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.


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Hugo expected measured Gene Rank description final
Results: HTML CSV LaTeX Showing element 51 to 100 of 3206 in total
Hugo  : no value
expected
measured
Rank
description
final
0.146383 0.0314375 2528 KERATIN ASSOCIATED PROTEIN 4-2; KERATIN ASSOCIATED PROTEIN 4.2. [RefSeq;Acc:NM_033062] 0.21476196
0.1468 0.0378274 924 FATTY ACID DESATURASE 1; LINOLEOYL-COA DESATURASE (DELTA-6-DESATURASE)-LIKE 1; DELTA-5 DESATURASE; DELTA-5 FATTY ACID DESATURASE. [RefSeq;Acc:NM_013402] 0.257679837
0.14739 0.0399967 534 SMALL NUCLEAR RIBONUCLEOPROTEIN E (SNRNP-E) (SM PROTEIN E) (SM-E) (SME). [SWISSPROT;Acc:P08578] 0.271366443
0.150941 0.0364961 1550 ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 7 (ADP-RIBOSYLATION FACTOR-LIKE PROTEIN LAK). [SWISSPROT;Acc:P56559] 0.241790501
0.151058 0.042516 357 0.281454805
0.15167 0.036822 1495 IMPORTIN 7; RAN-BINDING PROTEIN 7. [RefSeq;Acc:NM_006391] 0.242777082
0.1519 0.0313747 2723 0.206548387
0.15268 0.039713 878 PUTATIVE PRE-MRNA SPLICING FACTOR RNA HELICASE (ATP-DEPENDENT RNA HELICASE #3) (DEAH-BOX PROTEIN 16). [SWISSPROT;Acc:O60231] 0.260106104
0.154523 0.037776 1386 BA271B5.1 (SIMILAR TO RIBOSOMAL PROTEIN S7). [SPTREMBL;Acc:Q9H1S9] 0.244468461
0.154846 0.0415188 644 0.268129626
0.155406 0.0406169 813 DEAD-BOX PROTEIN ABSTRAKT HOMOLOG. [SWISSPROT;Acc:Q9UJV9] 0.261359922
0.155451 0.0333153 2555 METABOTROPIC GLUTAMATE RECEPTOR 3 PRECURSOR (MGLUR3). [SWISSPROT;Acc:Q14832] 0.214313835
0.155989 0.0384625 1273 KAPPA B-RAS 1. [RefSeq;Acc:NM_020345] 0.246571874
0.156754 0.0397033 1040 "ATP-DEPENDENT DNA HELICASE II, 70 KDA SUBUNIT (LUPUS KU AUTOANTIGEN PROTEIN P70) (KU70) (70 KDA SUBUNIT OF KU ANTIGEN) (THYROID-LUPUS AUTOANTIGEN) (TLAA) (CTC BOX BINDING FACTOR 75 KDA SUBUNIT) (CTCBF) (CTC75). [SWISSPROT;Acc:P12956]" 0.253284127
0.157168 0.06383 78 ASPARTATE BETA-HYDROXYLASE ISOFORM B; JUNCTIN ISOFORM 1; JUNCTATE; ASPARTYL/ASPARAGINYL-BETA-HYDROXYLASE; PEPTIDE-ASPARTATE BETA-DIOXYGENASE; HUMBUG. [RefSeq;Acc:NM_032468] 0.406125929
0.157329 0.0410035 847 0.260622644
0.158546 0.038631 1433 RNA HELICASE-RELATED PROTEIN; RNA HELICASE-LIKE PROTEIN; SF3B125 DEAD-BOX PROTEIN. [RefSeq;Acc:NM_007372] 0.243657992
0.159817 0.0424293 698 15 KDA SELENOPROTEIN PRECURSOR. [SWISSPROT;Acc:O60613] 0.265486775
0.163636 0.0436424 672 0.266704148
0.163741 0.038359 1823 0.234266311
0.163824 0.0394801 1567 NEFA-INTERACTING NUCLEAR PROTEIN NIP30. [RefSeq;Acc:NM_024946] 0.240990941
0.165297 0.0312313 2866 HEPATOMA-DERIVED GROWTH FACTOR-RELATED PROTEIN 2. [RefSeq;Acc:NM_032631] 0.188940513
0.165745 0.0588477 127 ERO1-LIKE. [RefSeq;Acc:NM_014584] 0.355049624
0.16661 0.0561104 180 TRINUCLEOTIDE REPEAT CONTAINING 15. [RefSeq;Acc:NM_015575] 0.336776904
0.170278 0.0503334 308 MITOCHONDRIAL 28S RIBOSOMAL PROTEIN S32 (S32MT) (MRP-S32) (PTD007) (HSPC204). [SWISSPROT;Acc:Q9Y6G3] 0.295595438
0.171674 0.0483186 356 0.281455549
0.173966 0.0415385 1668 MESODERM INDUCTION EARLY RESPONSE 1. [RefSeq;Acc:NM_020948] 0.238773668
0.176719 0.0753031 28 DOK-LIKE PROTEIN. [RefSeq;Acc:NM_024872] 0.426117735
0.178175 0.0382656 2526 KERATIN ASSOCIATED PROTEIN 4-14; KERATIN ASSOCIATED PROTEIN 4.14. [RefSeq;Acc:NM_033059] 0.214764136
0.178458 0.0383264 2525 KERATIN ASSOCIATED PROTEIN 4.9 (FRAGMENT). [SPTREMBL;Acc:Q9BYQ8] 0.214764258
0.178742 0.0388043 2441 MYO-INOSITOL 1-PHOSPHATE SYNTHASE A1. [RefSeq;Acc:NM_016368] 0.217096709
0.180015 0.0555455 261 APOBEC-1 COMPLEMENTATION FACTOR ISOFORM 1; APOBEC-1 STIMULATING PROTEIN; APO-B RNA EDITING PROTEIN. [RefSeq;Acc:NM_014576] 0.308560398
0.180231 0.0856348 17 0.475139127
0.180466 0.0556846 262 0.308560061
0.181705 0.0560669 263 RNA-BINDING PROTEIN. [RefSeq;Acc:NM_019027] 0.308560029
0.188688 0.0405241 2507 ALPHA-PARVIN (CALPONIN-LIKE INTEGRIN-LINKED KINASE BINDING PROTEIN) (CH-ILKBP). [SWISSPROT;Acc:Q9NVD7] 0.214767765
0.188793 0.044904 1700 0.237847802
0.19065 0.0423362 2308 DJ718P11.1.2 (NOVEL CLASS II AMINOTRANSFERASE SIMILAR TO SERINE PALMOTYLTRANSFERASE (ISOFORM 2)) (FRAGMENT). [SPTREMBL;Acc:Q9UGB5] 0.222062418
0.196598 0.0371369 2872 0.188897649
0.196899 0.0372023 2862 CGI-142; HEPATOMA-DERIVED GROWTH FACTOR 2. [RefSeq;Acc:NM_016073] 0.188941031
0.19742 0.042399 2521 KERATIN ASSOCIATED PROTEIN 4-12; KERATIN ASSOCIATED PROTEIN 4.12. [RefSeq;Acc:NM_031854] 0.214765475
0.203458 0.0436957 2522 0.21476521
0.204356 0.0488461 1642 0.239024545
0.209553 0.0250043 3024 SYNBINDIN (TRS23 HOMOLOG) (HEMATOPOIETIC STEM/PROGENITOR CELL PROTEIN 172) (HSPC172) (PTD009) (CGI-104). [SWISSPROT;Acc:Q9Y296] 0.119322081
0.210535 0.050323 1646 MYOSIN VI. [SWISSPROT;Acc:Q9UM54] 0.23902439
0.216002 0.0568574 777 HUNTINGTIN-ASSOCIATED PROTEIN-INTERACTING PROTEIN (DUO PROTEIN). [SWISSPROT;Acc:O60229] 0.263226266
0.217847 0.0454701 2677 GALACTOSE-1-PHOSPHATE URIDYLYLTRANSFERASE (EC 2.7.7.12) (GAL-1-P URIDYLYLTRANSFERASE) (UDP-GLUCOSE--HEXOSE-1-PHOSPHATE URIDYLYLTRANSFERASE). [SWISSPROT;Acc:P07902] 0.208724931
0.221164 0.0308655 2978 HOMEOBOX PROTEIN HOX-C6 (HOX-3C) (HHO.C8) (CP25). [SWISSPROT;Acc:P09630] 0.139559332
0.222701 0.0310799 2983 HOMEOBOX PROTEIN HOX-A4 (HOX-1D) (HOX-1.4). [SWISSPROT;Acc:Q00056] 0.13955887
0.223379 0.0431276 2835 "SUCCINATE DEHYDROGENASE [UBIQUINONE] CYTOCHROME B SMALL SUBUNIT, MITOCHONDRIAL PRECURSOR (CYBS) (SUCCINATE-UBIQUINONE REDUCTASE MEMBRANE ANCHOR SUBUNIT) (QPS2) (CII-4) (SUCCINATE DEHYDROGENASE COMPLEX SUBUNIT D) (SUCCINATE-UBIQUINONE OXIDOREDUCTASE CYTOCH" 0.193069178

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/