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:
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expected Rank Gene measured description Hugo final
Results: HTML CSV LaTeX Showing element 952 to 1001 of 3206 in total
expected
Rank
measured
description
Hugo
final
0.285651 1536 0.0691225 "5-FORMYLTETRAHYDROFOLATE CYCLO-LIGASE (EC 6.3.3.2) (5,10-METHENYL- TETRAHYDROFOLATE SYNTHETASE) (METHENYL-THF SYNTHETASE) (MTHFS). [SWISSPROT;Acc:P49914]" MTHFS 0.241982349
0.285702 2135 0.0651336 HETEROGENOUS NUCLEAR RIBONUCLEOPROTEIN U (HNRNP U) (SCAFFOLD ATTACHMENT FACTOR A) (SAF-A). [SWISSPROT;Acc:Q00839] HNRNPU 0.227977403
0.285736 2890 0.050962 SPTY2D1 0.178353445
0.286165 2102 0.0653467 INTS8 0.228353223
0.286244 2103 0.0653647 GON4L 0.228353083
2104 "PROTEIN KINASE C, EPSILON TYPE (EC 2.7.1.-) (NPKC-EPSILON). [SWISSPROT;Acc:Q02156]" PRKCE
0.28704 539 0.0778103 SRBD1 0.271078247
0.287738 898 0.0746561 WILMS' TUMOR 1-ASSOCIATING PROTEIN (WT1-ASSOCIATED PROTEIN). [SWISSPROT;Acc:Q15007] WTAP 0.259458605
0.287741 1448 0.0700456 BASIC PROLINE-RICH PEPTIDE P-E (IB-9). [SWISSPROT;Acc:P02811] no value 0.243432809
0.287777 2799 0.0572133 "ATAXIN 2; OLIVOPONTOCEREBELLAR ATAXIA 2, AUTOSOMAL DOMINANT. [RefSeq;Acc:NM_002973]" 0.198811232
0.28817 936 0.0739754 RHO INTERACTING PROTEIN 3. [RefSeq;Acc:NM_015134] 0.256707499
0.288355 1179 0.0718676 FAM58A 0.249233063
0.289339 651 0.0774957 DAZ ASSOCIATED PROTEIN 1 ISOFORM B; DELETED IN AZOOSPERMIA ASSOCIATED PROTEIN 1. [RefSeq;Acc:NM_018959] DAZAP1 0.267837035
0.289906 2247 0.0647928 TRANSPORTIN-SR; IMPORTIN 12. [RefSeq;Acc:NM_012470] TNPO3 0.223495892
0.289996 1153 0.0724168 SPROUTY HOMOLOG 2 (SPRY-2). [SWISSPROT;Acc:O43597] SPRY2 0.249716548
0.290115 2565 0.061947 TETRATRICOPEPTIDE REPEAT PROTEIN 4 (MY044 PROTEIN). [SWISSPROT;Acc:O95801] no value 0.213525671
0.290193 2885 0.0532406 PROTEIN KINASE NYD-SP25. [RefSeq;Acc:NM_033516] TPD52L3 0.183466176
0.290228 1014 0.0736761 HIV-1 REV BINDING PROTEIN-LIKE; REV/REX ACTIVATION DOMAIN BINDING PROTEIN-RELATED. [RefSeq;Acc:NM_006076] HRBL 0.253855934
0.29029 199 0.0936195 MAX DIMERIZATION PROTEIN 3; LIKELY ORTHOLOG OF MOUSE MAX DIMERIZATION PROTEIN 3. [RefSeq;Acc:NM_031300] RAB24 0.322503359
0.290291 1077 0.0732296 PHD FINGER PROTEIN 9. [RefSeq;Acc:NM_018062] FANCL 0.252262729
0.290389 1034 0.0735677 SODIUM/POTASSIUM-TRANSPORTING ATPASE ALPHA-3 CHAIN (EC 3.6.3.9) (SODIUM PUMP 3) (NA+/K+ ATPASE 3) (ALPHA(III)). [SWISSPROT;Acc:P13637] ATP1A3 0.253341897
0.290417 2349 0.0640044 PIH1D2 0.220387925
0.290783 890 0.0755679 TRANSCRIPTION FACTOR IIIA (FACTOR A) (TFIIIA). [SWISSPROT;Acc:Q92664] GTF3A 0.259877297
0.291157 1568 0.070166 MITOCHONDRIAL 28S RIBOSOMAL PROTEIN S22 (S22MT) (MRP-S22) (GK002). [SWISSPROT;Acc:P82650] MRPS22 0.240990256
0.291272 1175 0.0726422 MOTHERS AGAINST DECAPENTAPLEGIC HOMOLOG 1 (SMAD 1) (MOTHERS AGAINST DPP HOMOLOG 1) (MAD-RELATED PROTEIN 1) (TRANSFORMING GROWTH FACTOR- BETA SIGNALING PROTEIN-1) (BSP-1) (HSMAD1) (JV4-1). [SWISSPROT;Acc:Q15797] SMAD1 0.24939644
0.291643 748 0.0771388 PUTATIVE RNA-BINDING PROTEIN 7 (RNA BINDING MOTIF PROTEIN 7). [SWISSPROT;Acc:Q9Y580] RBM7 0.264497348
751 0.0771387 C15orf44 0.264497005
0.291777 992 0.0744186 INOSITOL POLYPHOSPHATE MULTIKINASE. [RefSeq;Acc:NM_152230] IPMK 0.255053003
0.291858 496 0.0800469 MITOCHONDRIAL RIBOSOMAL PROTEIN L18. [RefSeq;Acc:NM_014161] MRPL18 0.274266595
0.29203 2423 0.0637011 TRANSCRIPTION ELONGATION FACTOR A PROTEIN 1 (TRANSCRIPTION ELONGATION FACTOR S-II PROTEIN 1) (TRANSCRIPTION ELONGATION FACTOR TFIIS.O). [SWISSPROT;Acc:P23193] no value 0.218132041
0.292225 1604 0.0701119 60S RIBOSOMAL PROTEIN L28. [SWISSPROT;Acc:P46779] RPL28 0.239924373
0.292332 988 0.0745937 HECT TYPE E3 UBIQUITIN LIGASE. [RefSeq;Acc:NM_015052] HECW1 0.255167754
0.292836 1177 0.0730322 ETHANOLAMINE KINASE (EC 2.7.1.82) (EKI). [SWISSPROT;Acc:Q9HBU6] ETNK1 0.249396249
0.293231 3049 0.0312821 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-5 LIKE SUBUNIT. [SWISSPROT;Acc:Q9Y3K8] no value 0.10668074
0.293943 2919 0.0498692 HIRA-INTERACTING PROTEIN 5 (CGI-33). [SWISSPROT;Acc:Q9UMS0] NFU1 0.169656022
0.294313 1071 0.0742909 PROTEASOME SUBUNIT BETA TYPE 10 PRECURSOR (EC 3.4.25.1) (PROTEASOME MECL-1) (MACROPAIN SUBUNIT MECL-1) (MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT MECL-1). [SWISSPROT;Acc:P40306] CTRL 0.252421402
0.294737 1041 0.0746521 RAD17 HOMOLOG ISOFORM 1; RAD17-LIKE PROTEIN; CELL CYCLE CHECKPOINT PROTEIN (RAD17); RF-C ACTIVATOR 1 HOMOLOG. [RefSeq;Acc:NM_002873] RAD17 0.253283775
0.295201 1866 0.0688073 DIPHOSPHOMEVALONATE DECARBOXYLASE (EC 4.1.1.33) (MEVALONATE PYROPHOSPHATE DECARBOXYLASE) (MEVALONATE (DIPHOSPHO)DECARBOXYLASE). [SWISSPROT;Acc:P53602] MVD 0.23308627
0.295267 2583 0.062927 RHESUS BLOOD GROUP-ASSOCIATED GLYCOPROTEIN (ERYTHROCYTE PLASMA MEMBRANE 50 KDA GLYCOPROTEIN) (RH50A). [SWISSPROT;Acc:Q02094] RHAG 0.213118974
0.29571 2570 0.06311 HISTONE DEACETYLASE 9 (HD9) (HD7B) (HD7). [SWISSPROT;Acc:Q9UKV0] HDAC9 0.213418552
0.295729 87 0.113929 PLEKHG6 0.38524798
0.296516 892 0.0770577 TMEM53 0.259877039
0.296523 1355 0.0726736 TTLL12 0.245085879
1356 ZINC-FINGER PROTEIN ZPR1 (ZINC FINGER PROTEIN 259). [SWISSPROT;Acc:O75312] ZNF259
0.296552 1450 0.0721789 PROBABLE CALCIUM-TRANSPORTING ATPASE KIAA0703 (EC 3.6.3.8). [SWISSPROT;Acc:O75185] ATP2C2 0.243393739
0.296607 196 0.0956601 MAX-INTERACTING TRANSCRIPTIONAL REPRESSOR MAD4 (MAX-ASSOCIATED PROTEIN 4) (MAX DIMERIZATION PROTEIN 4). [SWISSPROT;Acc:Q14582] MXD4 0.322514641
0.29681 3048 0.031665 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-10 SUBUNIT. [SWISSPROT;Acc:P50151] GNG10 0.106684411
0.297409 726 0.0787172 NARDILYSIN PRECURSOR (EC 3.4.24.61) (N-ARGININE DIBASIC CONVERTASE) (NRD CONVERTASE) (NRD-C). [SWISSPROT;Acc:O43847] NRD1 0.26467659
0.297814 2596 0.0634018 "5-AMINOLEVULINIC ACID SYNTHASE, NONSPECIFIC, MITOCHONDRIAL PRECURSOR (EC 2.3.1.37) (DELTA-AMINOLEVULINATE SYNTHASE) (DELTA-ALA SYNTHETASE) (ALAS-H). [SWISSPROT;Acc:P13196]" ALAS1 0.212890596
0.297931 2494 0.0641898 METHIONYL-TRNA SYNTHETASE (EC 6.1.1.10) (METHIONINE--TRNA LIGASE) (METRS). [SWISSPROT;Acc:P56192] MARS 0.2154519

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/