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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expected Gene measured Rank Hugo description final
Results: HTML CSV LaTeX Showing element 1302 to 1351 of 3206 in total
expected
measured
Rank
Hugo
description
final
0.40396 0.104198 917 VPS33B VACUOLAR PROTEIN SORTING 33B (HVPS33B). [SWISSPROT;Acc:Q9H267] 0.25794138
0.40427 0.101255 1133 TYRP1 "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]" 0.250463799
0.404396 0.0999509 1260 no value ISCHEMIA/REPERFUSION INDUCIBLE PROTEIN. [RefSeq;Acc:NM_024640] 0.247160951
0.404444 0.192159 22 NAV2 NEURON NAVIGATOR 2 ISOFORM L; RETINOIC ACID INDUCIBLE IN NEUROBLASTOMA; PORE MEMBRANE AND/OR FILAMENT INTERACTING LIKE PROTEIN 2; HELICASE HELAD1. [RefSeq;Acc:NM_145117] 0.475118929
0.40494 0.0936292 1966 MED22 SURFEIT LOCUS PROTEIN 5. [SWISSPROT;Acc:Q15528] 0.231217464
0.406091 0.0937028 2003 TXNDC10 0.230743356
0.406247 0.0987602 1458 MEGF10 MEGF10 PROTEIN. [RefSeq;Acc:NM_032446] 0.243103826
0.406955 0.100674 1251 no value "SIMILAR TO RIBOSOMAL PROTEIN, LARGE, P0. [SPTREMBL;Acc:Q96FQ9]" 0.247383617
0.407134 0.0967911 1706 ACTR1A ALPHA-CENTRACTIN (CENTRACTIN) (CENTROSOME-ASSOCIATED ACTIN HOMOLOG) (ACTIN-RPV) (ARP1). [SWISSPROT;Acc:P42024] 0.237737698
0.407281 0.0882127 2475 EPB41L1 BAND 4.1-LIKE PROTEIN 1 (NEURONAL PROTEIN 4.1) (4.1N). [SWISSPROT;Acc:Q9H4G0] 0.216589284
0.407712 0.0833819 2745 PPCS 0.204511763
0.40795 0.0991443 1463 RIOK1 RIO KINASE 1 ISOFORM 1; AD034 PROTEIN. [RefSeq;Acc:NM_031480] 0.243030518
0.408247 0.0398596 3086 PCSK5 PROPROTEIN CONVERTASE SUBTILISIN/KEXIN TYPE 5 PRECURSOR (EC 3.4.21.-) (PROPROTEIN CONVERTASE PC5) (SUBTILISIN/KEXIN-LIKE PROTEASE PC5) (CONVERTASE PC5) (PC6) (HPC6). [SWISSPROT;Acc:Q92824] 0.09763599
0.408587 0.0992034 1489 ERBB3 RECEPTOR PROTEIN-TYROSINE KINASE ERBB-3 PRECURSOR (EC 2.7.1.112) (C-ERBB3) (TYROSINE KINASE-TYPE CELL SURFACE RECEPTOR HER3). [SWISSPROT;Acc:P21860] 0.242796271
1490 ERBB4 RECEPTOR PROTEIN-TYROSINE KINASE ERBB-4 PRECURSOR (EC 2.7.1.112) (P180ERBB4) (TYROSINE KINASE-TYPE CELL SURFACE RECEPTOR HER4). [SWISSPROT;Acc:Q15303]
0.409455 0.120354 315 TXNL4A SPLICEOSOMAL U5 SNRNP-SPECIFIC 15 KDA PROTEIN (DIM1 PROTEIN HOMOLOG) (THIOREDOXIN-LIKE U5 SNRNP PROTEIN U5-15KD). [SWISSPROT;Acc:O14834] 0.293937063
0.410377 0.106987 846 SLC46A2 THYMIC STROMAL CO-TRANSPORTER. [RefSeq;Acc:NM_033051] 0.260704182
0.410433 0.133951 192 NEDD9 ENHANCER OF FILAMENTATION 1 (HEF1) (CRK-ASSOCIATED SUBSTRATE-RELATED PROTEIN) (CAS-L) (CASL) (PP105) (NEURAL PRECURSOR CELL EXPRESSED DEVELOPMENTALLY DOWN-REGULATED 9). [SWISSPROT;Acc:Q14511] 0.326365083
0.410816 0.0997445 1491 HACL1 2-HYDROXYPHYTANOYL-COA LYASE (EC 4.1.-.-) (2-HPCL) (HSPC279). [SWISSPROT;Acc:Q9UJ83] 0.242796045
0.411298 0.0973611 1748 GDAP1 GANGLIOSIDE-INDUCED DIFFERENTIATION-ASSOCIATED PROTEIN 1. [RefSeq;Acc:NM_018972] 0.236716687
0.411431 0.086385 2648 PRKCI "PROTEIN KINASE C, IOTA TYPE (EC 2.7.1.37) (NPKC-IOTA) (ATYPICAL PROTEIN KINASE C-LAMDA/IOTA) (APKC-LAMBDA/IOTA). [SWISSPROT;Acc:P41743]" 0.209962302
0.411799 0.10892 744 INTS10 0.264497971
0.413762 0.110995 634 CYP4F12 CYTOCHROME P450 4F12 (EC 1.14.14.1) (CYPIVF12). [SWISSPROT;Acc:Q9HCS2] 0.268258081
0.41404 0.116954 350 MAPKBP1 0.282470293
0.414669 0.145659 154 C11orf60 0.351265708
0.415411 0.0800859 2839 AQP1 AQUAPORIN-CHIP (WATER CHANNEL PROTEIN FOR RED BLOOD CELLS AND KIDNEY PROXIMAL TUBULE) (AQUAPORIN 1) (AQP-1) (URINE WATER CHANNEL). [SWISSPROT;Acc:P29972] 0.192787143
0.415438 0.173246 47 GADD45B GROWTH ARREST AND DNA-DAMAGE-INDUCIBLE PROTEIN GADD45 BETA (NEGATIVE GROWTH-REGULATORY PROTEIN MYD118) (MYELOID DIFFERENTIATION PRIMARY RESPONSE PROTEIN MYD118). [SWISSPROT;Acc:O75293] 0.417020109
0.415448 0.0438075 3056 GNAZ "GUANINE NUCLEOTIDE-BINDING PROTEIN G(Z), ALPHA SUBUNIT (G(X) ALPHA CHAIN) (GZ-ALPHA). [SWISSPROT;Acc:P19086]" 0.10544641
0.415778 0.0900531 2473 EPB41 PROTEIN 4.1 (BAND 4.1) (P4.1) (EPB4.1) (4.1R). [SWISSPROT;Acc:P11171] 0.216589382
0.416 0.100408 1553 ATIC BIFUNCTIONAL PURINE BIOSYNTHESIS PROTEIN PURH [INCLUDES: PHOSPHORIBOSYLAMINOIMIDAZOLECARBOXAMIDE FORMYLTRANSFERASE (EC 2.1.2.3) (AICAR TRANSFORMYLASE); IMP CYCLOHYDROLASE (EC 3.5.4.10) (INOSINICASE) (IMP SYNTHETASE) (ATIC)]. [SWISSPROT;Acc:P31939] 0.241365385
1554 PFAS PHOSPHORIBOSYLFORMYLGLYCINAMIDINE SYNTHASE (EC 6.3.5.3) (FGAM SYNTHASE) (FGAMS) (FORMYLGLYCINAMIDE RIBOTIDE AMIDOTRANSFERASE) (FGARAT) (FORMYLGLYCINAMIDE RIBOTIDE SYNTHETASE). [SWISSPROT;Acc:O15067]
0.41666 0.0929892 2250 ZCCHC7 0.223177651
0.416755 0.0914148 2395 MARS2 0.219349018
0.417352 0.174044 48 GADD45A GROWTH ARREST AND DNA-DAMAGE-INDUCIBLE PROTEIN GADD45 ALPHA (DNA- DAMAGE INDUCIBLE TRANSCRIPT 1) (DDIT1). [SWISSPROT;Acc:P24522] 0.417019686
0.417367 0.0655808 2937 TSG101 TUMOR SUSCEPTIBILITY GENE 101 PROTEIN. [SWISSPROT;Acc:Q99816] 0.157129816
0.417534 0.101184 1522 RBM22 0.242337151
0.417668 0.117602 355 EXOC6B EXOCYST COMPLEX COMPONENT SEC15B. [SWISSPROT;Acc:Q9Y2D4] 0.281568135
0.418978 0.0936132 2248 CDC23 CELL DIVISION CYCLE PROTEIN 23; ANAPHASE-PROMOTING COMPLEX SUBUNIT 8. [RefSeq;Acc:NM_004661] 0.223432257
0.419099 0.102811 1333 MYBL2 MYB-RELATED PROTEIN B (B-MYB). [SWISSPROT;Acc:P10244] 0.245314353
0.419545 0.109193 875 BARX2 HOMEOBOX PROTEIN BARH-LIKE 2. [SWISSPROT;Acc:Q9UMQ3] 0.260265287
0.419564 0.0877868 2668 NFE2L3 NUCLEAR FACTOR (ERYTHROID-DERIVED 2)-LIKE 3; NF-E2-RELATED FACTOR 3. [RefSeq;Acc:NM_004289] 0.209233395
0.419969 0.0974156 1923 SLC35B1 "SOLUTE CARRIER FAMILY 35, MEMBER B1; UDP-GALACTOSE TRANSPORTER RELATED. [RefSeq;Acc:NM_005827]" 0.231959026
0.419992 0.0986496 1792 DHDH DIMERIC DIHYDRODIOL DEHYDROGENASE; 3-DEOXYGLUCOSONE REDUCTASE. [RefSeq;Acc:NM_014475] 0.234884474
0.421142 0.044407 3057 GNAT1 "GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-1 SUBUNIT (TRANSDUCIN ALPHA-1 CHAIN). [SWISSPROT;Acc:P11488]" 0.105444244
0.421972 0.0966625 2081 C6orf153 0.229073256
0.422452 0.135419 210 GSTO2 BA127L20.1 (NOVEL GLUTATHIONE-S-TRANSFERASE). [SPTREMBL;Acc:Q9H4Y5] 0.320554761
0.422875 0.0915902 2474 EPB41L2 BAND 4.1-LIKE PROTEIN 2 (GENERALLY EXPRESSED PROTEIN 4.1) (4.1G). [SWISSPROT;Acc:O43491] 0.216589299
0.422881 0.101079 1641 RAD23A UV EXCISION REPAIR PROTEIN RAD23 HOMOLOG A (HHR23A). [SWISSPROT;Acc:P54725] 0.23902469
0.423045 0.113218 654 no value CYSTEINE-RICH PROTEIN 1 (CYSTEINE-RICH INTESTINAL PROTEIN) (CRIP) (CYSTEINE-RICH HEART PROTEIN) (HCRHP). [SWISSPROT;Acc:P50238] 0.267626375
0.42318 0.113522 623 CYP4F11 CYTOCHROME P450 4F11 (EC 1.14.14.1) (CYPIVF11). [SWISSPROT;Acc:Q9HBI6] 0.26825937

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/