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