Supplemental Table 5

Transcripts, Genes / encoded Proteins specific for Skullbase Chordoma / Transcripts, Genes / encoded Proteins specific for Spine Chordoma / Transcripts, Genes / encoded Proteins common in Spine & Skullbase Chordoma
UP - Regulated / UP - Regulated / UP - Regulated
Transcription Factors:
ZIC1, ZIC4 (development)
LHX4 (development & differentiation, Wnt-bCat-TCF pathway (PW))
ncRNA:
ITPK1-AS1 (asRNA for ITPK1)
TMEM108-AS1 (asRNA for TMEM108)
CSNK1G2-AS1 (asRNA for CSNK1G2)
TNK2-AX1 (asRNA for TNK2)
Posttranscriptional & Protein Expression Regulator:
NANOS1 (posttranscriptional repressor, preserves germline stem-cell status, promotes tumor cell invasion, upregulated at RB1-deficiency)
Intracellular Metabolism / Catabolism:
AKR1B15 (steroid metabolism, detoxification)
DIO1 (thyroid hormone T3 signaling, antiapoptotic)
Intracellular Transport:
SLC25A18 (mitochondrial inner membrane transport of glutamate, amine compounds, and carbohydrates)
Cell Division:
KIF18B (microtubule component, regulator of cell division, driver in carcinogenesis)
SPC25 (part of kinetochore-Ndc80 complex in mitotic spindle for chromosome segregation)
Intracellular Signaling:
PBK (PDZ binding kinase, activates oncogenic FOXM1-PBK-bCat signaling PW, inhibits p53-p21 pathway to activate cell cycle progression)
Secretory, ECM, Membrane & Receptor Proteins for Signaling:
CPLX2 (synaptic vesicle exocytosis)
NIPAL4 (membrane receptor)
ESM1 (proteoglycan)
HCRTR1 (G-protein-coupled orexin receptor)
Secretory, ECM & Membrane & Channel Proteins structural, metabolic & Transport:
CLDN18 (tight junction, membrane remodeling)
MUC6 (immune response)
HEXA (N-acetyl hexosamine catabolism)
CDSN (corneodesmosin)
HAS1 (hyaluronan synthase 1)
SFTPB (surfactant protein B)
Unknown Functions:
LOC100506142 (ncRNA)
ENSG00000273319 (ncRNA)
ENSG00000233559
LINC01291
LOC100127955
LINC0129
LOC101929595
LOC400627
ENSG00000270071
AKR7A2P1 (aldo-keto reductase family 7, member A2 pseudogene 1)
BC042374
AK097829
C7orf71
ENSG00000248223
C5orf66 / Transcription Factors:
SALL3 (development, represses DNMT3A-induced DNA methylation)
HOXA4, A5, A10 (development)
HOXB6 (development)
HOXC6, C8, C10 (development)
ZNF385B (pro- & anti-apoptotic)
ZNF695 (cell cycle activation)
Transcriptional Regulator:
HOPX (differentiation & proliferation, marker of quiescent stem cells, recruits HDAC, inhibits SRF, activates ABC transporter for multidrug resistance)
ncRNA:
piR-49021 (epigenetics & gene silencing)
HOXA-AS2 (asRNA for HOXA cluster)
SNORD45 (RNA processing)
FOXO22-AS1 (asRNA for FOXO22)
Intracellular Metabolism / Catabolism:
ASB1 (proteasomal degradation)
AKR1B10 (drug resistance)
ABHD16B (hydrolase activity)
GDA (guanine deaminase)
PSAPL (preproprotein involved in lysosomal degradation, multifunctional)
Intracellular Transport:
AP3B2 (vesicle component involved in transport to lysosomes)
Intracellular Signaling:
HPCAL4 (hippocalcin like 4)
ALPK2 (activator of DNA repair & apoptosis, increases invasive & metastatic potential)
ARHGAP40 (inhibits small GTPase signaling)
DDIT4L (inhibits mTOR PWs involved in growth, stem cell differentiation & inhibition of apoptosis)
Secretory, ECM, Membrane & Receptor Proteins for Signaling:
MRGPRX3 (G protein-coupled receptor, cell differentiation)
SHH (development, cell-cell differentiation)
POPDC3 (cAMP signaling pathway)
PKD1L2 (component of calcium channel pores, G protein binding)
ADGRD1 (adhesion G protein-coupled receptor, cell adhesion & migration, cell growth, oncogenic)
Secretory, ECM, Membrane & Channel Proteins structural, metabolic & Transport:
SLC15A5 (oligopeptide transport)
RAB3B (RAS oncogene family member)
Immune, Defense Response / Tumor Suppressor:
TRIL (inflammatory & innate immune response via TLR4 receptor signaling)
Unknown Functions:
LOC729739
ENSG00000256151
ENSG00000262477
ENSG00000260884
ENSG00000260597
LOC643201 (ncRNA, pseudogene)
AX746504 (lincRNA in bladder cancer)
LINC00475 / Transcription Factors:
T (brachyury drives EMT, development)
LMX1A (development & differentiation)
HOXA1, A2, A3 (development)
FOXD1 (development & differentiation, autoimmunity, inflammation, drug resistance)
DNA / RNA Processing & Repair:
EME1 (increases tumor survival & drug resistance)
ncRNA:
NAV2-AS5 (asRNA for NAV2, which regulates neuron growth & migration)
MALAT1 (regulation of gene expression)
HOTAIRM1 (asRNA for HOXA cluster)
Pseudogene:
SPDYE7P (intracellular kinase signaling)
Intracellular Metabolism / Catabolism:
SPTLC3 (serine palmitoyltransferase)
PAPSS2 (dvlp. of bone & skeletal system, prevents cell senescence)
Intracellular Signaling:
PPEF1 (protein phosphatase)
GPER1 (G protein-coupled estrogen receptor 1)
Secretory, ECM, Membrane & Receptor Proteins for Signaling:
IQGAP3 (cell proliferation)
CD109 (inhibits TGF-beta signaling)
Secretory, ECM, Membrane & Channel Proteins structural, metabolic & Transport:
COL2A1 (collagen, type II, alpha 1)
HRNR (hornerin)
ACAN (aggrecan, part of ECM)
PRSS51 (extracellular protein metabolism)
FN1 (cell adhesion, migration, metastasis)
ADAMTS7 (disintegrin & metalloproteinase)
NAV2 (cell growth &, migration, tumorigenesis & metastasis)
Unknown Functions:
BC047626
LOC101928909
NPIPB3 (nuclear pore complex interacting protein family, member B3, signaling & immune response)
SYCP2L (DNA repair, chromosomal rearrangements, RNA splicing)
SAMD5 (SAM domain, SAMD5-SASH1 fusion, cell cycle regulation)
LOC100126784 (ncRNA)
DOWN - Regulated / DOWN - Regulated / DOWN - Regulated
Transcription Factors:
PAX3 (development & differentiation, multifunctional)
ESRRG (activates DNMT1-induced DNA methylation)
OVOL2 (epithelial dvlp. & diff.)
TFAP2B (development)
ncRNA:
SOX21-AS1 (asRNA for SOX21, probably regulation of gene expression)
Intracellular Metabolism / Catabolism:
ALDH1A2 (retinoic acid signaling)
PLD5 (signaling)
Intracellular structural / motor Proteins:
KRT23 (cytoskeleton)
CCDC42B (ciliogenesis)
CNN1 (cytoskeleton, tumor suppressing)
ACTG2 (inhibits cell growth)
Intracellular Transport:
SEC14L3 (lipid & phosphatidylinositol transport)
Intracellular Signaling:
CRYM (regulates thyroid hormone T3 & pipecolate PWs)
Secretory, ECM, Membrane & Receptor Proteins for Signaling:
OXGR1 (tumor suppressing)
NTF3 (cell development, differentiation & growth)
Secretory, ECM, Membrane & Channel Proteins structural, metabolic & Transport:
SLC5A1 (glucose : sodium symporter)
ATP12A (ATPase H+/K+ transporting non-gastric alpha2 subunit)
GCNT3 (glucosaminyl N-acetyl transferase 3, mucin type, glycoprotein metabolism)
ART3 (ADP-ribosyl transferase, protein metabolism)
CLDN22 (tight junctions)
HEPACAM2 (tumor suppressor)
SLC5A7 (choline transport)
ABCC8 (multidrug resistance)
HCN1 (hyperpolarization activated cyclic nucleotide activated potassium channel1)
Immune, Defense Response / Tumor Suppressor:
SLPI (secretory leucocyte peptidase inhibitor)
Unknown Functions:
ENSG00000260265
LOC642366
C8orf22
ENSG00000255693
LINC00284
LINC02185 / Transcription Factors:
FOXG1 (transcriptional repressor, neuron development & differentiation)
FOXJ1 (main regulator of motile ciliogenesis, controlled by Shh & Wnt signaling PWs, tumor suppressing)
SPDEF (tumor suppressor)
Transcriptional Regulator:
TOX3 (structural modification of chromatin & DNA)
Intracellular Metabolism / Catabolism:
ALOX15 (Shh induced inflammatory responses)
GSTA2 (detoxification)
FUT6 (glycosyltransferase)
CYP2B6 (detoxification)
Intracellular Signaling:
SULT1E1 (inflammation, lipid metabolism)
NEURL3 (ubiquitin signaling to activate Notch signaling PW for tissue dvlp., diff., maturation)
C10orf90 (ciliogenesis, ubiquitin signaling to activate tumor suppressor p53 - p21 PW)
Secretory, ECM, Membrane & Receptor Proteins for Signaling:
NRG3 (ligand for ERBB3 & 4 receptors, inhibits neuron migration)
ADGRF1 (adhesion G protein-coupled receptor F1)
NPY5R (drug resistance)
Secretory, ECM, Membrane & Channel Proteins structural, metabolic & Transport:
SLC34A2 (pH-sensitive sodium-dependent phosphate transporter, tumor suppressing)
FER1L6 (membrane protein for vesicle fusion)
B3GNT3 (metabolic enzyme involved in tumor suppressor signaling)
HS6ST3 (heparin sulfate 6-O-sulfotransferase 3, sulfate & glycosaminoglycan metabolism)
FRMPD2 (tight junctions, cell polarization, immunity)
CLDN3 (tight junctions, metastasis suppressor via inhibition of Wnt / EMT)
SLCO1B3 (organic anion transporter, uptake of endogenous & xenobiotic compounds)
RSPH1 (motile ciliogenesis, meiosis, mitosis)
Immune, Defense Response / Tumor Suppressor:
PRB3 (defense response against polyphenols & pathogen infections)
Unknown Functions:
TMEM213 (transmembrane protein of ER)
WDR49
AK131337 (carbohydrate catabolism)
ANKUB1
PRR15 (involved in loss of function of APC tumor suppressor, disruption of Wnt signaling)
C10orf107
C1orf210 (trafficking between endosome membrane & plasma membrane)
LOC283299
ARMC3 (similar to catenins beta & gamma, multifunctional)
CCDC60
LINC01207 / Transcription Factors:
ELF5 (regulates terminal differentiation, tumor suppressor, inhibits EMT via Snail2)
PAX7 (development, tumor suppressor)
SIX3 (development, activates SHH, represses WNT)
ncRNA:
RMST (lincRNA interacts with SOX2 to regulate neurogenesis)
Intracellular Metabolism / Catabolism:
PIP (prolactin induced protein, involved in proteolysis, multifunctional)
AGR2 (protein disulfide isomerase, post-translational protein modification)
CAPN13 (endopeptidase linked to apoptosis & proteolysis PWs of ECM & cytoskeleton)
Intracellular Signaling:
DAB1 (reelin signaling for brain development, neurogenesis & cell migration)
Secretory, ECM, Membrane & Receptor Proteins for Signaling:
ZG16B (cell adhesion, IFNAR & kinase signaling)
C6orf58 (FGFR & Erk signaling)
ODAM (tumor suppressor)
FAM3D (inflammation)
PROM1 (suppresses diff. of SC & EMT),
CHRM1 (cholinergic receptor muscarinic 1, G protein-coupled)
Secretory, ECM, Membrane & Channel Proteins structural, metabolic & Transport:
STATH (part of the ECM, involved in Ca2+ storage & homoeostasis)
CRISP3 (cysteine-rich secretory protein3, involved in immune response)
MUC7 (immune response)
LPO (lactoperoxidase, antimicrobial)
AQP5 (aquaporin 5)
SLC5A8 (tumor suppressing by sequestering survivin)
SLC13A2 (dicarboxylic acid transmembrane transport)
MUC5AC (immune response)
UGT2A1 (secretion of lipophilic molecules)
CRISP2 (immune response)
Immune, Defense Response / Tumor Suppressor:
PIGR (polymeric immunoglobulin receptor)
LTF (iron homeostasis, innate immune rsp.)
DMBT1 (promotes tumor cell interaction with immune system)
TCN1 (vitamin B12 transport)
MSMB (autocrine, paracrine factor)
BPIFA1, B1, B2, B3
FDCSP (follicular dendritic cell secreted protein)
SCGB3A1 (secretoglobin, family 3A, member 1, tumor suppressor)
VTCN1 (immune checkpoint molecule, tumor suppressor)
Unknown Functions:
PLEKHS1
LOC644838

Supplemental Table 5:

The three gene groups of differentially expressed genes and transcripts from Supplemental Table 4 were used to create these panel lists of 30 to 41 genes and transcripts strongest differentially up- and downregulated, and categorized according to their biological functions and subcellular locations, including short annotations in parenthesis.