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 2202 to 2251 of 3206 in total
expected
measured
Rank
Hugo
description
final
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
0.981155 0.270501 455 GTPBP3 MITOCHONDRIAL GTP BINDING PROTEIN ISOFORM V. [RefSeq;Acc:NM_032620] 0.275696501

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/