7 / LUM / NM_002345 / 16.38 / Lumican precursor
8 / XP_294590.1 / XM_294590 / 15.76 / PREDICTED: similar to bA13B9.3
9 / TNC / NM_002160 / 14.91 / Tenascin precursor
10 / TXNDC5 / NM_022085 / 14.58 / Muted protein homolog.
11 / ITGBL1 / NM_004791 / 13.47 / integrin, beta-like 1
12 / PALM2 / NM_007203 / 12.94 / A-kinase anchor protein 2
13 / ITGB1 / NM_133376 / 12.45 / Integrin beta-1 precursor
14 / CALML3 / NM_005185 / 12.42 / Calmodulin-related protein NB-1
15 / POSTN / NM_006475 / 12.03 / Periostin precursor
16 / CPVL / NM_031311 / 11.77 / Probable serine carboxypeptidase CPVL precursor
17 / LNK / NM_005475 / 11.48 / Lymphocyte specific adapter protein Lnk
18 / KRT10 / NM_000421 / 11.48 / Keratin, type I cytoskeletal 10
19 / ARP3 / NM_005721 / 11.07 / Actin-like protein 3
20 / COTL1 / NM_021149 / 9.76 / Coactosin-like protein.
21 / ARPC1B / NM_005720 / 9.69 / ARP2/3 complex 41 kDa subunit
22 / SPP1 / NM_000582 / 9.66 / Osteopontin precursor
23 / SDCBP / NM_005625 / 9.42 / Syntenin 1
24 / IGJ / NM_144646 / 8.99 / Immunoglobulin J chain.
25 / HLA-B / NM_005514 / 8.93 / HLA class I histocompatibility antigen, B-42 alpha chain precursor
26 / CCL2 / NM_002982 / 8.84 / Small inducible cytokine A2 precursor
27 / SEPP1 / NM_005410 / 8.68 / Selenoprotein P precursor
28 / BTBD1 / NM_025238 / 8.47 / BTB/POZ domain containing protein 1
29 / RPN1 / NM_002950 / 8.44 / Dolichyl-diphosphooligosaccharide—protein glycosyltransferase 67 kDa subunit precursor
30 / PRSS23 / NM_007173 / 8.24 / Serine protease 23 precursor
31 / NP_115952.1 / NM_032563 / 0.01 / late cornified envelope 3D
32 / BBOX1 / NM_003986 / 0.02 / Gamma-butyrobetaine dioxygenase
33 / KRT25A / NM_181534 / 0.02 / keratin 25A
34 / MAGEA6 / NM_005361 / 0.02 / Melanoma-associated antigen 6
35 / C1QG / NM_172369 / 0.03 / Complement C1q subcomponent, C chain precursor.
36 / PIP / NM_002652 / 0.09 / Prolactin-inducible protein precursor
37 / KRT6E / NM_173086 / 0.09 / Keratin, type II cytoskeletal 6E
38 / S100A8 / NM_002964 / 0.10 / Calgranulin A
39 / NP_055215.1 / NM_014400 / 0.10 / GPI-anchored metastasis-associated protein homolog
40 / XP_043500.1 / XM_043500 / 0.10 / PREDICTED: similar to death-associated protein
41 / PP14C / NM_030949 / 0.10 / Protein phosphatase 1 regulatory subunit 14C
42 / MFAP5 / NM_003480 / 0.11 / Microfibrillar-associated protein 5 precursor
43 / FGA / NM_021871 / 0.12 / Fibrinogen alpha/alpha-E chain precursor
44 / ICBR / NM_021571 / 0.12 / Caspase-1 inhibitor Iceberg
45 / KRT25A / NM_181539 / 0.13 / keratin 25A
46 / WFDC12 / NM_080869 / 0.13 / WAP four-disulfide core domain protein 12 precursor
47 / SCGB1D2 / NM_006551 / 0.14 / Lipophilin B precursor
48 / ANGPTL1 / NM_004673 / 0.15 / angiopoietin-like 1 precursor
49 / CLDN1 / NM_021101 / 0.16 / Claudin-1
50 / CKMT1 / NM_020990 / 0.17 / Creatine kinase, ubiquitous mitochondrial precursor
51 / GPR87 / NM_023915 / 0.17 / Probable G-protein coupled receptor 87
52 / NFIB / NM_005596 / 0.18 / Nuclear factor 1 B-type
53 / CGA / NM_000735 / 0.19 / Glycoprotein hormones alpha chain precursor
54 / MSMB / NM_002443 / 0.20 / Beta-microseminoprotein precursor
55 / KLK11 / NM_144947 / 0.20 / Kallikrein 11 precursor
56 / NP_996849.1 / NM_206966 / 0.22 / similar to AVLV472
57 / MYH11 / NM_022844 / 0.22 / Myosin heavy chain, smooth muscle isoform
58 / F10 / NM_000504 / 0.22 / Coagulation factor X precursor
59 / XG / NM_175569 / 0.22 / XG glycoprotein precursor
60 / HOP / NM_139211 / 0.22 / Homeodomain-only protein
Table 5 Top 30 differentially regulated genes in KS sample B.
1 / CHSP1 / NM_014316 / 1056.03 / Calcium-regulated heat stable protein 1
2 / MAP3K7 / NM_145333 / 86.48 / Mitogen-activated protein kinase kinase kinase 7
3 / MFRP / NM_015645 / 26.68 / Complement C1q tumor necrosis factor-related protein 5 precursor
4 / PRAME / NM_006115 / 25.48 / Melanoma antigen preferentially expressed in tumors
5 / 209L1 / NM_214679 / 24.65 / CD209 antigen-like protein 1
6 / SLC1A5 / NM_005628 / 22.29 / Neutral amino acid transporter B
7 / SVIL / NM_021738 / 21.45 / Supervillin
8 / PDHA1 / NM_000284 / 19.24 / Pyruvate dehydrogenase E1 component alpha subunit, somatic form, mitochondrial precursor
9 / TPD52L2 / NM_003288 / 16.82 / Tumor protein D54
10 / SERPINA / NM_001085 / 14.72 / Alpha-1-antichymotrypsin precursor
11 / HECW2 / NM_020760 / 14.22 / HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2
12 / PGM2L1 / NM_173582 / 11.97 / phosphoglucomutase 2-like 1
13 / SUMF2 / NM_015411 / 11.10 / Sulfatase modifying factor 2 precursor
14 / RASSF2 / NM_014737 / 9.75 / Ras association domain family 2.
15 / TRAP1 / NM_016292 / 8.83 / Heat shock protein 75 kDa, mitochondrial precursor
16 / CG38 / NM_015964 / 8.49 / Protein CGI-38.
17 / NDUFB7 / NM_004146 / 8.07 / NADH-ubiquinone oxidoreductase B18 subunit
18 / FEN1 / NM_004111 / 7.43 / Flap endonuclease-1
19 / ELOVL4 / NM_022726 / 7.28 / Elongation of very long chain fatty acids protein 4
20 / ATP1A1 / NM_000701 / 7.23 / Sodium/potassium-transporting ATPase alpha-1 chain precursor
21 / CD200 / NM_001004196 / 6.46 / OX-2 membrane glycoprotein precursor
22 / SOX17 / NM_022454 / 6.13 / Transcription factor SOX-17.
23 / XP_372941.2 / XM_372941 / 5.34 / PREDICTED: similar to Ig kappa chain V region
24 / TACSTD1 / NM_002354 / 5.28 / Tumor-associated calcium signal transducer 1 precursor
25 / ITGA4 / NM_000885 / 5.04 / Integrin alpha-4 precursor
26 / NP_001009567.1 / NM_002438 / 4.93 / mannose receptor, C type 1-like 1
27 / GZMA / NM_006144 / 4.83 / Granzyme A precursor
28 / K467 / NM_207392 / 4.79 / KIPV467 protein precursor
29 / O60474 / NM_015892 / 4.71 / B cell RAG associated protein
30 / ATP6V / NM_001693 / 4.58 / Vacuolar ATP synthase subunit B, brain isoform
31 / TMEFF1 / NM_080655 / 0.01 / transmembrane protein with EGF-like and two follistatin-like domains 1
32 / C21orf63 / NM_058187 / 0.01 / precursor
33 / TRIM8 / NM_030912 / 0.02 / Tripartite motif protein 8
34 / ZDHHC14 / NM_024630 / 0.02 / Zinc finger DHHC domain containing protein 14
35 / CCL15 / NM_032964 / 0.02 / Small inducible cytokine A15 precursor
36 / LYSC / NM_000239 / 0.04 / Lysozyme C precursor
37 / TNFSF10 / NM_003810 / 0.05 / Tumor necrosis factor ligand superfamily member 10
38 / PSMD3 / NM_002809 / 0.06 / 26S proteasome non-ATPase regulatory subunit 3
39 / HCK / NM_002110 / 0.06 / Tyrosine-protein kinase HCK
40 / LPL / NM_000237 / 0.07 / Lipoprotein lipase precursor
41 / OAS3 / NM_006187 / 0.08 / 2'-5'-oligoadenylate synthetase 3
42 / SPRR1B / NM_003125 / 0.08 / Cornifin B
43 / ITGA9 / NM_002207 / 0.08 / Integrin alpha-9 precursor
44 / RALY / NM_016732 / 0.08 / RNA-binding protein Raly
45 / SIA8A / NM_003034 / 0.08 / Alpha-N-acetylneuraminide alpha 2,8sialyltransferase
46 / MYCT1 / NM_025107 / 0.09 / myc target 1
47 / HLA-A / NM_002116 / 0.09 / HLA class I histocompatibility antigen, A-80 alpha chain precursor
48 / SEPW1 / NM_003009 / 0.09 / Selenoprotein W.
49 / RGS1 / NM_002922 / 0.09 / Regulator of G-protein signaling 1
50 / HMOX2 / NM_002134 / 0.11 / Heme oxygenase 2
51 / EDARADD / NM_080738 / 0.11 / Ectodysplasin A receptor associated adapter protein
52 / HSPA8 / XM_376576 / 0.11 / Heat shock cognate 71 kDa protein
53 / GILZ / NM_198057 / 0.11 / Glucocorticoid-induced leucine zipper protein
54 / HLA-DPB1 / NM_002121 / 0.12 / HLA class II histocompatibility antigen, SB beta chain
55 / HLA-B / NM_005514 / 0.12 / HLA class I histocompatibility antigen, B-42 alpha chain precursor
56 / RPL13A / NM_012423 / 0.13 / 60S ribosomal protein L13a
57 / HLA-J / XR_000297 / 0.14 / HLA class I histocompatibility antigen, alpha chain G precursor
58 / SND1 / NM_014390 / 0.15 / Staphylococcal nuclease domain containing protein 1
59 / TSTA3 / NM_003313 / 0.15 / GDP-L-fucose synthetase
60 / PTTG1IP / NM_004339 / 0.16 / Pituitary tumor-transforming gene 1 protein-interacting protein precursor