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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expected Gene measured Rank Hugo description final
Results: HTML CSV LaTeX Showing element 1152 to 1201 of 3206 in total
expected
measured
Rank
Hugo
description
final
0.351165 0.0948257 582 no value "SERINE/THREONINE PROTEIN PHOSPHATASE 2A, 55 KDA REGULATORY SUBUNIT B, ALPHA ISOFORM (PP2A, SUBUNIT B, B-ALPHA ISOFORM) (PP2A, SUBUNIT B, B55-ALPHA ISOFORM) (PP2A, SUBUNIT B, PR55-ALPHA ISOFORM) (PP2A, SUBUNIT B, R2-ALPHA ISOFORM). [SWISSPROT;Acc:Q0" 0.270031751
0.35143 0.147881 42 CUTL2 HOMEOBOX PROTEIN CUX-2 (CUT-LIKE 2) (FRAGMENT). [SWISSPROT;Acc:O14529] 0.420797883
0.351521 0.10034 327 MAP2K4 DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 4 (EC 2.7.1.-) (MAP KINASE KINASE 4) (JNK ACTIVATING KINASE 1) (C-JUN N- TERMINAL KINASE KINASE 1) (JNKK) (SAPK/ERK KINASE 1) (SEK1). [SWISSPROT;Acc:P45985] 0.285445251
0.352238 0.0795635 2197 PPP1R13B "PROTEIN PHOSPHATASE 1, REGULATORY (INHIBITOR) SUBUNIT 13B; APOPTOSIS-STIMULATING PROTEIN OF P53, 1. [RefSeq;Acc:NM_015316]" 0.225879945
0.352242 0.0951162 583 PPP2R2D UNCHARACTERIZED HEMATOPOIETIC STEM/PROGENITOR CELLS PROTEIN MDS026. [SPTREMBL;Acc:Q9NZ48] 0.270030831
0.352603 0.0444453 3004 no value ENDO-BETA-N-ACETYLGLUCOSAMINIDASE. [RefSeq;Acc:NM_022759] 0.126049126
0.352624 0.0775947 2370 WARS2 "TRYPTOPHANYL-TRNA SYNTHETASE, MITOCHONDRIAL PRECURSOR (EC 6.1.1.2) (TRYPTOPHAN--TRNA LIGASE) (TRPRS) ((MT)TRPRS). [SWISSPROT;Acc:Q9UGM6]" 0.220049401
2371 WARS TRYPTOPHANYL-TRNA SYNTHETASE (EC 6.1.1.2) (TRYPTOPHAN--TRNA LIGASE) (TRPRS) (IFP53) (HWRS). [SWISSPROT;Acc:P23381]
0.353426 0.070265 2800 ATXN2L ATAXIN 2 RELATED PROTEIN ISOFORM A; ATAXIN-2 DOMAIN PROTEIN. [RefSeq;Acc:NM_007245] 0.198811067
0.353554 0.0968147 509 SNUPN "RNA, U TRANSPORTER 1; SNURPORTIN-1. [RefSeq;Acc:NM_005701]" 0.273832852
0.353982 0.0365299 3070 C1orf156 0.103197055
0.354268 0.102544 321 KY 0.289453182
0.354697 0.0751775 2607 HMGCS1 "HYDROXYMETHYLGLUTARYL-COA SYNTHASE, CYTOPLASMIC (EC 2.3.3.10) (HMG-COA SYNTHASE) (3-HYDROXY-3-METHYLGLUTARYL COENZYME A SYNTHASE). [SWISSPROT;Acc:Q01581]" 0.211948508
0.355321 0.086609 1431 no value ENTHOPROTIN; EPSIN 4; CLATHRIN INTERACTING PROTEIN LOCALIZED IN THE TRANS-GOLGI REGION. [RefSeq;Acc:NM_014666] 0.24374861
0.355368 0.0883685 1187 FREQ NEURONAL CALCIUM SENSOR 1 (NCS-1) (FREQUENIN HOMOLOG) (FREQUENIN-LIKE PROTEIN) (FREQUENIN-LIKE UBIQUITOUS PROTEIN). [SWISSPROT;Acc:P36610] 0.248667578
0.355998 0.0954996 629 CYP4X1 LIKELY ORTHOLOG OF RAT CYTOCHROME P450 4X1. [RefSeq;Acc:NM_178033] 0.26825881
0.356213 0.078258 2384 ANAPC10 ANAPHASE-PROMOTING COMPLEX SUBUNIT 10; ANAPHASE-PROMOTING COMPLEX 10. [RefSeq;Acc:NM_014885] 0.219694396
0.356254 0.0961987 584 PPP2R2B "SERINE/THREONINE PROTEIN PHOSPHATASE 2A, 55 KDA REGULATORY SUBUNIT B, BETA ISOFORM (PP2A, SUBUNIT B, B-BETA ISOFORM) (PP2A, SUBUNIT B, B55- BETA ISOFORM) (PP2A, SUBUNIT B, PR55-BETA ISOFORM) (PP2A, SUBUNIT B, R2-BETA ISOFORM). [SWISSPROT;Acc:Q00005" 0.270028407
0.356265 0.0721926 2758 SAPS2 0.202637363
0.356373 0.0958474 608 LANCL2 LANC LANTIBIOTIC SYNTHETASE COMPONENT C-LIKE 2; TESTIS-SPECIFIC ADRIAMYCIN SENSITIVITY PROTEIN; LANC (BACTERIAL LANTIBIOTIC SYNTHETASE COMPONENT C)-LIKE 2; G PROTEIN-COUPLED RECEPTOR 69B. [RefSeq;Acc:NM_018697] 0.268952474
0.356562 0.0993399 393 TIMM22 MITOCHONDRIAL IMPORT INNER MEMBRANE TRANSLOCASE SUBUNIT TIM22. [SWISSPROT;Acc:Q9Y584] 0.278604843
394 ATPAF2 ATP SYNTHASE MITOCHONDRIAL F1 COMPLEX ASSEMBLY FACTOR 2. [RefSeq;Acc:NM_145691]
395 UQCRB UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 14 KDA PROTEIN (EC 1.10.2.2) (COMPLEX III SUBUNIT VI) (QP-C). [SWISSPROT;Acc:P14927]
0.356578 0.0824177 1972 POLR1E RNA POLYMERASE I ASSOCIATED FACTOR 53. [RefSeq;Acc:NM_022490] 0.231135123
0.356839 0.120377 177 REV1 REV1-LIKE; REV1 PROTEIN; REV1 (YEAST HOMOLOG)- LIKE. [RefSeq;Acc:NM_016316] 0.337342611
0.35711 0.0828779 1913 no value HISTONE H4. [SWISSPROT;Acc:P02304] 0.232079471
0.358007 0.0960386 627 CYP4B1 CYTOCHROME P450 4B1 (EC 1.14.14.1) (CYPIVB1) (P450-HP). [SWISSPROT;Acc:P13584] 0.268259001
0.358823 0.0811054 2193 APEX1 DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE (EC 4.2.99.18) (AP ENDONUCLEASE 1) (APEX NUCLEASE) (APEN) (REF-1 PROTEIN). [SWISSPROT;Acc:P27695] 0.226031776
0.359971 0.116127 194 MXD1 MAD PROTEIN (MAX DIMERIZER). [SWISSPROT;Acc:Q05195] 0.322600987
0.360019 0.0766446 2599 ALAS2 "5-AMINOLEVULINIC ACID SYNTHASE, ERYTHROID-SPECIFIC, MITOCHONDRIAL PRECURSOR (EC 2.3.1.37) (DELTA-AMINOLEVULINATE SYNTHASE) (DELTA-ALA SYNTHETASE) (ALAS-E). [SWISSPROT;Acc:P22557]" 0.212890431
0.361827 0.0838403 1932 PUF60 FUSE-BINDING PROTEIN-INTERACTING REPRESSOR ISOFORM B; SIAH BINDING PROTEIN 1; PYRIMIDINE TRACT BINDING SPLICING FACTOR; RO RIBONUCLEOPROTEIN-BINDING PROTEIN 1; POLY-U BINDING SPLICING FACTOR PUF60. [RefSeq;Acc:NM_014281] 0.231713775
0.362026 0.0899489 1198 STX6 SYNTAXIN 6. [SWISSPROT;Acc:O43752] 0.248459779
0.362464 0.0900162 1203 FAM40B 0.248345215
0.362904 0.101036 400 GTF2B TRANSCRIPTION INITIATION FACTOR IIB (GENERAL TRANSCRIPTION FACTOR TFIIB) (S300-II). [SWISSPROT;Acc:Q00403] 0.278409717
0.363171 0.11305 256 NOLA1 "NUCLEOLAR PROTEIN FAMILY A, MEMBER 1; GAR1 PROTEIN. [RefSeq;Acc:NM_018983]" 0.311285868
0.363712 0.0829182 2133 HNRPUL1 E1B-55KDA-ASSOCIATED PROTEIN 5 ISOFORM A. [RefSeq;Acc:NM_007040] 0.227977631
0.363797 0.0861167 1751 no value VACUOLAR ATP SYNTHASE SUBUNIT G 2 (EC 3.6.3.14) (V-ATPASE G SUBUNIT 2) (VACUOLAR PROTON PUMP G SUBUNIT 2) (V-ATPASE 13 KDA SUBUNIT 2). [SWISSPROT;Acc:O95670] 0.236716356
0.363819 0.0761231 2667 MAFF TRANSCRIPTION FACTOR MAFF (V-MAF MUSCULOAPONEUROTIC FIBROSARCOMA ONCOGENE HOMOLOG F) (U-MAF). [SWISSPROT;Acc:Q9ULX9] 0.209233438
0.364414 0.077662 2585 RHCG RH TYPE C GLYCOPROTEIN. [RefSeq;Acc:NM_016321] 0.213114754
0.364571 0.0840355 2021 no value "LON PROTEASE HOMOLOG, MITOCHONDRIAL PRECURSOR (EC 3.4.21.-) (LON PROTEASE-LIKE PROTEIN) (LONP) (LONHS). [SWISSPROT;Acc:P36776]" 0.230505169
0.36491 0.0884483 1513 ATPBD4 0.242383875
0.365289 0.0890817 1428 MAPRE3 MICROTUBULE-ASSOCIATED PROTEIN RP/EB FAMILY MEMBER 3 (PROTEIN EB3). [SWISSPROT;Acc:Q9UPY8] 0.243866363
0.365399 0.0927584 1019 no value INTERSECTIN 1 (SH3 DOMAIN-CONTAINING PROTEIN 1A) (SH3P17). [SWISSPROT;Acc:Q15811] 0.253855101
0.365592 0.0699506 2851 PPP1R7 "PROTEIN PHOSPHATASE 1, REGULATORY SUBUNIT 7; SDS22. [RefSeq;Acc:NM_002712]" 0.19133515
0.365653 0.0841705 2035 DARS2 0.230192286
0.366045 0.0801834 2401 no value WILLIAMS-BEUREN SYNDROME CRITICAL REGION PROTEIN 20 COPY B. [RefSeq;Acc:NM_145645] 0.219053395
0.366305 0.0391008 3042 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-7 SUBUNIT. [SWISSPROT;Acc:O60262] 0.106743834
3043 GNG12 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-12 SUBUNIT. [SWISSPROT;Acc:Q9UBI6]
0.367477 0.0978055 675 NSFL1C P47 PROTEIN ISOFORM A. [RefSeq;Acc:NM_016143] 0.266154072
0.36752 0.0996239 544 BRDT TESTIS-SPECIFIC BROMODOMAIN PROTEIN. [RefSeq;Acc:NM_001726] 0.27107069

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/