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 Rank measured Hugo description final
Results: HTML CSV LaTeX Showing element 652 to 701 of 3206 in total
expected
Rank
measured
Hugo
description
final
0.188793 1700 0.044904 no value 0.237847802
0.189914 382 0.0530069 TOMM20 MITOCHONDRIAL IMPORT RECEPTOR SUBUNIT TOM20 HOMOLOG (MITOCHONDRIAL 20 KDA OUTER MEMBRANE PROTEIN) (OUTER MITOCHONDRIAL MEMBRANE RECEPTOR TOM20). [SWISSPROT;Acc:Q15388] 0.279110018
0.189922 3012 0.0231389 CD209 CD209 ANTIGEN; DENDRITIC CELL-SPECIFIC ICAM3-GRABBING NONINTEGRIN. [RefSeq;Acc:NM_021155] 0.1218337
0.190263 2833 0.036734 PTPRB PROTEIN-TYROSINE PHOSPHATASE BETA PRECURSOR (EC 3.1.3.48) (R-PTP- BETA). [SWISSPROT;Acc:P23467] 0.193069593
0.19065 2308 0.0423362 no value DJ718P11.1.2 (NOVEL CLASS II AMINOTRANSFERASE SIMILAR TO SERINE PALMOTYLTRANSFERASE (ISOFORM 2)) (FRAGMENT). [SPTREMBL;Acc:Q9UGB5] 0.222062418
0.191372 162 0.0661546 DNAJB11 DNAJ HOMOLOG SUBFAMILY B MEMBER 11 PRECURSOR (ER-ASSOCIATED DNAJ PROTEIN 3) (ERJ3) (ER-ASSOCIATED HSP40 CO-CHAPERONE) (HDJ9) (PWP1- INTERACTING PROTEIN 4). [SWISSPROT;Acc:Q9UBS4] 0.345685889
0.191403 2660 0.0401827 SLC13A2 "SOLUTE CARRIER FAMILY 13, MEMBER 2 (RENAL SODIUM/DICARBOXYLATE COTRANSPORTER) (NA(+)/DICARBOXYLATE COTRANSPORTER 1) (NADC-1). [SWISSPROT;Acc:Q13183]" 0.209937671
0.191876 1404 0.0468234 EPN3 EPSIN 3. [RefSeq;Acc:NM_017957] 0.244029477
0.192302 1350 0.0471496 HIVEP1 ZINC FINGER PROTEIN 40 (HUMAN IMMUNODEFICIENCY VIRUS TYPE I ENHANCER- BINDING PROTEIN 1) (HIV-EP1) (MAJOR HISTOCOMPATIBILITY COMPLEX BINDING PROTEIN 1) (MBP-1) (POSITIVE REGULATORY DOMAIN II BINDING FACTOR 1) (PRDII-BF1). [SWISSPROT;Acc:P15822] 0.245185177
0.192307 1288 0.0473076 ZNF622 ZINC FINGER-LIKE PROTEIN 9. [RefSeq;Acc:NM_033414] 0.246000406
0.193087 2213 0.0434449 LRRC48 0.225001683
0.193844 1562 0.0467541 ARRDC3 0.241194466
0.196031 74 0.0796134 HEY2 HAIRY/ENHANCER-OF-SPLIT RELATED WITH YRPW MOTIF 2; GRIDLOCK; HES-RELATED REPRESSOR PROTEIN 1. [RefSeq;Acc:NM_012259] 0.406126582
0.196275 405 0.0546138 CENTG3 CENTAURIN GAMMA 3. [SWISSPROT;Acc:Q96P47] 0.278251433
406 MOSC1
407 MOSC2
0.196556 484 0.0539161 HNRNPA2B1 HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEINS A2/B1 (HNRNP A2 / HNRNP B1). [SWISSPROT;Acc:P22626] 0.274304015
0.196587 1799 0.0461397 FAM57B 0.234703719
0.196598 2872 0.0371369 no value 0.188897649
0.196899 2861 0.0372023 TMEM131 RW1 PROTEIN (FRAGMENT). [SWISSPROT;Acc:Q92545] 0.188941031
2862 no value CGI-142; HEPATOMA-DERIVED GROWTH FACTOR 2. [RefSeq;Acc:NM_016073]
2863 ORAI3
2864 PARK2 "PARKINSON DISEASE (AUTOSOMAL RECESSIVE, JUVENILE) 2, PARKIN ISOFORM 1; PARKIN. [RefSeq;Acc:NM_004562]"
0.19727 2696 0.0410294 ENDOG "ENDONUCLEASE G, MITOCHONDRIAL PRECURSOR (EC 3.1.30.-) (ENDO G). [SWISSPROT;Acc:Q14249]" 0.207986009
0.19742 2521 0.042399 no value KERATIN ASSOCIATED PROTEIN 4-12; KERATIN ASSOCIATED PROTEIN 4.12. [RefSeq;Acc:NM_031854] 0.214765475
0.197588 919 0.0509651 RALGPS1 RAL GUANINE NUCLEOTIDE EXCHANGE FACTOR RALGPS1A. [RefSeq;Acc:NM_014636] 0.257936211
0.197664 146 0.0694539 NDUFA6 NADH-UBIQUINONE OXIDOREDUCTASE B14 SUBUNIT (EC 1.6.5.3) (EC 1.6.99.3) (COMPLEX I-B14) (CI-B14). [SWISSPROT;Acc:P56556] 0.351373543
0.197784 2298 0.0439756 DLX3 HOMEOBOX PROTEIN DLX-3. [SWISSPROT;Acc:O60479] 0.222341544
0.198227 1865 0.0462274 DCTN5 DYNACTIN 4. [RefSeq;Acc:NM_032486] 0.233204357
0.198284 2992 0.026835 HS3ST3A1 HEPARAN SULFATE D-GLUCOSAMINYL 3-O-SULFOTRANSFERASE 3A1; HEPARIN-GLUCOSAMINE 3-O-SULFOTRANSFERASE. [RefSeq;Acc:NM_006042] 0.135336184
0.198705 2875 0.0374428 CTNNAL1 "CATENIN (CADHERIN-ASSOCIATED PROTEIN), ALPHA-LIKE 1; ALPHA-CATULIN. [RefSeq;Acc:NM_003798]" 0.188434111
2876 SLC4A1AP "SOLUTE CARRIER FAMILY 4 (ANION EXCHANGER), MEMBER 1, ADAPTOR PROTEIN; KIDNEY ANION EXCHANGER ADAPTOR PROTEIN; KANADAPTIN; LUNG CANCER ONCOGENE 3. [RefSeq;Acc:NM_018158]"
0.199072 938 0.0510434 CHAT CHOLINE O-ACETYLTRANSFERASE (EC 2.3.1.6) (CHOACTASE) (CHOLINE ACETYLASE) (CHAT). [SWISSPROT;Acc:P28329] 0.256406727
0.199308 2290 0.0443146 DLX5 HOMEOBOX PROTEIN DLX-5. [SWISSPROT;Acc:P56178] 0.222342304
0.200292 1686 0.0476887 SNX17 SORTING NEXIN 17. [SWISSPROT;Acc:Q15036] 0.23809588
0.200615 1289 0.0493513 SLC45A2 MEMBRANE-ASSOCIATED TRANSPORTER PROTEIN (AIM-1 PROTEIN) (MELANOMA ANTIGEN AIM1). [SWISSPROT;Acc:Q9UMX9] 0.24600005
0.200737 2359 0.0442218 PGC GASTRICSIN PRECURSOR (EC 3.4.23.3) (PEPSINOGEN C). [SWISSPROT;Acc:P20142] 0.220297205
0.201854 2523 0.0433512 STARD4 STAR-RELATED LIPID TRANSFER PROTEIN 4 (STARD4) (START DOMAIN- CONTAINING PROTEIN 4). [SWISSPROT;Acc:Q96DR4] 0.214765127
0.203458 2522 0.0436957 no value 0.21476521
0.203469 3015 0.0247893 CLEC4M CD209 ANTIGEN-LIKE; PUTATIVE TYPE II MEMBRANE PROTEIN. [RefSeq;Acc:NM_014257] 0.121833301
0.203611 859 0.0530266 PRPF4 U4/U6 SMALL NUCLEAR RIBONUCLEOPROTEIN PRP4 (U4/U6 SNRNP 60 KDA PROTEIN) (WD SPLICING FACTOR PRP4) (HPRP4). [SWISSPROT;Acc:O43172] 0.26043092
0.203814 2134 0.046465 NETO1 NEUROPILIN- AND TOLLOID-LIKE PROTEIN 1 ISOFORM 3 PRECURSOR. [RefSeq;Acc:NM_138966] 0.22797747
0.203883 1082 0.0513934 BBOX1 "GAMMA-BUTYROBETAINE,2-OXOGLUTARATE DIOXYGENASE (EC 1.14.11.1) (GAMMA-BUTYROBETAINE HYDROXYLASE) (GAMMA-BBH). [SWISSPROT;Acc:O75936]" 0.252073003
0.204307 2524 0.043878 STARD6 STAR-RELATED LIPID TRANSFER PROTEIN 6 (STARD6) (START DOMAIN- CONTAINING PROTEIN 6). [SWISSPROT;Acc:P59095] 0.214765035
0.204356 1642 0.0488461 no value 0.239024545
0.204515 2887 0.0368025 DPP9 DIPEPTIDYLPEPTIDASE 9; DIPEPTIDYL PEPTIDASE 9; DIPEPTIDYL PEPTIDASE IV-RELATED PROTEIN-2. [RefSeq;Acc:NM_139159] 0.179950126
0.204773 2182 0.0463914 PAK2 SERINE/THREONINE-PROTEIN KINASE PAK 2 (EC 2.7.1.-) (P21-ACTIVATED KINASE 2) (PAK-2) (PAK65) (GAMMA-PAK) (S6/H4 KINASE). [SWISSPROT;Acc:Q13177] 0.226550375
0.205148 487 0.0562729 HNRPA3 HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN A3 (HNRNP A3) (D10S102). [SWISSPROT;Acc:P51991] 0.274303917
0.20547 2063 0.0471781 BECN1 BECLIN 1 (COILED-COIL MYOSIN-LIKE BCL2-INTERACTING PROTEIN) (PROTEIN GT197). [SWISSPROT;Acc:Q14457] 0.229610649
0.205572 378 0.0573826 GULP1 PTB DOMAIN ADAPTOR PROTEIN CED-6; ENGULFMENT ADAPTER PROTEIN. [RefSeq;Acc:NM_016315] 0.279136264

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/