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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measured Hugo Gene description expected Rank final
Results: HTML CSV LaTeX Showing element 802 to 851 of 3206 in total
measured
Hugo
description
expected
Rank
final
0.0527752 SLC2A6 "SOLUTE CARRIER FAMILY 2, FACILITATED GLUCOSE TRANSPORTER, MEMBER 6 (GLUCOSE TRANSPORTER TYPE 6) (GLUCOSE TRANSPORTER TYPE 9). [SWISSPROT;Acc:Q9UGQ3]" 0.213145 1244 0.247602336
0.0530069 TOMM20 MITOCHONDRIAL IMPORT RECEPTOR SUBUNIT TOM20 HOMOLOG (MITOCHONDRIAL 20 KDA OUTER MEMBRANE PROTEIN) (OUTER MITOCHONDRIAL MEMBRANE RECEPTOR TOM20). [SWISSPROT;Acc:Q15388] 0.189914 382 0.279110018
0.0530266 PRPF4 U4/U6 SMALL NUCLEAR RIBONUCLEOPROTEIN PRP4 (U4/U6 SNRNP 60 KDA PROTEIN) (WD SPLICING FACTOR PRP4) (HPRP4). [SWISSPROT;Acc:O43172] 0.203611 859 0.26043092
0.0532303 RAC2 RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 2 (P21-RAC2) (SMALL G PROTEIN) (GX). [SWISSPROT;Acc:P15153] 0.219077 1479 0.242975301
0.0532406 TPD52L3 PROTEIN KINASE NYD-SP25. [RefSeq;Acc:NM_033516] 0.290193 2885 0.183466176
0.0533745 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] 0.229226 1869 0.232846623
0.0533885 no value 0.517345 3069 0.103197093
0.0534133 PAPD5 TOPOISOMERASE-RELATED FUNCTION PROTEIN 4-2. [RefSeq;Acc:NM_022447] 0.239746 2266 0.222791204
0.0536444 RNF44 RING FINGER PROTEIN 44. [RefSeq;Acc:NM_014901] 0.240498 2260 0.223055493
0.0536744 WDR32 0.268503 2792 0.199902422
0.0539161 HNRNPA2B1 HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEINS A2/B1 (HNRNP A2 / HNRNP B1). [SWISSPROT;Acc:P22626] 0.196556 484 0.274304015
0.0540721 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] 0.232231 1871 0.232837563
0.0542439 TRMT6 0.177846 273 0.305004892
0.0544673 CCDC95 0.15506 153 0.351265962
PBK T-LAK CELL-ORIGINATED PROTEIN KINASE; SPERMATOGENESIS-RELATED PROTEIN KINASE; PDZ-BINDING KINASE; PBK; MAPKK-LIKE PROTEIN KINASE; SERINE/THREONINE PROTEIN KINASE. [RefSeq;Acc:NM_018492] 152
0.0544712 no value APOPTOSIS INHIBITOR FKSG2. [SWISSPROT;Acc:Q9HAU6] 0.239562 2148 0.227378299
0.0545554 EXOC2 EXOCYST COMPLEX COMPONENT SEC5. [SWISSPROT;Acc:Q96KP1] 0.261799 2682 0.208386587
0.0546138 CENTG3 CENTAURIN GAMMA 3. [SWISSPROT;Acc:Q96P47] 0.196275 405 0.278251433
MOSC1 406
MOSC2 407
0.0546688 VARS VALYL-TRNA SYNTHETASE 2 (EC 6.1.1.9) (VALINE--TRNA LIGASE 2) (VALRS 2) (G7A). [SWISSPROT;Acc:P26640] 0.233559 1832 0.234068479
0.0547796 RIOK2 0.231086 1724 0.237052872
0.0547985 IPO11 RAN BINDING PROTEIN 11. [RefSeq;Acc:NM_016338] 0.233549 1802 0.234633846
0.0548378 NETO2 NEUROPILIN- AND TOLLOID-LIKE PROTEIN 2 PRECURSOR. [RefSeq;Acc:NM_018092] 0.24054 2131 0.227977883
RUNX2 "RUNT-RELATED TRANSCRIPTION FACTOR 2 (CORE-BINDING FACTOR, ALPHA 1 SUBUNIT) (CBF-ALPHA 1) (ACUTE MYELOID LEUKEMIA 3 PROTEIN) (ONCOGENE AML-3) (POLYOMAVIRUS ENHANCER BINDING PROTEIN 2 ALPHA A SUBUNIT) (PEBP2-ALPHA A) (PEA2-ALPHA A) (SL3-3 ENHANCER FACTOR 1 " 2130
0.054901 C10orf58 0.181906 289 0.301809726
0.0549835 BCMO1 "BETA-CAROTENE 15, 15'-DIOXYGENASE; BETA-CAROTENE 15,15'-MONOOXYGENASE. [RefSeq;Acc:NM_017429]" 0.182179 283 0.301810307
INMT INDOLETHYLAMINE N-METHYLTRANSFERASE (EC 2.1.1.49) (AROMATIC ALKYLAMINE N-METHYLTRANSFERASE) (INDOLAMINE N-METHYLTRANSFERASE) (ARYLAMINE N- METHYLTRANSFERASE) (AMINE N-METHYLTRANSFERASE). [SWISSPROT;Acc:O95050] 285
WDR4 WD-REPEAT PROTEIN 4. [SWISSPROT;Acc:P57081] 284
0.0550688 RASAL2 RAS GTPASE-ACTIVATING PROTEIN NGAP (RAS PROTEIN ACTIVATOR LIKE 1). [SWISSPROT;Acc:Q9UJF2] 0.533628 3073 0.103196984
0.0552487 ZMYND11 ADENOVIRUS 5 E1A-BINDING PROTEIN (BS69 PROTEIN). [SWISSPROT;Acc:Q15326] 0.210853 789 0.262024728
0.0555356 SERPINC1 ANTITHROMBIN-III PRECURSOR (ATIII) (PRO0309). [SWISSPROT;Acc:P01008] 0.230542 1585 0.240891464
0.0555455 no value APOBEC-1 COMPLEMENTATION FACTOR ISOFORM 1; APOBEC-1 STIMULATING PROTEIN; APO-B RNA EDITING PROTEIN. [RefSeq;Acc:NM_014576] 0.180015 261 0.308560398
0.0555486 CYP2D6 CYTOCHROME P450 2D6 (EC 1.14.14.1) (CYPIID6) (P450-DB1) (DEBRISOQUINE 4-HYDROXYLASE). [SWISSPROT;Acc:P10635] 0.258646 2520 0.214766901
0.0555683 OCRL INOSITOL POLYPHOSPHATE 5-PHOSPHATASE OCRL-1 (EC 3.1.3.36) (LOWE'S OCULOCEREBRORENAL SYNDROME PROTEIN). [SWISSPROT;Acc:Q01968] 0.23248 1648 0.239024002
0.0555879 GCLM GLUTAMATE--CYSTEINE LIGASE REGULATORY SUBUNIT (EC 6.3.2.2) (GAMMA- GLUTAMYLCYSTEINE SYNTHETASE) (GAMMA-ECS) (GCS LIGHT CHAIN) (GLUTAMATE--CYSTEINE LIGASE MODIFIER SUBUNIT). [SWISSPROT;Acc:P48507] 0.271808 2746 0.204511641
0.0556491 MPDU1 MANNOSE-P-DOLICHOL UTILIZATION DEFECT 1 PROTEIN (SUPPRESSOR OF LEC15 AND LEC35 GLYCOSYLATION MUTATION HOMOLOG) (SL15). [SWISSPROT;Acc:O75352] 0.249916 2276 0.222671218
0.0556846 no value 0.180466 262 0.308560061
0.0557223 MED30 TRAP/MEDIATOR COMPLEX COMPONENT TRAP25. [RefSeq;Acc:NM_080651] 0.278747 2791 0.199902779
0.0558136 COQ7 UBIQUINONE BIOSYNTHESIS PROTEIN COQ7 HOMOLOG (COENZYME Q BIOSYNTHESIS PROTEIN 7 HOMOLOG) (TIMING PROTEIN CLK-1 HOMOLOG). [SWISSPROT;Acc:Q99807] 0.558604 3082 0.09991622
0.0558685 FER PROTO-ONCOGENE TYROSINE-PROTEIN KINASE FER (EC 2.7.1.112) (P94-FER) (C-FER). [SWISSPROT;Acc:P16591] 0.254301 2388 0.219694378
0.0558748 AP1S3 ADAPTER-RELATED PROTEIN COMPLEX 1 SIGMA 1C SUBUNIT (SIGMA-ADAPTIN 1C) (ADAPTOR PROTEIN COMPLEX AP-1 SIGMA-1C SUBUNIT) (GOLGI ADAPTOR HA1/AP1 ADAPTIN SIGMA-1C SUBUNIT) (CLATHRIN ASSEMBLY PROTEIN COMPLEX 1 SIGMA- 1C SMALL CHAIN) (SIGMA 1C SUBUNIT OF AP-1 CL 0.22389 1159 0.249563625
0.0559551 ENO3 BETA ENOLASE (EC 4.2.1.11) (2-PHOSPHO-D-GLYCERATE HYDRO-LYASE) (SKELETAL MUSCLE ENOLASE) (MSE) (ENOLASE 3). [SWISSPROT;Acc:P13929] 0.24878 2219 0.224918
0.0559574 TMEM132C 0.22361 1144 0.250245517
0.0559756 C1orf14 0.634694 3119 0.088193051
0.0560483 PIK3R2 PHOSPHATIDYLINOSITOL 3-KINASE REGULATORY BETA SUBUNIT (PI3-KINASE P85-BETA SUBUNIT) (PTDINS-3-KINASE P85-BETA). [SWISSPROT;Acc:O00459] 0.251275 2258 0.223055616
0.0560669 no value RNA-BINDING PROTEIN. [RefSeq;Acc:NM_019027] 0.181705 263 0.308560029
0.0561104 TRINUCLEOTIDE REPEAT CONTAINING 15. [RefSeq;Acc:NM_015575] 0.16661 180 0.336776904
0.0561617 BLOOD GROUP RH(CE) POLYPEPTIDE (RHESUS C/E ANTIGENS) (RH30A) (RHIXB) (RH POLYPEPTIDE 1) (RHPI). [SWISSPROT;Acc:P18577] 0.26352 2582 0.213121205
0.0562476 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] 0.237616 1750 0.236716383

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/