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 Gene measured Rank Hugo description final
Results: HTML CSV LaTeX Showing element 2201 to 2250 of 3206 in total
expected
measured
Rank
Hugo
description
final
0.929536 0.23379 1094 CSNK2A1P "CASEIN KINASE II, ALPHA CHAIN (CK II) (EC 2.7.1.37). [SWISSPROT;Acc:P19138]" 0.251512583
0.930463 0.218499 1796 PDCD5 PROGRAMMED CELL DEATH PROTEIN 5 (TFAR19 PROTEIN) (TF-1 CELL APOPTOSIS RELATED GENE-19 PROTEIN). [SWISSPROT;Acc:O14737] 0.234828252
0.9315 0.163112 2896 CCNB1 G2/MITOTIC-SPECIFIC CYCLIN B1. [SWISSPROT;Acc:P14635] 0.175106817
0.932647 0.25098 600 ZIC3 ZINC FINGER PROTEIN ZIC 3 (ZINC FINGER PROTEIN OF THE CEREBELLUM 3). [SWISSPROT;Acc:O60481] 0.269105031
0.9333 0.25596 497 R3HDM2 0.274252652
0.933978 0.253813 529 PPP1R12A "PROTEIN PHOSPHATASE 1, REGULATORY (INHIBITOR) SUBUNIT 12A; MYOSIN PHOSPHATASE, TARGET SUBUNIT 1. [RefSeq;Acc:NM_002480]" 0.271754795
0.939561 0.230116 1363 DDX24 ATP-DEPENDENT RNA HELICASE DDX24 (DEAD-BOX PROTEIN 24). [SWISSPROT;Acc:Q9GZR7] 0.244918638
0.939792 0.208679 2310 DCAKD 0.22204807
0.939933 0.260039 446 NPLOC4 0.276656953
0.940372 0.214415 2129 KIAA1432 BA207C16.2 (FRAGMENT). [SPTREMBL;Acc:Q9NQL7] 0.22801083
0.940952 0.206722 2381 USP52 0.219694522
0.941277 0.318787 172 PEF1 PEF PROTEIN WITH A LONG N-TERMINAL HYDROPHOBIC DOMAIN (PEFLIN). [RefSeq;Acc:NM_012392] 0.338675013
0.941317 0.136683 2966 FOXP4 FORKHEAD BOX P4; FORK HEAD-RELATED PROTEIN LIKE A; WINGED-HELIX REPRESSOR FOXP4. [RefSeq;Acc:NM_138457] 0.145204007
0.944489 0.224133 1717 ATP6V0A4 "ATPASE, H+ TRANSPORTING, LYSOSOMAL V0 SUBUNIT A ISOFORM 4; VACUOLAR PROTON PUMP 116 KDA ACCESSORY SUBUNIT; VACUOLAR PROTON PUMP, SUBUNIT 2; H(+)-TRANSPORTING TWO-SECTOR ATPASE, NONCATALYTIC ACCESSORY PROTEIN 1B; ATPASE, H+ TRANSPORTING, LYSOSOMAL (VACUOLA" 0.237306099
0.945419 0.219925 1894 CKM "CREATINE KINASE, M CHAIN (EC 2.7.3.2) (M-CK). [SWISSPROT;Acc:P06732]" 0.232621726
0.945656 0.214133 2186 ARHGEF7 RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 7 (PAK-INTERACTING EXCHANGE FACTOR BETA) (BETA-PIX) (COOL-1) (P85). [SWISSPROT;Acc:Q14155] 0.226438578
0.945747 0.222245 1790 ARG1 ARGINASE 1 (EC 3.5.3.1) (LIVER-TYPE ARGINASE). [SWISSPROT;Acc:P05089] 0.234994137
0.946559 0.205001 2477 PARS2 SIMILAR TO TRNA SYNTHETASE CLASS II. [RefSeq;Acc:NM_152268] 0.216574984
0.947072 0.228182 1575 ACTG1 "ACTIN, CYTOPLASMIC 2 (GAMMA-ACTIN). [SWISSPROT;Acc:P02571]" 0.240934163
0.94731 0.205647 2448 ZMPSTE24 CAAX PRENYL PROTEASE 1 HOMOLOG (EC 3.4.24.-) (PRENYL PROTEIN-SPECIFIC ENDOPROTEASE 1) (FARNESYLATED-PROTEINS CONVERTING ENZYME 1) (FACE-1) (ZINC METALLOPROTEINASE STE24 HOMOLOG). [SWISSPROT;Acc:O75844] 0.21708522
0.94872 0.137759 2965 FOXP1 FORKHEAD BOX PROTEIN P1 (HSPC215). [SWISSPROT;Acc:Q9H334] 0.145205118
0.951909 0.257341 577 ACOT4 PEROXISOMAL ACYL-COA THIOESTERASE 2B; LIKELY ORTHOLOG OF MOUSE PEROXISOMAL ACYL-COA THIOESTERASE 2B. [RefSeq;Acc:NM_152331] 0.270342018
0.952373 0.222313 1858 POLR2G DNA-DIRECTED RNA POLYMERASE II 19 KDA POLYPEPTIDE (EC 2.7.7.6) (RPB7). [SWISSPROT;Acc:P52433] 0.233430599
0.952641 0.116797 3008 SEPT6 SEPTIN 6. [SWISSPROT;Acc:Q14141] 0.122603373
0.953667 0.263953 439 MLLT4 AF-6 PROTEIN. [SWISSPROT;Acc:P55196] 0.276776904
0.954128 0.189189 2804 HTATIP2 "HIV-1 TAT INTERACTIVE PROTEIN 2, 30KDA; TAT-INTERACTING PROTEIN (30KD); HIV-1 TAT INTERACTIVE PROTEIN 2, 30 KDA; HIV-1 TAT INTERACTIVE PROTEIN 2, 30 KD. [RefSeq;Acc:NM_006410]" 0.198284717
0.954199 0.21824 2090 NUPL1 NUCLEOPORIN LIKE 1. [RefSeq;Acc:NM_014089] 0.228715394
0.955286 0.342509 122 SOS2 SON OF SEVENLESS PROTEIN HOMOLOG 2 (SOS-2). [SWISSPROT;Acc:Q07890] 0.358540793
0.956345 0.375556 84 EIF5 EUKARYOTIC TRANSLATION INITIATION FACTOR 5 (EIF-5). [SWISSPROT;Acc:P55010] 0.392699287
0.957852 0.260139 530 RBM24 0.271585798
0.959291 0.221383 1995 no value INTEGRAL MEMBRANE PROTEIN CII-3B. [SPTREMBL;Acc:O75609] 0.230777731
0.96599 0.189314 2813 OTUB1 UBIQUITIN-SPECIFIC PROTEASE OTUBAIN 1. [RefSeq;Acc:NM_017670] 0.195979254
0.967917 0.232181 1606 KATNAL1 0.239876973
0.968071 0.229236 1743 no value 40S RIBOSOMAL PROTEIN S28. [SWISSPROT;Acc:P25112] 0.236796681
0.968184 0.193542 2796 PAK7 SERINE/THREONINE-PROTEIN KINASE PAK 7 (EC 2.7.1.-) (P21-ACTIVATED KINASE 7) (PAK-7) (PAK-5). [SWISSPROT;Acc:Q9P286] 0.199902085
0.968873 0.21385 2341 RARS2 ARGINYL-TRNA SYNTHETASE-LIKE; ARGININE-TRNA LIGASE. [RefSeq;Acc:NM_020320] 0.220720363
0.969013 0.208649 2500 PMPCB "MITOCHONDRIAL PROCESSING PEPTIDASE BETA SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 3.4.24.64) (BETA-MPP) (P-52). [SWISSPROT;Acc:O75439]" 0.215321157
0.969143 0.253043 829 no value PURINE NUCLEOSIDE PHOSPHORYLASE (EC 2.4.2.1) (INOSINE PHOSPHORYLASE) (PNP). [SWISSPROT;Acc:P00491] 0.261099755
0.969328 0.590586 6 CHRAC1 CHROMATIN ACCESSIBILITY COMPLEX PROTEIN 1 (CHRAC-1) (CHRAC-15) (HUCHRAC15) (DNA POLYMERASE EPSILON SUBUNIT P15). [SWISSPROT;Acc:Q9NRG0] 0.609273641
0.970087 0.210228 2465 BRD9 0.21671046
0.971531 0.230384 1723 VPS45 VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 45 (H-VPS45) (HLVPS45). [SWISSPROT;Acc:Q9NRW7] 0.237134996
0.972163 0.218789 2211 MLH1 DNA MISMATCH REPAIR PROTEIN MLH1 (MUTL PROTEIN HOMOLOG 1). [SWISSPROT;Acc:P40692] 0.225053823
0.972411 0.221521 2144 ICT1 IMMATURE COLON CARCINOMA TRANSCRIPT 1 (DIGESTION SUBSTRACTION 1) (DS- 1). [SWISSPROT;Acc:Q14197] 0.227805938
0.973079 0.23697 1439 NLE1 0.243525962
0.973151 0.256243 771 DVL3 SEGMENT POLARITY PROTEIN DISHEVELLED HOMOLOG DVL-3 (DISHEVELLED-3) (DSH HOMOLOG 3). [SWISSPROT;Acc:Q92997] 0.263312682
0.973671 0.287802 311 UBB UBIQUITIN. [SWISSPROT;Acc:P02248] 0.295584443
0.975402 0.215454 2338 WRNIP1 WERNER HELICASE INTERACTING PROTEIN ISOFORM 1; PUTATIVE HELICASE RUVBL; WERNER HELICASE INTERACTING PROTEIN. [RefSeq;Acc:NM_020135] 0.220887388
0.976589 0.203468 2683 RTN3 RETICULON PROTEIN 3 (NEUROENDOCRINE-SPECIFIC PROTEIN-LIKE 2) (NSP-LIKE PROTEIN II) (NSPLII). [SWISSPROT;Acc:O95197] 0.208345578
0.977987 0.195503 2788 REEP5 POLYPOSIS LOCUS PROTEIN 1 (TB2 PROTEIN). [SWISSPROT;Acc:Q00765] 0.199903475
0.979382 0.22609 1994 DOHH 0.230849658

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/