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 2202 to 2251 of 3206 in total
expected
Rank
description
measured
final
Hugo
0.930463 1796 PROGRAMMED CELL DEATH PROTEIN 5 (TFAR19 PROTEIN) (TF-1 CELL APOPTOSIS RELATED GENE-19 PROTEIN). [SWISSPROT;Acc:O14737] 0.218499 0.234828252 PDCD5
0.9315 2896 G2/MITOTIC-SPECIFIC CYCLIN B1. [SWISSPROT;Acc:P14635] 0.163112 0.175106817 CCNB1
0.932647 600 ZINC FINGER PROTEIN ZIC 3 (ZINC FINGER PROTEIN OF THE CEREBELLUM 3). [SWISSPROT;Acc:O60481] 0.25098 0.269105031 ZIC3
0.9333 497 0.25596 0.274252652 R3HDM2
0.933978 529 "PROTEIN PHOSPHATASE 1, REGULATORY (INHIBITOR) SUBUNIT 12A; MYOSIN PHOSPHATASE, TARGET SUBUNIT 1. [RefSeq;Acc:NM_002480]" 0.253813 0.271754795 PPP1R12A
0.939561 1363 ATP-DEPENDENT RNA HELICASE DDX24 (DEAD-BOX PROTEIN 24). [SWISSPROT;Acc:Q9GZR7] 0.230116 0.244918638 DDX24
0.939792 2310 0.208679 0.22204807 DCAKD
0.939933 446 0.260039 0.276656953 NPLOC4
0.940372 2129 BA207C16.2 (FRAGMENT). [SPTREMBL;Acc:Q9NQL7] 0.214415 0.22801083 KIAA1432
0.940952 2381 0.206722 0.219694522 USP52
0.941277 172 PEF PROTEIN WITH A LONG N-TERMINAL HYDROPHOBIC DOMAIN (PEFLIN). [RefSeq;Acc:NM_012392] 0.318787 0.338675013 PEF1
0.941317 2966 FORKHEAD BOX P4; FORK HEAD-RELATED PROTEIN LIKE A; WINGED-HELIX REPRESSOR FOXP4. [RefSeq;Acc:NM_138457] 0.136683 0.145204007 FOXP4
0.944489 1717 "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" 0.224133 0.237306099 ATP6V0A4
0.945419 1894 "CREATINE KINASE, M CHAIN (EC 2.7.3.2) (M-CK). [SWISSPROT;Acc:P06732]" 0.219925 0.232621726 CKM
0.945656 2186 RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 7 (PAK-INTERACTING EXCHANGE FACTOR BETA) (BETA-PIX) (COOL-1) (P85). [SWISSPROT;Acc:Q14155] 0.214133 0.226438578 ARHGEF7
0.945747 1790 ARGINASE 1 (EC 3.5.3.1) (LIVER-TYPE ARGINASE). [SWISSPROT;Acc:P05089] 0.222245 0.234994137 ARG1
0.946559 2477 SIMILAR TO TRNA SYNTHETASE CLASS II. [RefSeq;Acc:NM_152268] 0.205001 0.216574984 PARS2
0.947072 1575 "ACTIN, CYTOPLASMIC 2 (GAMMA-ACTIN). [SWISSPROT;Acc:P02571]" 0.228182 0.240934163 ACTG1
0.94731 2448 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] 0.205647 0.21708522 ZMPSTE24
0.94872 2965 FORKHEAD BOX PROTEIN P1 (HSPC215). [SWISSPROT;Acc:Q9H334] 0.137759 0.145205118 FOXP1
0.951909 577 PEROXISOMAL ACYL-COA THIOESTERASE 2B; LIKELY ORTHOLOG OF MOUSE PEROXISOMAL ACYL-COA THIOESTERASE 2B. [RefSeq;Acc:NM_152331] 0.257341 0.270342018 ACOT4
0.952373 1858 DNA-DIRECTED RNA POLYMERASE II 19 KDA POLYPEPTIDE (EC 2.7.7.6) (RPB7). [SWISSPROT;Acc:P52433] 0.222313 0.233430599 POLR2G
0.952641 3008 SEPTIN 6. [SWISSPROT;Acc:Q14141] 0.116797 0.122603373 SEPT6
0.953667 439 AF-6 PROTEIN. [SWISSPROT;Acc:P55196] 0.263953 0.276776904 MLLT4
0.954128 2804 "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]" 0.189189 0.198284717 HTATIP2
0.954199 2090 NUCLEOPORIN LIKE 1. [RefSeq;Acc:NM_014089] 0.21824 0.228715394 NUPL1
0.955286 122 SON OF SEVENLESS PROTEIN HOMOLOG 2 (SOS-2). [SWISSPROT;Acc:Q07890] 0.342509 0.358540793 SOS2
0.956345 84 EUKARYOTIC TRANSLATION INITIATION FACTOR 5 (EIF-5). [SWISSPROT;Acc:P55010] 0.375556 0.392699287 EIF5
0.957852 530 0.260139 0.271585798 RBM24
0.959291 1995 INTEGRAL MEMBRANE PROTEIN CII-3B. [SPTREMBL;Acc:O75609] 0.221383 0.230777731 no value
0.96599 2813 UBIQUITIN-SPECIFIC PROTEASE OTUBAIN 1. [RefSeq;Acc:NM_017670] 0.189314 0.195979254 OTUB1
0.967917 1606 0.232181 0.239876973 KATNAL1
0.968071 1743 40S RIBOSOMAL PROTEIN S28. [SWISSPROT;Acc:P25112] 0.229236 0.236796681 no value
0.968184 2796 SERINE/THREONINE-PROTEIN KINASE PAK 7 (EC 2.7.1.-) (P21-ACTIVATED KINASE 7) (PAK-7) (PAK-5). [SWISSPROT;Acc:Q9P286] 0.193542 0.199902085 PAK7
0.968873 2341 ARGINYL-TRNA SYNTHETASE-LIKE; ARGININE-TRNA LIGASE. [RefSeq;Acc:NM_020320] 0.21385 0.220720363 RARS2
0.969013 2500 "MITOCHONDRIAL PROCESSING PEPTIDASE BETA SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 3.4.24.64) (BETA-MPP) (P-52). [SWISSPROT;Acc:O75439]" 0.208649 0.215321157 PMPCB
0.969143 829 PURINE NUCLEOSIDE PHOSPHORYLASE (EC 2.4.2.1) (INOSINE PHOSPHORYLASE) (PNP). [SWISSPROT;Acc:P00491] 0.253043 0.261099755 no value
0.969328 6 CHROMATIN ACCESSIBILITY COMPLEX PROTEIN 1 (CHRAC-1) (CHRAC-15) (HUCHRAC15) (DNA POLYMERASE EPSILON SUBUNIT P15). [SWISSPROT;Acc:Q9NRG0] 0.590586 0.609273641 CHRAC1
0.970087 2465 0.210228 0.21671046 BRD9
0.971531 1723 VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 45 (H-VPS45) (HLVPS45). [SWISSPROT;Acc:Q9NRW7] 0.230384 0.237134996 VPS45
0.972163 2211 DNA MISMATCH REPAIR PROTEIN MLH1 (MUTL PROTEIN HOMOLOG 1). [SWISSPROT;Acc:P40692] 0.218789 0.225053823 MLH1
0.972411 2144 IMMATURE COLON CARCINOMA TRANSCRIPT 1 (DIGESTION SUBSTRACTION 1) (DS- 1). [SWISSPROT;Acc:Q14197] 0.221521 0.227805938 ICT1
0.973079 1439 0.23697 0.243525962 NLE1
0.973151 771 SEGMENT POLARITY PROTEIN DISHEVELLED HOMOLOG DVL-3 (DISHEVELLED-3) (DSH HOMOLOG 3). [SWISSPROT;Acc:Q92997] 0.256243 0.263312682 DVL3
0.973671 311 UBIQUITIN. [SWISSPROT;Acc:P02248] 0.287802 0.295584443 UBB
0.975402 2338 WERNER HELICASE INTERACTING PROTEIN ISOFORM 1; PUTATIVE HELICASE RUVBL; WERNER HELICASE INTERACTING PROTEIN. [RefSeq;Acc:NM_020135] 0.215454 0.220887388 WRNIP1
0.976589 2683 RETICULON PROTEIN 3 (NEUROENDOCRINE-SPECIFIC PROTEIN-LIKE 2) (NSP-LIKE PROTEIN II) (NSPLII). [SWISSPROT;Acc:O95197] 0.203468 0.208345578 RTN3
0.977987 2788 POLYPOSIS LOCUS PROTEIN 1 (TB2 PROTEIN). [SWISSPROT;Acc:Q00765] 0.195503 0.199903475 REEP5
0.979382 1994 0.22609 0.230849658 DOHH
0.981155 455 MITOCHONDRIAL GTP BINDING PROTEIN ISOFORM V. [RefSeq;Acc:NM_032620] 0.270501 0.275696501 GTPBP3

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/