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 expected Rank description measured final Hugo
Results: HTML CSV LaTeX Showing element 702 to 751 of 3206 in total
expected
Rank
description
measured
final
Hugo
0.205631 1754 VACUOLAR ATP SYNTHASE SUBUNIT G 3 (EC 3.6.3.14) (V-ATPASE G SUBUNIT 3) (VACUOLAR PROTON PUMP G SUBUNIT 3) (V-ATPASE 13 KDA SUBUNIT 3). [SWISSPROT;Acc:Q96LB4] 0.0486762 0.236716254 ATP6V1G3
0.206095 1184 EPSIN 2 ISOFORM B; EPS15 BINDING PROTEIN. [RefSeq;Acc:NM_014964] 0.0512587 0.248713943 EPN2
0.206215 2382 PROTO-ONCOGENE TYROSINE-PROTEIN KINASE FES/FPS (EC 2.7.1.112) (C-FES). [SWISSPROT;Acc:P07332] 0.0453043 0.219694494 FES
0.206986 2628 MITOGEN-ACTIVATED PROTEIN KINASE 14 (EC 2.7.1.37) (MITOGEN-ACTIVATED PROTEIN KINASE P38ALPHA) (MAP KINASE P38ALPHA) (CYTOKINE SUPPRESSIVE ANTI-INFLAMMATORY DRUG BINDING PROTEIN) (CSAID BINDING PROTEIN) (CSBP) (MAX-INTERACTING PROTEIN 2) (MAP KINASE MXI2) 0.0434669 0.209999227 MAPK14
0.208298 1915 TYROSYL-TRNA SYNTHETASE (EC 6.1.1.1) (TYROSYL--TRNA LIGASE) (TYRRS). [SWISSPROT;Acc:P54577] 0.0483307 0.232026712 YARS
0.208398 3041 MITOCHONDRIAL SOLUTE CARRIER PROTEIN. [RefSeq;Acc:NM_145305] 0.0228794 0.109787042 SLC25A43
0.208597 2971 TUBULIN-SPECIFIC CHAPERONE C (TUBULIN-FOLDING COFACTOR C) (CFC). [SWISSPROT;Acc:Q15814] 0.0292681 0.140309305 TBCC
2972 DEAD-BOX PROTEIN. [RefSeq;Acc:NM_018665] DDX43
0.20874 2676 N-ACETYLGALACTOSAMINE KINASE (EC 2.7.1.-) (GALNAC KINASE) (GALACTOKINASE 2). [SWISSPROT;Acc:Q01415] 0.0435693 0.208725208 GALK2
0.208966 2123 0.0476698 0.228122278 TCP11L2
0.209553 3024 SYNBINDIN (TRS23 HOMOLOG) (HEMATOPOIETIC STEM/PROGENITOR CELL PROTEIN 172) (HSPC172) (PTD009) (CGI-104). [SWISSPROT;Acc:Q9Y296] 0.0250043 0.119322081 no value
3025 SEDLIN. [SWISSPROT;Acc:O14582] ZNF547
0.210056 170 0.0714655 0.340221179 EPC2
0.210535 1646 MYOSIN VI. [SWISSPROT;Acc:Q9UM54] 0.050323 0.23902439 no value
0.210671 2997 OLIGOSACCHARYL TRANSFERASE STT3 SUBUNIT HOMOLOG (B5) (INTEGRAL MEMBRANE PROTEIN 1) (TMC). [SWISSPROT;Acc:P46977] 0.0284601 0.135092633 STT3A
0.210853 789 ADENOVIRUS 5 E1A-BINDING PROTEIN (BS69 PROTEIN). [SWISSPROT;Acc:Q15326] 0.0552487 0.262024728 ZMYND11
0.211181 2362 "SOLUTE CARRIER FAMILY 20 (PHOSPHATE TRANSPORTER), MEMBER 1; GLVR-1; PIT-1; GIBBON APE LEUKEMIA VIRUS RECEPTOR 1. [RefSeq;Acc:NM_005415]" 0.0465225 0.220296807 SLC20A1
0.213145 1244 "SOLUTE CARRIER FAMILY 2, FACILITATED GLUCOSE TRANSPORTER, MEMBER 6 (GLUCOSE TRANSPORTER TYPE 6) (GLUCOSE TRANSPORTER TYPE 9). [SWISSPROT;Acc:Q9UGQ3]" 0.0527752 0.247602336 SLC2A6
0.213303 260 NS1-ASSOCIATED PROTEIN 1. [RefSeq;Acc:NM_006372] 0.0658169 0.308560592 SYNCRIP
0.215105 2183 SERINE/THREONINE-PROTEIN KINASE PAK 3 (EC 2.7.1.-) (P21-ACTIVATED KINASE 3) (PAK-3) (BETA-PAK) (OLIGOPHRENIN-3). [SWISSPROT;Acc:O75914] 0.048732 0.226549825 PAK3
0.216002 777 HUNTINGTIN-ASSOCIATED PROTEIN-INTERACTING PROTEIN (DUO PROTEIN). [SWISSPROT;Acc:O60229] 0.0568574 0.263226266 no value
0.217449 2901 P66 ALPHA. [RefSeq;Acc:NM_017660] 0.0379885 0.174700734 GATAD2A
0.217657 2600 UBIQUITIN-ACTIVATING ENZYME E1 (A1S9 PROTEIN). [SWISSPROT;Acc:P22314] 0.046337 0.212890006 UBE1
0.217847 2677 GALACTOSE-1-PHOSPHATE URIDYLYLTRANSFERASE (EC 2.7.7.12) (GAL-1-P URIDYLYLTRANSFERASE) (UDP-GLUCOSE--HEXOSE-1-PHOSPHATE URIDYLYLTRANSFERASE). [SWISSPROT;Acc:P07902] 0.0454701 0.208724931 no value
0.217862 441 "ATPASE INHIBITOR, MITOCHONDRIAL PRECURSOR. [SWISSPROT;Acc:Q9UII2]" 0.0602832 0.276703601 ATPIF1
442 POLYAMINE OXIDASE ISOFORM 1; POLYAMINE OXIDASE; FLAVIN-CONTAINING SPERMINE OXIDASE; PUTATIVE CYCLIN G1 INTERACTING PROTEIN; FLAVIN CONTAINING AMINE OXIDASE. [RefSeq;Acc:NM_019025] SMOX
0.21806 610 DJ947L8.1.6 (NOVEL CUB AND SUSHI (SCR REPEAT) DOMAIN PROTEIN) (FRAGMENT). [SPTREMBL;Acc:Q9H4W2] 0.0586244 0.268845272 CSMD1
0.218331 2611 TOPOISOMERASE (DNA) II BINDING PROTEIN. [RefSeq;Acc:NM_007027] 0.0461407 0.211333709 TOPBP1
0.219077 1479 RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 2 (P21-RAC2) (SMALL G PROTEIN) (GX). [SWISSPROT;Acc:P15153] 0.0532303 0.242975301 RAC2
0.22041 3038 PANTOTHENATE KINASE 1 (EC 2.7.1.33) (PANTOTHENIC ACID KINASE 1) (HPANK1) (HPANK). [SWISSPROT;Acc:Q8TE04] 0.0241982 0.109787215 PANK1
3039 "28S RIBOSOMAL PROTEIN S17, MITOCHONDRIAL PRECURSOR (MRP-S17) (HSPC011). [SWISSPROT;Acc:Q9Y2R5]" MRPS17
0.220425 2218 ALPHA ENOLASE (EC 4.2.1.11) (2-PHOSPHO-D-GLYCERATE HYDRO-LYASE) (NON- NEURAL ENOLASE) (NNE) (ENOLASE 1) (PHOSPHOPYRUVATE HYDRATASE). [SWISSPROT;Acc:P06733] 0.0495777 0.22491868 ENO1
0.22089 2216 GAMMA ENOLASE (EC 4.2.1.11) (2-PHOSPHO-D-GLYCERATE HYDRO-LYASE) (NEURAL ENOLASE) (NSE) (ENOLASE 2). [SWISSPROT;Acc:P09104] 0.0496823 0.224918738 ENO2
0.221164 2978 HOMEOBOX PROTEIN HOX-C6 (HOX-3C) (HHO.C8) (CP25). [SWISSPROT;Acc:P09630] 0.0308655 0.139559332 no value
0.221972 2656 SECRETORY CARRIER-ASSOCIATED MEMBRANE PROTEIN 1. [SWISSPROT;Acc:O15126] 0.0466014 0.209942695 SCAMP1
0.222289 2106 "PROTEIN KINASE C, ETA TYPE (EC 2.7.1.-) (NPKC-ETA) (PKC-L). [SWISSPROT;Acc:P24723]" 0.0507599 0.228350931 PRKCH
0.222515 941 VOLTAGE-GATED POTASSIUM CHANNEL BETA-3 SUBUNIT (K+ CHANNEL BETA-3 SUBUNIT) (KV-BETA-3). [SWISSPROT;Acc:O43448] 0.0570543 0.256406534 KCNAB3
0.222701 2983 HOMEOBOX PROTEIN HOX-A4 (HOX-1D) (HOX-1.4). [SWISSPROT;Acc:Q00056] 0.0310799 0.13955887 no value
0.223127 2974 HOMEOBOX PROTEIN HOX-D4 (HOX-4B) (HOX-5.1) (HHO.C13). [SWISSPROT;Acc:P09016] 0.0311395 0.139559533 HOXD4
0.223156 2837 THYMUS-SPECIFIC SERINE PROTEASE PRECURSOR (EC 3.4.-.-). [SWISSPROT;Acc:Q9NQE7] 0.0430845 0.193068974 PRSS16
0.22325 16 SERINE/THREONINE-PROTEIN KINASE NEK2 (EC 2.7.1.37) (NIMA-RELATED PROTEIN KINASE 2) (NIMA-LIKE PROTEIN KINASE 1) (HSPK 21). [SWISSPROT;Acc:P51955] 0.106175 0.475587906 NEK2
0.223379 2835 "SUCCINATE DEHYDROGENASE [UBIQUINONE] CYTOCHROME B SMALL SUBUNIT, MITOCHONDRIAL PRECURSOR (CYBS) (SUCCINATE-UBIQUINONE REDUCTASE MEMBRANE ANCHOR SUBUNIT) (QPS2) (CII-4) (SUCCINATE DEHYDROGENASE COMPLEX SUBUNIT D) (SUCCINATE-UBIQUINONE OXIDOREDUCTASE CYTOCH" 0.0431276 0.193069178 no value
0.223469 2976 HOMEOBOX PROTEIN HOX-C4 (HOX-3E) (CP19). [SWISSPROT;Acc:P09017] 0.0311872 0.139559402
0.2235 3114 CCAAT-BINDING TRANSCRIPTION FACTOR SUBUNIT B (CBF-B) (NF-Y PROTEIN CHAIN A) (NF-YA) (CAAT-BOX DNA BINDING PROTEIN SUBUNIT A). [SWISSPROT;Acc:P23511] 0.0202662 0.09067651 NFYA
0.22361 1144 0.0559574 0.250245517 TMEM132C
0.22389 1159 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 0.0558748 0.249563625 AP1S3
0.223943 2140 0.0510195 0.227823598 KIAA1109
0.223986 26 DOCKING PROTEIN 2 (P56(DOK-2)) (DOWNSTREAM OF TYROSINE KINASE 2). [SWISSPROT;Acc:O60496] 0.0954445 0.42611815 DOK2
0.224664 2982 HOMEOBOX PROTEIN HOX-B4 (HOX-2F) (HOX-2.6). [SWISSPROT;Acc:P17483] 0.0313539 0.139559075 HOXB4
0.224949 449 0.0621484 0.276277734 TSNARE1

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/