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 651 to 700 of 3206 in total
expected
Rank
description
measured
final
Hugo
0.188735 107 SEQUESTOSOME 1; UBIQUITIN-BINDING PROTEIN P62; PHOSPHOTYROSINE INDEPENDENT LIGAND FOR THE LCK SH2 DOMAIN P62. [RefSeq;Acc:NM_003900] 0.0692099 0.366704109 SQSTM1
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

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/