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

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/