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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Rank Gene description expected Hugo measured final
Results: HTML CSV LaTeX Showing element 1101 to 1150 of 3206 in total
Rank
description
expected
Hugo
measured
final
1101 U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM6 (SM PROTEIN F). [SWISSPROT;Acc:Q9Y4Y8] 0.623964 LSM6 0.156724 0.251174747
1102 "PROTEIN KINASE, INTERFERON-INDUCIBLE DOUBLE STRANDED RNA DEPENDENT ACTIVATOR; PROTEIN ACTIVATOR OF THE INTERFERON-INDUCED PROTEIN KINASE. [RefSeq;Acc:NM_003690]" 0.753541 PRKRAP1 0.189161 0.251029473
1103 0.530672 THG1L 0.133213 0.251027
1104 "U2 SMALL NUCLEAR RIBONUCLEOPROTEIN B"". [SWISSPROT;Acc:P08579]" 0.135722 SNRPB2 0.0340698 0.251026363
1105 CYTIDINE DEAMINASE (EC 3.5.4.5) (CYTIDINE AMINOHYDROLASE). [SWISSPROT;Acc:P32320] 1.62535 CDA 0.407912 0.250968714
1106 0.440965 C2orf25 0.110645 0.250915606
1107 "5-METHYLTETRAHYDROFOLATE--HOMOCYSTEINE METHYLTRANSFERASE (EC 2.1.1.13) (METHIONINE SYNTHASE, VITAMIN-B12 DEPENDENT) (MS). [SWISSPROT;Acc:Q99707]" 0.147123 MTR 0.0369154 0.250915221
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; 0.303457 DDB1 0.0761267 0.250864867
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]" 0.45456 PCCB 0.114033 0.250864572
1110 0.151938 WDR22 0.0381158 0.250864168
1111 CPZ GENE PRODUCT. [RefSeq;Acc:NM_003652] 0.12113 CPZ 0.0303816 0.250818129
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] 0.121992 CPN1 0.0305978 0.250818086
1113 CARBOXYPEPTIDASE H PRECURSOR (EC 3.4.17.10) (CPH) (CARBOXYPEPTIDASE E) (CPE) (ENKEPHALIN CONVERTASE) (PROHORMONE PROCESSING CARBOXYPEPTIDASE). [SWISSPROT;Acc:P16870] 0.156752 CPE 0.0393162 0.250817852
1114 POTENTIAL CARBOXYPEPTIDASE-LIKE PROTEIN X2 PRECURSOR. [SWISSPROT;Acc:Q8N436] 0.120464 CPXM2 0.0302145 0.250817672
1115 POTENTIAL CARBOXYPEPTIDASE X PRECURSOR (EC 3.4.17.-) (METALLOCARBOXYPEPTIDASE CPX-1). [SWISSPROT;Acc:Q96SM3] CPXM1
1116 DENDRITIC CELL PROTEIN. [RefSeq;Acc:NM_006360] 1.36198 EIF3M 0.341608 0.250817193
1117 0.464479 PAF1 0.116498 0.250814353
1118 PARAFIBROMIN. [RefSeq;Acc:NM_024529] 0.464305 CDC73 0.116454 0.250813582
1119 0.153758 GTDC1 0.0385624 0.250799308
1120 1.1302 AGGF1 0.283453 0.250798974
1121 "SPLICING FACTOR, ARGININE/SERINE-RICH 8 (SUPPRESSOR OF WHITE APRICOT PROTEIN HOMOLOG). [SWISSPROT;Acc:Q12872]" 0.620608 SFRS8 0.155587 0.250700926
1122 TRANSCRIPTION FACTOR IIB. [RefSeq;Acc:NM_013242] 0.155152 C16orf80 0.0388966 0.25069995899999997
1123 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 1 (26S PROTEASOME REGULATORY SUBUNIT S1) (26S PROTEASOME SUBUNIT P112). [SWISSPROT;Acc:Q99460] 1.05182 PSMD1 0.263669 0.250678823
1124 RNA POLYMERASE II SUBUNIT 5-MEDIATING PROTEIN (RPB5-MEDIATING PROTEIN). [SWISSPROT;Acc:O94763] 0.155056 C19orf2 0.0388692 0.250678465
1125 ADHESION REGULATING MOLECULE 1 PRECURSOR (110 KDA CELL MEMBRANE GLYCOPROTEIN) (GP110). [SWISSPROT;Acc:Q16186] 0.464548 ADRM1 0.116452 0.250678078
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] 0.154436 UCHL5 0.0387137 0.250677951
1127 "CYTOCHROME OXIDASE BIOGENESIS PROTEIN OXA1, MITOCHONDRIAL PRECURSOR (OXA1-LIKE PROTEIN) (OXA1HS). [SWISSPROT;Acc:Q15070]" 0.673879 OXA1L 0.168913 0.250657759
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] 0.518618 TYR 0.129983 0.250633414
1130 PHOSPHOLIPID SCRAMBLASE 2 (PL SCRAMBLASE 2) (CA(2+)-DEPENDENT PHOSPHOLIPID SCRAMBLASE 2). [SWISSPROT;Acc:Q9NRY7] 1.00989 PLSCR2 0.252989 0.250511442
1131 PYRIDOXINE 5'-PHOSPHATE OXIDASE. [RefSeq;Acc:NM_018129] 0.166987 PNPO 0.0418316 0.250508123
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] 0.466478 BUB1B 0.116856 0.250506991
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]" 0.40427 TYRP1 0.101255 0.250463799
1134 DOPACHROME TAUTOMERASE PRECURSOR (EC 5.3.3.12) (DT) (DCT) (DOPACHROME DELTA-ISOMERASE) (TYROSINASE-RELATED PROTEIN 2) (TRP-2) (TRP2). [SWISSPROT;Acc:P40126] 0.402579 DCT 0.10083 0.250460158
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] 0.601708 PSMB7 0.150695 0.250445399
1136 PHOSPHOLIPID SCRAMBLASE 3 (PL SCRAMBLASE 3) (CA(2+)-DEPENDENT PHOSPHOLIPID SCRAMBLASE 3). [SWISSPROT;Acc:Q9NRY6] 0.79556 no value 0.199227 0.250423601
1137 PHOSPHOLIPID SCRAMBLASE 4 (PL SCRAMBLASE 4) (CA(2+)-DEPENDENT PHOSPHOLIPID SCRAMBLASE 4). [SWISSPROT;Acc:Q9NRQ2] 0.793992 PLSCR4 0.198834 0.250423178
1138 "TYROSINASE-RELATED GENE SEGMENT, EXON 5 (FRAGMENT). [SPTREMBL;Acc:Q15677]" 0.383295 TYRL 0.0959848 0.250420172
1139 MSTP028 PROTEIN. [RefSeq;Acc:NM_031954] 1.38684 KCTD10 0.347203 0.250355484
1140 TAR DNA-BINDING PROTEIN-43 (TDP-43). [SWISSPROT;Acc:Q13148] 2.60974 TARDBP 0.653337 0.250345628
1141 "SWI/SNF RELATED, MATRIX ASSOCIATED, ACTIN DEPENDENT REGULATOR OF CHROMATIN SUBFAMILY B MEMBER 1 (INTEGRASE INTERACTOR 1 PROTEIN) (HSNF5) (BAF47). [SWISSPROT;Acc:Q12824]" 0.43247 SMARCB1 0.108251 0.250308692
1142 "TUMOR NECROSIS FACTOR, ALPHA-INDUCED PROTEIN 1, ENDOTHELIAL (B12 PROTEIN). [SWISSPROT;Acc:Q13829]" 1.12603 TNFAIP1 0.281828 0.250284628
1143 POLYMERASE DELTA-INTERACTING PROTEIN 1; TNFAIP1-LIKE. [RefSeq;Acc:NM_178863] 1.11156 KCTD13 0.278202 0.250280687
1144 0.22361 TMEM132C 0.0559574 0.250245517
1145 0.185855 TMEM132D 0.0465063 0.250228942
1146 0.18098 TMEM132B 0.0452858 0.250225439
1147 0.177917 TMEM132E 0.0445191 0.250223981
1148 GBP PROTEIN ISOFORM A. [RefSeq;Acc:NM_017870] 0.169541 TMEM132A 0.0424223 0.250218531
1149 PUTATIVE GTP-BINDING PROTEIN PTD004 (PRO2455). [SWISSPROT;Acc:Q9NTK5] 0.618161 OLA1 0.154662 0.250196955
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] 3.08939 PSMB1 0.771753 0.249807567

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/