Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Network Type I Analysis

Type 1 network in which we propagated the absolute log regulation ratio abs(log(r/g)). We used the filtered lowest boundary of the confidence interval for the microarray measurement based and used the high confidence interaction map. Because type-I networks tend to favour highly connected proteins we tested a normalisation scheme in which we would run the network once with real values (the measured column) and once with simulated values where each measured point is set to 1 instead of the actual signal (the expected column). Afterwards we divided the measured value by the expected value. This normalisation scheme works to a certain extend but will lead to a variance that is directly related to the connectivity of each protein. In the end we dropped the use of Type-I networks due to the many technical problems they pose.


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Gene Rank description measured expected final Hugo
Results: HTML CSV LaTeX Showing element 1108 to 1157 of 3206 in total
Rank
description
measured
expected
final
Hugo
1108 DNA DAMAGE BINDING PROTEIN 1 (DAMAGE-SPECIFIC DNA BINDING PROTEIN 1) (DDB P127 SUBUNIT) (DDBA) (UV-DAMAGED DNA-BINDING PROTEIN 1) (UV-DDB 1) (XERODERMA PIGMENTOSUM GROUP E COMPLEMENTING PROTEIN) (XPCE) (X- ASSOCIATED PROTEIN 1) (XAP-1). [SWISSPROT; 0.0761267 0.303457 0.250864867 DDB1
1109 "PROPIONYL-COA CARBOXYLASE BETA CHAIN, MITOCHONDRIAL PRECURSOR (EC 6.4.1.3) (PCCASE BETA SUBUNIT) (PROPANOYL-COA:CARBON DIOXIDE LIGASE BETA SUBUNIT). [SWISSPROT;Acc:P05166]" 0.114033 0.45456 0.250864572 PCCB
1110 0.0381158 0.151938 0.250864168 WDR22
1111 CPZ GENE PRODUCT. [RefSeq;Acc:NM_003652] 0.0303816 0.12113 0.250818129 CPZ
1112 CARBOXYPEPTIDASE N CATALYTIC CHAIN PRECURSOR (EC 3.4.17.3) (ARGININE CARBOXYPEPTIDASE) (KININASE 1) (SERUM CARBOXYPEPTIDASE N) (SCPN) (ANAPHYLATOXIN INACTIVATOR) (PLASMA CARBOXYPEPTIDASE B). [SWISSPROT;Acc:P15169] 0.0305978 0.121992 0.250818086 CPN1
1113 CARBOXYPEPTIDASE H PRECURSOR (EC 3.4.17.10) (CPH) (CARBOXYPEPTIDASE E) (CPE) (ENKEPHALIN CONVERTASE) (PROHORMONE PROCESSING CARBOXYPEPTIDASE). [SWISSPROT;Acc:P16870] 0.0393162 0.156752 0.250817852 CPE
1114 POTENTIAL CARBOXYPEPTIDASE-LIKE PROTEIN X2 PRECURSOR. [SWISSPROT;Acc:Q8N436] 0.0302145 0.120464 0.250817672 CPXM2
1115 POTENTIAL CARBOXYPEPTIDASE X PRECURSOR (EC 3.4.17.-) (METALLOCARBOXYPEPTIDASE CPX-1). [SWISSPROT;Acc:Q96SM3] CPXM1
1116 DENDRITIC CELL PROTEIN. [RefSeq;Acc:NM_006360] 0.341608 1.36198 0.250817193 EIF3M
1117 0.116498 0.464479 0.250814353 PAF1
1118 PARAFIBROMIN. [RefSeq;Acc:NM_024529] 0.116454 0.464305 0.250813582 CDC73
1119 0.0385624 0.153758 0.250799308 GTDC1
1120 0.283453 1.1302 0.250798974 AGGF1
1121 "SPLICING FACTOR, ARGININE/SERINE-RICH 8 (SUPPRESSOR OF WHITE APRICOT PROTEIN HOMOLOG). [SWISSPROT;Acc:Q12872]" 0.155587 0.620608 0.250700926 SFRS8
1122 TRANSCRIPTION FACTOR IIB. [RefSeq;Acc:NM_013242] 0.0388966 0.155152 0.25069995899999997 C16orf80
1123 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 1 (26S PROTEASOME REGULATORY SUBUNIT S1) (26S PROTEASOME SUBUNIT P112). [SWISSPROT;Acc:Q99460] 0.263669 1.05182 0.250678823 PSMD1
1124 RNA POLYMERASE II SUBUNIT 5-MEDIATING PROTEIN (RPB5-MEDIATING PROTEIN). [SWISSPROT;Acc:O94763] 0.0388692 0.155056 0.250678465 C19orf2
1125 ADHESION REGULATING MOLECULE 1 PRECURSOR (110 KDA CELL MEMBRANE GLYCOPROTEIN) (GP110). [SWISSPROT;Acc:Q16186] 0.116452 0.464548 0.250678078 ADRM1
1126 UBIQUITIN CARBOXYL-TERMINAL HYDROLASE ISOZYME L5 (EC 3.4.19.12) (UCH- L5) (UBIQUITIN THIOLESTERASE L5) (UBIQUITIN C-TERMINAL HYDROLASE UCH37) (CGI-70) (AD-019). [SWISSPROT;Acc:Q9Y5K5] 0.0387137 0.154436 0.250677951 UCHL5
1127 "CYTOCHROME OXIDASE BIOGENESIS PROTEIN OXA1, MITOCHONDRIAL PRECURSOR (OXA1-LIKE PROTEIN) (OXA1HS). [SWISSPROT;Acc:Q15070]" 0.168913 0.673879 0.250657759 OXA1L
1128 "60S RIBOSOMAL PROTEIN L34, MITOCHONDRIAL PRECURSOR (L34MT). [SWISSPROT;Acc:Q9BQ48]" MRPL34
1129 TYROSINASE PRECURSOR (EC 1.14.18.1) (MONOPHENOL MONOOXYGENASE) (TUMOR REJECTION ANTIGEN AB) (SK29-AB) (LB24-AB). [SWISSPROT;Acc:P14679] 0.129983 0.518618 0.250633414 TYR
1130 PHOSPHOLIPID SCRAMBLASE 2 (PL SCRAMBLASE 2) (CA(2+)-DEPENDENT PHOSPHOLIPID SCRAMBLASE 2). [SWISSPROT;Acc:Q9NRY7] 0.252989 1.00989 0.250511442 PLSCR2
1131 PYRIDOXINE 5'-PHOSPHATE OXIDASE. [RefSeq;Acc:NM_018129] 0.0418316 0.166987 0.250508123 PNPO
1132 MITOTIC CHECKPOINT SERINE/THREONINE-PROTEIN KINASE BUB1 BETA (EC 2.7.1.-) (HBUBR1) (MAD3/BUB1-RELATED PROTEIN KINASE) (MITOTIC CHECKPOINT KINASE MAD3L). [SWISSPROT;Acc:O60566] 0.116856 0.466478 0.250506991 BUB1B
1133 "5,6-DIHYDROXYINDOLE-2-CARBOXYLIC ACID OXIDASE PRECURSOR (EC 1.14.18.-) (DHICA OXIDASE) (TYROSINASE-RELATED PROTEIN 1) (TRP-1) (TRP1) (TRP) (CATALASE B) (GLYCOPROTEIN-75) (MELANOMA ANTIGEN GP75). [SWISSPROT;Acc:P17643]" 0.101255 0.40427 0.250463799 TYRP1
1134 DOPACHROME TAUTOMERASE PRECURSOR (EC 5.3.3.12) (DT) (DCT) (DOPACHROME DELTA-ISOMERASE) (TYROSINASE-RELATED PROTEIN 2) (TRP-2) (TRP2). [SWISSPROT;Acc:P40126] 0.10083 0.402579 0.250460158 DCT
1135 PROTEASOME SUBUNIT BETA TYPE 7 PRECURSOR (EC 3.4.25.1) (PROTEASOME SUBUNIT Z) (MACROPAIN CHAIN Z) (MULTICATALYTIC ENDOPEPTIDASE COMPLEX CHAIN Z). [SWISSPROT;Acc:Q99436] 0.150695 0.601708 0.250445399 PSMB7
1136 PHOSPHOLIPID SCRAMBLASE 3 (PL SCRAMBLASE 3) (CA(2+)-DEPENDENT PHOSPHOLIPID SCRAMBLASE 3). [SWISSPROT;Acc:Q9NRY6] 0.199227 0.79556 0.250423601 no value
1137 PHOSPHOLIPID SCRAMBLASE 4 (PL SCRAMBLASE 4) (CA(2+)-DEPENDENT PHOSPHOLIPID SCRAMBLASE 4). [SWISSPROT;Acc:Q9NRQ2] 0.198834 0.793992 0.250423178 PLSCR4
1138 "TYROSINASE-RELATED GENE SEGMENT, EXON 5 (FRAGMENT). [SPTREMBL;Acc:Q15677]" 0.0959848 0.383295 0.250420172 TYRL
1139 MSTP028 PROTEIN. [RefSeq;Acc:NM_031954] 0.347203 1.38684 0.250355484 KCTD10
1140 TAR DNA-BINDING PROTEIN-43 (TDP-43). [SWISSPROT;Acc:Q13148] 0.653337 2.60974 0.250345628 TARDBP
1141 "SWI/SNF RELATED, MATRIX ASSOCIATED, ACTIN DEPENDENT REGULATOR OF CHROMATIN SUBFAMILY B MEMBER 1 (INTEGRASE INTERACTOR 1 PROTEIN) (HSNF5) (BAF47). [SWISSPROT;Acc:Q12824]" 0.108251 0.43247 0.250308692 SMARCB1
1142 "TUMOR NECROSIS FACTOR, ALPHA-INDUCED PROTEIN 1, ENDOTHELIAL (B12 PROTEIN). [SWISSPROT;Acc:Q13829]" 0.281828 1.12603 0.250284628 TNFAIP1
1143 POLYMERASE DELTA-INTERACTING PROTEIN 1; TNFAIP1-LIKE. [RefSeq;Acc:NM_178863] 0.278202 1.11156 0.250280687 KCTD13
1144 0.0559574 0.22361 0.250245517 TMEM132C
1145 0.0465063 0.185855 0.250228942 TMEM132D
1146 0.0452858 0.18098 0.250225439 TMEM132B
1147 0.0445191 0.177917 0.250223981 TMEM132E
1148 GBP PROTEIN ISOFORM A. [RefSeq;Acc:NM_017870] 0.0424223 0.169541 0.250218531 TMEM132A
1149 PUTATIVE GTP-BINDING PROTEIN PTD004 (PRO2455). [SWISSPROT;Acc:Q9NTK5] 0.154662 0.618161 0.250196955 OLA1
1150 PROTEASOME SUBUNIT BETA TYPE 1 (EC 3.4.25.1) (PROTEASOME COMPONENT C5) (MACROPAIN SUBUNIT C5) (MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT C5) (PROTEASOME GAMMA CHAIN). [SWISSPROT;Acc:P20618] 0.771753 3.08939 0.249807567 PSMB1
1151 SPROUTY HOMOLOG 4 (SPRY-4). [SWISSPROT;Acc:Q9C004] 0.0568291 0.227574 0.249717015 no value
1152 SPROUTY HOMOLOG 3 (SPRY-3). [SWISSPROT;Acc:O43610] 0.0570101 0.228299 0.249716819 SPRY3
1153 SPROUTY HOMOLOG 2 (SPRY-2). [SWISSPROT;Acc:O43597] 0.0724168 0.289996 0.249716548 SPRY2
1154 SPROUTY HOMOLOG 1 (SPRY-1) (FRAGMENT). [SWISSPROT;Acc:O43609] 0.0563765 0.225762 0.249716516 SPRY1
1155 0.126888 0.508241 0.249661086 PAPLN
1156 0.0411817 0.164951 0.249660202 CYB5D2
1157 PROTEASOME SUBUNIT BETA TYPE 3 (EC 3.4.25.1) (PROTEASOME THETA CHAIN) (PROTEASOME CHAIN 13) (PROTEASOME COMPONENT C10-II). [SWISSPROT;Acc:P49720] 0.781534 3.13091 0.249618801 PSMB3

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Hugo is the bloody hugo identifier as demanded by the BMC Bioinformatics idiots
- http://analysis.yellowcouch.org/