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 description Rank expected measured Hugo final
Results: HTML CSV LaTeX Showing element 451 to 500 of 3206 in total
description
Rank
expected
measured
Hugo
final
3205 2.59675 0.000571223 C1orf166 0.000219976
"1,4-ALPHA-GLUCAN BRANCHING ENZYME (EC 2.4.1.18) (GLYCOGEN BRANCHING ENZYME) (BRANCHER ENZYME). [SWISSPROT;Acc:Q04446]" 523 0.525483 0.142881 GBE1 0.271904134
"10 KDA HEAT SHOCK PROTEIN, MITOCHONDRIAL (HSP10) (10 KDA CHAPERONIN) (CPN10). [SWISSPROT;Acc:Q04984]" 951 0.251688 0.0645342 HSPE1 0.25640555
"2-OXOGLUTARATE DEHYDROGENASE E1 COMPONENT, MITOCHONDRIAL PRECURSOR (EC 1.2.4.2) (ALPHA-KETOGLUTARATE DEHYDROGENASE). [SWISSPROT;Acc:Q02218]" 2093 1.36954 0.313207 OGDH 0.228695036
"2-OXOISOVALERATE DEHYDROGENASE ALPHA SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 1.2.4.4) (BRANCHED-CHAIN ALPHA-KETO ACID DEHYDROGENASE E1 COMPONENT ALPHA CHAIN) (BCKDH E1-ALPHA). [SWISSPROT;Acc:P12694]" 2344 0.130409 0.0287655 TMEM91 0.220579101
"2-OXOISOVALERATE DEHYDROGENASE BETA SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 1.2.4.4) (BRANCHED-CHAIN ALPHA-KETO ACID DEHYDROGENASE E1 COMPONENT BETA CHAIN) (BCKDH E1-BETA). [SWISSPROT;Acc:P21953]" 432 0.63809 0.176985 BCKDHB 0.277366829
"28S RIBOSOMAL PROTEIN S12, MITOCHONDRIAL PRECURSOR (MPR-S12) (MT- RPS12). [SWISSPROT;Acc:O15235]" 1985 2.1041 0.485913 MRPS12 0.230936267
"28S RIBOSOMAL PROTEIN S16, MITOCHONDRIAL PRECURSOR (MRP-S16) (CGI- 132). [SWISSPROT;Acc:Q9Y3D3]" 2280 0.575175 0.12797 MRPS16 0.222488808
"28S RIBOSOMAL PROTEIN S17, MITOCHONDRIAL PRECURSOR (MRP-S17) (HSPC011). [SWISSPROT;Acc:Q9Y2R5]" 3039 0.22041 0.0241982 MRPS17 0.109787215
"28S RIBOSOMAL PROTEIN S18A, MITOCHONDRIAL PRECURSOR (MRP-S18-A) (MRPS18A) (MRP-S18-3). [SWISSPROT;Acc:Q9NVS2]" 2561 0.149576 0.0319993 MRPS18A 0.213933385
"28S RIBOSOMAL PROTEIN S26, MITOCHONDRIAL PRECURSOR (MRP-S26) (MRP- S13). [SWISSPROT;Acc:Q9BYN8]" 1324 0.160458 0.0393961 MRPS26 0.245522816
"28S RIBOSOMAL PROTEIN S9, MITOCHONDRIAL PRECURSOR (MRP-S9). [SWISSPROT;Acc:P82933]" 2072 2.79379 0.640883 MRPS9 0.229395552
"3-HYDROXYANTHRANILATE 3,4-DIOXYGENASE (EC 1.13.11.6) (3-HAO) (3-HYDROXYANTHRANILIC ACID DIOXYGENASE) (3-HYDROXYANTHRANILATE OXYGENASE). [SWISSPROT;Acc:P46952]" 1312 0.170469 0.0418885 HAAO 0.245725029
"3-KETOACYL-COA THIOLASE, PEROXISOMAL PRECURSOR (EC 2.3.1.16) (BETA- KETOTHIOLASE) (ACETYL-COA ACYLTRANSFERASE) (PEROXISOMAL 3-OXOACYL- COA THIOLASE). [SWISSPROT;Acc:P09110]" 2608 3.15431 0.668547 ACAA1 0.211947145
"4-AMINOBUTYRATE AMINOTRANSFERASE, MITOCHONDRIAL PRECURSOR (EC 2.6.1.19) (GAMMA-AMINO-N-BUTYRATE TRANSAMINASE) (GABA TRANSAMINASE) (GABA AMINOTRANSFERASE) (GABA-AT) (GABA-T). [SWISSPROT;Acc:P80404]" 2115 0.743642 0.16968 no value 0.22817431
"40S RIBOSOMAL PROTEIN S4, X ISOFORM (SINGLE COPY ABUNDANT MRNA PROTEIN) (SCR10). [SWISSPROT;Acc:P12750]" 2040 3.07604 0.707942 0.230147202
"40S RIBOSOMAL PROTEIN S4, Y ISOFORM 2. [SWISSPROT;Acc:Q8TD47]" 2041 2.90083 0.667613 RPS4Y2 0.23014551
"5'-AMP-ACTIVATED PROTEIN KINASE, BETA-1 SUBUNIT (AMPK BETA-1 CHAIN) (AMPKB). [SWISSPROT;Acc:Q9Y478]" 246 1.13895 0.355846 PRKAB1 0.312433382
"5'-AMP-ACTIVATED PROTEIN KINASE, BETA-2 SUBUNIT (AMPK BETA-2 CHAIN). [SWISSPROT;Acc:O43741]" 241 1.29474 0.404521 PRKAB2 0.312434157
"5'-AMP-ACTIVATED PROTEIN KINASE, CATALYTIC ALPHA-1 CHAIN (EC 2.7.1.-) (AMPK ALPHA-1 CHAIN). [SWISSPROT;Acc:Q13131]" 240 1.75288 0.547661 PRKAA1 0.312434964
"5'-AMP-ACTIVATED PROTEIN KINASE, CATALYTIC ALPHA-2 CHAIN (EC 2.7.1.-) (AMPK ALPHA-2 CHAIN). [SWISSPROT;Acc:P54646]" 244 2.01815 0.630538 PRKAA2 0.312433664
"5'-AMP-ACTIVATED PROTEIN KINASE, GAMMA-1 SUBUNIT (AMPK GAMMA-1 CHAIN) (AMPKG). [SWISSPROT;Acc:P54619]" 242 0.577642 0.180475 PRKAG1 0.312433999
"5'-AMP-ACTIVATED PROTEIN KINASE, GAMMA-2 SUBUNIT (AMPK GAMMA-2 CHAIN) (AMPK GAMMA2) (H91620P). [SWISSPROT;Acc:Q9UGJ0]" 245 0.70777 0.221131 PRKAG2 0.312433418
"5'-AMP-ACTIVATED PROTEIN KINASE, GAMMA-3 SUBUNIT (AMPK GAMMA-3 CHAIN) (AMPK GAMMA3). [SWISSPROT;Acc:Q9UGI9]" 243 0.567061 0.177169 PRKAG3 0.312433759
"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]" 1133 0.40427 0.101255 TYRP1 0.250463799
"5-AMINOLEVULINIC ACID SYNTHASE, ERYTHROID-SPECIFIC, MITOCHONDRIAL PRECURSOR (EC 2.3.1.37) (DELTA-AMINOLEVULINATE SYNTHASE) (DELTA-ALA SYNTHETASE) (ALAS-E). [SWISSPROT;Acc:P22557]" 2599 0.360019 0.0766446 ALAS2 0.212890431
"5-AMINOLEVULINIC ACID SYNTHASE, NONSPECIFIC, MITOCHONDRIAL PRECURSOR (EC 2.3.1.37) (DELTA-AMINOLEVULINATE SYNTHASE) (DELTA-ALA SYNTHETASE) (ALAS-H). [SWISSPROT;Acc:P13196]" 2596 0.297814 0.0634018 ALAS1 0.212890596
"5-FORMYLTETRAHYDROFOLATE CYCLO-LIGASE (EC 6.3.3.2) (5,10-METHENYL- TETRAHYDROFOLATE SYNTHETASE) (METHENYL-THF SYNTHETASE) (MTHFS). [SWISSPROT;Acc:P49914]" 1536 0.285651 0.0691225 MTHFS 0.241982349
"5-METHYLTETRAHYDROFOLATE--HOMOCYSTEINE METHYLTRANSFERASE (EC 2.1.1.13) (METHIONINE SYNTHASE, VITAMIN-B12 DEPENDENT) (MS). [SWISSPROT;Acc:Q99707]" 1107 0.147123 0.0369154 MTR 0.250915221
"54 KDA NUCLEAR RNA- AND DNA-BINDING PROTEIN (P54(NRB)) (P54NRB) (55 KDA NUCLEAR PROTEIN) (NMT55) (NON-POU DOMAIN-CONTAINING OCTAMER- BINDING PROTEIN) (DNA-BINDING P52/P100 COMPLEX, 52 KDA SUBUNIT). [SWISSPROT;Acc:Q15233]" 1676 0.847008 0.201833 NONO 0.238289367
"6-PHOSPHOFRUCTOKINASE, LIVER TYPE (EC 2.7.1.11) (PHOSPHOFRUCTOKINASE 1) (PHOSPHOHEXOKINASE) (PHOSPHOFRUCTO-1-KINASE ISOZYME B) (PFK-B). [SWISSPROT;Acc:P17858]" 2947 2.04623 0.310225 PFKL 0.151608079
"6-PHOSPHOFRUCTOKINASE, MUSCLE TYPE (EC 2.7.1.11) (PHOSPHOFRUCTOKINASE 1) (PHOSPHOHEXOKINASE) (PHOSPHOFRUCTO-1-KINASE ISOZYME A) (PFK-A) (PHOSPHOFRUCTOKINASE-M). [SWISSPROT;Acc:P08237]" 2948 2.07226 0.314149 PFKM 0.15159729
"6-PHOSPHOFRUCTOKINASE, TYPE C (EC 2.7.1.11) (PHOSPHOFRUCTOKINASE 1) (PHOSPHOHEXOKINASE) (PHOSPHOFRUCTO-1-KINASE ISOZYME C) (PFK-C) (6-PHOSPHOFRUCTOKINASE, PLATELET TYPE). [SWISSPROT;Acc:Q01813]" 2949 2.42367 0.367121 PFKP 0.151473179
"6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING (EC 1.1.1.44). [SWISSPROT;Acc:P52209]" 2339 0.303687 0.0670488 PGD 0.220782582
"60 KDA HEAT SHOCK PROTEIN, MITOCHONDRIAL PRECURSOR (HSP60) (60 KDA CHAPERONIN) (CPN60) (HEAT SHOCK PROTEIN 60) (HSP-60) (MITOCHONDRIAL MATRIX PROTEIN P1) (P60 LYMPHOCYTE PROTEIN) (HUCHA60). [SWISSPROT;Acc:P10809]" 2066 0.737338 0.16919 HSPD1 0.229460573
"60S RIBOSOMAL PROTEIN L11, MITOCHONDRIAL PRECURSOR (L11MT) (CGI-113). [SWISSPROT;Acc:Q9Y3B7]" 2198 2.51757 0.568484 MRPL11 0.225806631
"60S RIBOSOMAL PROTEIN L12, MITOCHONDRIAL PRECURSOR (L12MT) (5C5-2). [SWISSPROT;Acc:P52815]" 1958 4.73611 1.09511 MRPL12 0.231225626
"60S RIBOSOMAL PROTEIN L13, MITOCHONDRIAL (L13MT). [SWISSPROT;Acc:Q9BYD1]" 2019 2.56327 0.590899 MRPL13 0.230525462
"60S RIBOSOMAL PROTEIN L34, MITOCHONDRIAL PRECURSOR (L34MT). [SWISSPROT;Acc:Q9BQ48]" 1128 0.673879 0.168913 MRPL34 0.250657759
"60S RIBOSOMAL PROTEIN L36, MITOCHONDRIAL PRECURSOR (L36MT) (BRCA1- INTERACTING PROTEIN 1). [SWISSPROT;Acc:Q9P0J6]" 1980 5.32517 1.23017 MRPL36 0.231010465
"ACETYL-COA ACETYLTRANSFERASE, MITOCHONDRIAL PRECURSOR (EC 2.3.1.9) (ACETOACETYL-COA THIOLASE) (T2). [SWISSPROT;Acc:P24752]" 2604 3.13139 0.663698 ACAT1 0.211949965
"ACETYL-COENZYME A SYNTHETASE, CYTOPLASMIC (EC 6.2.1.1) (ACETATE--COA LIGASE) (ACYL-ACTIVATING ENZYME) (ACETYL-COA SYNTHETASE) (ACS) (ACECS). [SWISSPROT;Acc:Q9NR19]" 2609 2.37915 0.503361 ACSS2 0.21157178
"ACTIN, CYTOPLASMIC 2 (GAMMA-ACTIN). [SWISSPROT;Acc:P02571]" 1575 0.947072 0.228182 ACTG1 0.240934163
"ACTIVIN A RECEPTOR, TYPE IC; ACTIVIN RECEPTOR-LIKE KINASE 7. [RefSeq;Acc:NM_145259]" 1185 0.59173 0.147145 ACVR1C 0.248669157
"ACYL CARRIER PROTEIN, MITOCHONDRIAL PRECURSOR (ACP) (NADH-UBIQUINONE OXIDOREDUCTASE 9.6 KDA SUBUNIT) (CI-SDAP). [SWISSPROT;Acc:O14561]" 2595 4.36574 0.929425 NDUFAB1 0.212890598
"ACYL-COA DEHYDROGENASE, MEDIUM-CHAIN SPECIFIC, MITOCHONDRIAL PRECURSOR (EC 1.3.99.3) (MCAD). [SWISSPROT;Acc:P11310]" 2794 0.311942 0.0623579 ACADM 0.199902225
"ACYL-COA DEHYDROGENASE, SHORT/BRANCHED CHAIN SPECIFIC, MITOCHONDRIAL PRECURSOR (EC 1.3.99.-) (SBCAD) (2-METHYL BRANCHED CHAIN ACYL-COA DEHYDROGENASE) (2-MEBCAD) (2-METHYLBUTYRYL-COENZYME A DEHYDROGENASE) (2-METHYLBUTYRYL-COA DEHYDROGENASE). [SWISSP" 960 0.240043 0.0614814 no value 0.256126611
"ACYL-COA DEHYDROGENASE, VERY-LONG-CHAIN SPECIFIC, MITOCHONDRIAL PRECURSOR (EC 1.3.99.-) (VLCAD). [SWISSPROT;Acc:P49748]" 2814 0.399468 0.0780112 ACADVL 0.195287733
"ACYL-COENZYME A OXIDASE 1, PEROXISOMAL (EC 1.3.3.6) (PALMITOYL-COA OXIDASE) (AOX). [SWISSPROT;Acc:Q15067]" 2610 4.61324 0.974934 ACOX1 0.2113339
"ACYL-COENZYME A OXIDASE 2, PEROXISOMAL (EC 1.3.3.6) (BRANCHED-CHAIN ACYL-COA OXIDASE) (BRCACOX) (TRIHYDROXYCOPROSTANOYL-COA OXIDASE) (THCCOX) (THCA-COA OXIDASE). [SWISSPROT;Acc:Q99424]" 2679 3.18084 0.663483 ACOX2 0.208587354

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/