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.


Navigation/Query Panel:
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expected Gene measured Rank Hugo description final
Results: HTML CSV LaTeX Showing element 652 to 701 of 3206 in total
expected
measured
Rank
Hugo
description
final
0.188793 0.044904 1700 no value 0.237847802
0.189914 0.0530069 382 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 0.0231389 3012 CD209 CD209 ANTIGEN; DENDRITIC CELL-SPECIFIC ICAM3-GRABBING NONINTEGRIN. [RefSeq;Acc:NM_021155] 0.1218337
0.190263 0.036734 2833 PTPRB PROTEIN-TYROSINE PHOSPHATASE BETA PRECURSOR (EC 3.1.3.48) (R-PTP- BETA). [SWISSPROT;Acc:P23467] 0.193069593
0.19065 0.0423362 2308 no value DJ718P11.1.2 (NOVEL CLASS II AMINOTRANSFERASE SIMILAR TO SERINE PALMOTYLTRANSFERASE (ISOFORM 2)) (FRAGMENT). [SPTREMBL;Acc:Q9UGB5] 0.222062418
0.191372 0.0661546 162 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 0.0401827 2660 SLC13A2 "SOLUTE CARRIER FAMILY 13, MEMBER 2 (RENAL SODIUM/DICARBOXYLATE COTRANSPORTER) (NA(+)/DICARBOXYLATE COTRANSPORTER 1) (NADC-1). [SWISSPROT;Acc:Q13183]" 0.209937671
0.191876 0.0468234 1404 EPN3 EPSIN 3. [RefSeq;Acc:NM_017957] 0.244029477
0.192302 0.0471496 1350 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 0.0473076 1288 ZNF622 ZINC FINGER-LIKE PROTEIN 9. [RefSeq;Acc:NM_033414] 0.246000406
0.193087 0.0434449 2213 LRRC48 0.225001683
0.193844 0.0467541 1562 ARRDC3 0.241194466
0.196031 0.0796134 74 HEY2 HAIRY/ENHANCER-OF-SPLIT RELATED WITH YRPW MOTIF 2; GRIDLOCK; HES-RELATED REPRESSOR PROTEIN 1. [RefSeq;Acc:NM_012259] 0.406126582
0.196275 0.0546138 405 CENTG3 CENTAURIN GAMMA 3. [SWISSPROT;Acc:Q96P47] 0.278251433
406 MOSC1
407 MOSC2
0.196556 0.0539161 484 HNRNPA2B1 HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEINS A2/B1 (HNRNP A2 / HNRNP B1). [SWISSPROT;Acc:P22626] 0.274304015
0.196587 0.0461397 1799 FAM57B 0.234703719
0.196598 0.0371369 2872 no value 0.188897649
0.196899 0.0372023 2861 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 0.0410294 2696 ENDOG "ENDONUCLEASE G, MITOCHONDRIAL PRECURSOR (EC 3.1.30.-) (ENDO G). [SWISSPROT;Acc:Q14249]" 0.207986009
0.19742 0.042399 2521 no value KERATIN ASSOCIATED PROTEIN 4-12; KERATIN ASSOCIATED PROTEIN 4.12. [RefSeq;Acc:NM_031854] 0.214765475
0.197588 0.0509651 919 RALGPS1 RAL GUANINE NUCLEOTIDE EXCHANGE FACTOR RALGPS1A. [RefSeq;Acc:NM_014636] 0.257936211
0.197664 0.0694539 146 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 0.0439756 2298 DLX3 HOMEOBOX PROTEIN DLX-3. [SWISSPROT;Acc:O60479] 0.222341544
0.198227 0.0462274 1865 DCTN5 DYNACTIN 4. [RefSeq;Acc:NM_032486] 0.233204357
0.198284 0.026835 2992 HS3ST3A1 HEPARAN SULFATE D-GLUCOSAMINYL 3-O-SULFOTRANSFERASE 3A1; HEPARIN-GLUCOSAMINE 3-O-SULFOTRANSFERASE. [RefSeq;Acc:NM_006042] 0.135336184
0.198705 0.0374428 2875 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 0.0510434 938 CHAT CHOLINE O-ACETYLTRANSFERASE (EC 2.3.1.6) (CHOACTASE) (CHOLINE ACETYLASE) (CHAT). [SWISSPROT;Acc:P28329] 0.256406727
0.199308 0.0443146 2290 DLX5 HOMEOBOX PROTEIN DLX-5. [SWISSPROT;Acc:P56178] 0.222342304
0.200292 0.0476887 1686 SNX17 SORTING NEXIN 17. [SWISSPROT;Acc:Q15036] 0.23809588
0.200615 0.0493513 1289 SLC45A2 MEMBRANE-ASSOCIATED TRANSPORTER PROTEIN (AIM-1 PROTEIN) (MELANOMA ANTIGEN AIM1). [SWISSPROT;Acc:Q9UMX9] 0.24600005
0.200737 0.0442218 2359 PGC GASTRICSIN PRECURSOR (EC 3.4.23.3) (PEPSINOGEN C). [SWISSPROT;Acc:P20142] 0.220297205
0.201854 0.0433512 2523 STARD4 STAR-RELATED LIPID TRANSFER PROTEIN 4 (STARD4) (START DOMAIN- CONTAINING PROTEIN 4). [SWISSPROT;Acc:Q96DR4] 0.214765127
0.203458 0.0436957 2522 no value 0.21476521
0.203469 0.0247893 3015 CLEC4M CD209 ANTIGEN-LIKE; PUTATIVE TYPE II MEMBRANE PROTEIN. [RefSeq;Acc:NM_014257] 0.121833301
0.203611 0.0530266 859 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 0.046465 2134 NETO1 NEUROPILIN- AND TOLLOID-LIKE PROTEIN 1 ISOFORM 3 PRECURSOR. [RefSeq;Acc:NM_138966] 0.22797747
0.203883 0.0513934 1082 BBOX1 "GAMMA-BUTYROBETAINE,2-OXOGLUTARATE DIOXYGENASE (EC 1.14.11.1) (GAMMA-BUTYROBETAINE HYDROXYLASE) (GAMMA-BBH). [SWISSPROT;Acc:O75936]" 0.252073003
0.204307 0.043878 2524 STARD6 STAR-RELATED LIPID TRANSFER PROTEIN 6 (STARD6) (START DOMAIN- CONTAINING PROTEIN 6). [SWISSPROT;Acc:P59095] 0.214765035
0.204356 0.0488461 1642 no value 0.239024545
0.204515 0.0368025 2887 DPP9 DIPEPTIDYLPEPTIDASE 9; DIPEPTIDYL PEPTIDASE 9; DIPEPTIDYL PEPTIDASE IV-RELATED PROTEIN-2. [RefSeq;Acc:NM_139159] 0.179950126
0.204773 0.0463914 2182 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 0.0562729 487 HNRPA3 HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN A3 (HNRNP A3) (D10S102). [SWISSPROT;Acc:P51991] 0.274303917
0.20547 0.0471781 2063 BECN1 BECLIN 1 (COILED-COIL MYOSIN-LIKE BCL2-INTERACTING PROTEIN) (PROTEIN GT197). [SWISSPROT;Acc:Q14457] 0.229610649
0.205572 0.0573826 378 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/