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 752 to 801 of 3206 in total
expected
measured
Rank
Hugo
description
final
0.225027 0.0585668 872 OPN4 OPSIN 4 (MELANOPSIN). [SWISSPROT;Acc:Q9UHM6] 0.260265657
0.225301 0.0695188 264 HNRNPR HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN R (HNRNP R). [SWISSPROT;Acc:O43390] 0.30855966
0.225696 0.0525547 1868 FMO4 DIMETHYLANILINE MONOOXYGENASE [N-OXIDE FORMING] 4 (EC 1.14.13.8) (HEPATIC FLAVIN-CONTAINING MONOOXYGENASE 4) (FMO 4) (DIMETHYLANILINE OXIDASE 4). [SWISSPROT;Acc:P31512] 0.232856143
0.225762 0.0563765 1154 SPRY1 SPROUTY HOMOLOG 1 (SPRY-1) (FRAGMENT). [SWISSPROT;Acc:O43609] 0.249716516
0.225994 0.0416917 2882 AP3B1 ADAPTER-RELATED PROTEIN COMPLEX 3 BETA 1 SUBUNIT (BETA-ADAPTIN 3A) (AP-3 COMPLEX BETA-3A SUBUNIT) (BETA-3A-ADAPTIN). [SWISSPROT;Acc:O00203] 0.184481446
0.22609 0.0498274 2350 SLIT1 0.220387456
0.226516 0.052087 2048 AIP AH RECEPTOR-INTERACTING PROTEIN (AIP) (IMMUNOPHILIN HOMOLOG ARA9) (HBV-X ASSOCIATED PROTEIN 2). [SWISSPROT;Acc:O00170] 0.229948436
0.227574 0.0568291 1151 no value SPROUTY HOMOLOG 4 (SPRY-4). [SWISSPROT;Acc:Q9C004] 0.249717015
0.228299 0.0570101 1152 SPRY3 SPROUTY HOMOLOG 3 (SPRY-3). [SWISSPROT;Acc:O43610] 0.249716819
0.228574 0.0586077 946 KCNAB2 VOLTAGE-GATED POTASSIUM CHANNEL BETA-2 SUBUNIT (K+ CHANNEL BETA-2 SUBUNIT) (KV-BETA-2) (HKVBETA2). [SWISSPROT;Acc:Q13303] 0.256405803
0.228892 0.0480531 2658 SLC13A4 "SOLUTE CARRIER FAMILY 13, MEMBER 4 (NA+/SULFATE COTRANSPORTER SUT-1). [SWISSPROT;Acc:Q9UKG4]" 0.209937875
0.229168 0.0509775 2281 HRSP12 14.5 KDA TRANSLATIONAL INHIBITOR PROTEIN (P14.5) (UK114 ANTIGEN HOMOLOG). [SWISSPROT;Acc:P52758] 0.222445978
0.229226 0.0533745 1869 FMO1 DIMETHYLANILINE MONOOXYGENASE [N-OXIDE FORMING] 1 (EC 1.14.13.8) (FETAL HEPATIC FLAVIN-CONTAINING MONOOXYGENASE 1) (FMO 1) (DIMETHYLANILINE OXIDASE 1). [SWISSPROT;Acc:Q01740] 0.232846623
0.229333 0.0616259 616 ING4 P29ING4; CANDIDATE TUMOR SUPPRESSOR P33 ING1 HOMOLOG. [RefSeq;Acc:NM_016162] 0.268717978
0.229436 0.0481673 2659 SLC13A1 "SOLUTE CARRIER FAMILY 13, MEMBER 1 (RENAL SODIUM/SULFATE COTRANSPORTER) (NA(+)/SULFATE COTRANSPORTER) (HNASI-1). [SWISSPROT;Acc:Q9BZW2]" 0.209937848
0.229439 0.0828978 112 C11orf56 0.361306491
0.2297 0.0320568 2975 HOXC5 HOMEOBOX PROTEIN HOX-C5 (HOX-3D) (CP11). [SWISSPROT;Acc:Q00444] 0.139559425
0.230542 0.0555356 1585 SERPINC1 ANTITHROMBIN-III PRECURSOR (ATIII) (PRO0309). [SWISSPROT;Acc:P01008] 0.240891464
0.231055 0.0507615 2383 RPL29 60S RIBOSOMAL PROTEIN L29 (CELL SURFACE HEPARIN BINDING PROTEIN HIP). [SWISSPROT;Acc:P47914] 0.219694445
0.231086 0.0547796 1724 RIOK2 0.237052872
0.231274 0.0637349 460 no value COLLAGEN ALPHA 5(IV) CHAIN PRECURSOR. [SWISSPROT;Acc:P29400] 0.27558177699999997
0.231281 0.0576807 1172 ETNK2 ETHANOLAMINE KINASE-LIKE PROTEIN EKI2 (FLJ10761). [SWISSPROT;Acc:Q9NVF9] 0.249396621
0.231578 0.0525739 2168 GYG2 GLYCOGENIN-2 (EC 2.4.1.186) (GN-2) (GN2). [SWISSPROT;Acc:O15488] 0.227024588
0.232231 0.0540721 1871 FMO2 DIMETHYLANILINE MONOOXYGENASE [N-OXIDE FORMING] 2 (EC 1.14.13.8) (PULMONARY FLAVIN-CONTAINING MONOOXYGENASE 2) (FMO 2) (DIMETHYLANILINE OXIDASE 2) (FMO 1B1). [SWISSPROT;Acc:Q99518] 0.232837563
0.23248 0.0555683 1648 OCRL INOSITOL POLYPHOSPHATE 5-PHOSPHATASE OCRL-1 (EC 3.1.3.36) (LOWE'S OCULOCEREBRORENAL SYNDROME PROTEIN). [SWISSPROT;Acc:Q01968] 0.239024002
0.23257 0.0564981 1484 NDC80 "HIGHLY EXPRESSED IN CANCER, RICH IN LEUCINE HEPTAD REPEATS. [RefSeq;Acc:NM_006101]" 0.242929441
0.233092 0.0598365 935 TRIOBP PROTEIN TARA (TRIO-ASSOCIATED REPEAT ON ACTIN) (HRIHFB2122). [SWISSPROT;Acc:Q9H2D6] 0.256707652
0.233549 0.0547985 1802 IPO11 RAN BINDING PROTEIN 11. [RefSeq;Acc:NM_016338] 0.234633846
0.233559 0.0546688 1832 VARS VALYL-TRNA SYNTHETASE 2 (EC 6.1.1.9) (VALINE--TRNA LIGASE 2) (VALRS 2) (G7A). [SWISSPROT;Acc:P26640] 0.234068479
0.23369 0.0597214 972 DNAJB1 DNAJ HOMOLOG SUBFAMILY B MEMBER 1 (HEAT SHOCK 40 KDA PROTEIN 1) (HEAT SHOCK PROTEIN 40) (HSP40) (DNAJ PROTEIN HOMOLOG 1) (HDJ-1). [SWISSPROT;Acc:P25685] 0.255558218
0.233925 0.0593831 1018 C16orf35 CGTHBA PROTEIN (-14 GENE PROTEIN). [SWISSPROT;Acc:Q12980] 0.253855296
0.234118 0.0470468 2781 FARSB PHENYLALANYL-TRNA SYNTHETASE BETA CHAIN (EC 6.1.1.20) (PHENYLALANINE-- TRNA LIGASE BETA CHAIN) (PHERS) (HSPC173). [SWISSPROT;Acc:Q9NSD9] 0.200953365
0.234405 0.0569548 1474 RAC3 RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 3 (P21-RAC3). [SWISSPROT;Acc:O14658] 0.242976046
0.234495 0.0516003 2374 TSEN2 0.220048615
0.234744 0.056548 1581 SERPINB7 MEGSIN (TP55) (SERPIN B7). [SWISSPROT;Acc:O75635] 0.240892206
0.235377 0.0517945 2373 TSEN34 LENG5 PROTEIN. [RefSeq;Acc:NM_024075] 0.220049113
0.235627 0.0506049 2519 G3BP1 RAS-GTPASE-ACTIVATING PROTEIN BINDING PROTEIN 1 (GAP SH3-DOMAIN BINDING PROTEIN 1) (G3BP-1). [SWISSPROT;Acc:Q13283] 0.214766983
0.235798 0.0575359 1408 WBP11 WW DOMAIN BINDING PROTEIN 11; NPW38-BINDING PROTEIN NPWBP; SH3 DOMAIN-BINDING PROTEIN SNP70. [RefSeq;Acc:NM_016312] 0.244005038
1409 ELAC2 ELAC HOMOLOG 2; PUTATIVE PROSTATE CANCER SUSCEPTIBILITY PROTEIN; ELAC (E. COLI) HOMOLOG 2. [RefSeq;Acc:NM_018127]
0.235868 0.0524219 2304 SPTLC2 SERINE PALMITOYLTRANSFERASE 2 (EC 2.3.1.50) (LONG CHAIN BASE BIOSYNTHESIS PROTEIN 2) (LCB 2) (SERINE-PALMITOYL-COA TRANSFERASE 2) (SPT 2). [SWISSPROT;Acc:O15270] 0.222251005
0.237616 0.0562476 1750 ATP6V1H VACUOLAR ATP SYNTHASE SUBUNIT H (EC 3.6.3.14) (V-ATPASE H SUBUNIT) (VACUOLAR PROTON PUMP H SUBUNIT) (V-ATPASE 50/57 KDA SUBUNITS) (VACUOLAR PROTON PUMP SUBUNIT SFD) (CGI-11). [SWISSPROT;Acc:Q9UI12] 0.236716383
0.238547 0.056545 1729 NAPG "GAMMA-SOLUBLE NSF ATTACHMENT PROTEIN (SNAP-GAMMA) (N-ETHYLMALEIMIDE- SENSITIVE FACTOR ATTACHMENT PROTEIN, GAMMA). [SWISSPROT;Acc:Q99747]" 0.237039242
0.238723 0.0511995 2553 no value 0.214472422
0.23892 0.0666911 381 CAPSL 0.279135694
0.239274 0.0410645 2916 FKBP8 38 KDA FK-506 BINDING PROTEIN HOMOLOG (FKBPR38) (FK506-BINDING PROTEIN 8). [SWISSPROT;Acc:Q14318] 0.171621238
0.239562 0.0544712 2148 no value APOPTOSIS INHIBITOR FKSG2. [SWISSPROT;Acc:Q9HAU6] 0.227378299
0.239646 0.0503166 2649 PARD6G PARTITIONING DEFECTIVE-6 HOMOLOG GAMMA (PAR-6 GAMMA) (PAR6D). [SWISSPROT;Acc:Q9BYG4] 0.209962194
0.239746 0.0534133 2266 PAPD5 TOPOISOMERASE-RELATED FUNCTION PROTEIN 4-2. [RefSeq;Acc:NM_022447] 0.222791204
0.240043 0.0614814 960 no value "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" 0.256126611
0.240498 0.0536444 2260 RNF44 RING FINGER PROTEIN 44. [RefSeq;Acc:NM_014901] 0.223055493

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/