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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measured Rank Gene Hugo description expected final
Results: HTML CSV LaTeX Showing element 1108 to 1157 of 3206 in total
measured
Rank
Hugo
description
expected
final
0.0726324 1595 CENTB2 CENTAURIN BETA 2 (CNT-B2). [SWISSPROT;Acc:Q15057] 0.302313 0.240255629
0.0726422 1175 SMAD1 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] 0.291272 0.24939644
0.0726736 1355 TTLL12 0.296523 0.245085879
1356 ZNF259 ZINC-FINGER PROTEIN ZPR1 (ZINC FINGER PROTEIN 259). [SWISSPROT;Acc:O75312]
0.0727992 3162 MYH3 "MYOSIN HEAVY CHAIN, FAST SKELETAL MUSCLE, EMBRYONIC (MUSCLE EMBRYONIC MYOSIN HEAVY CHAIN) (SMHCE). [SWISSPROT;Acc:P11055]" 1.125 0.0647104
0.0728267 3106 NEUROD4 NEUROGENIC DIFFERENTIATION FACTOR 4 (NEUROD4). [SWISSPROT;Acc:Q9HD90] 0.789676 0.09222352
0.0730211 2425 XRCC3 DNA-REPAIR PROTEIN XRCC3 (X-RAY REPAIR CROSS-COMPLEMENTING PROTEIN 3). [SWISSPROT;Acc:O43542] 0.335124 0.21789278
0.0730322 1177 ETNK1 ETHANOLAMINE KINASE (EC 2.7.1.82) (EKI). [SWISSPROT;Acc:Q9HBU6] 0.292836 0.249396249
0.0730689 1655 APEX2 APURINIC/APYRIMIDINIC ENDONUCLEASE 2; APURINIC/APYRIMIDINIC ENDONUCLEASE-LIKE 2; APEX NUCLEASE-LIKE 2. [RefSeq;Acc:NM_014481] 0.305877 0.238883277
0.0732296 1077 FANCL PHD FINGER PROTEIN 9. [RefSeq;Acc:NM_018062] 0.290291 0.252262729
0.0733796 1475 no value RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1 (P21-RAC1) (RAS-LIKE PROTEIN TC25). [SWISSPROT;Acc:P15154] 0.302004 0.24297559
0.0734189 775 TRIO TRIPLE FUNCTIONAL DOMAIN PROTEIN (PTPRF INTERACTING PROTEIN). [SWISSPROT;Acc:O75962] 0.278919 0.2632266
0.0734554 2594 UBE1C "UBIQUITIN-ACTIVATING ENZYME E1C (UBA3 HOMOLOG, YEAST); UBIQUITIN-ACTIVATING ENZYME E1C (HOMOLOGOUS TO YEAST UBA3). [RefSeq;Acc:NM_003968]" 0.345038 0.212890754
0.0735334 2953 PPP2R5E "SERINE/THREONINE PROTEIN PHOSPHATASE 2A, 56 KDA REGULATORY SUBUNIT, EPSILON ISOFORM (PP2A, B SUBUNIT, B' EPSILON ISOFORM) (PP2A, B SUBUNIT, B56 EPSILON ISOFORM) (PP2A, B SUBUNIT, PR61 EPSILON ISOFORM) (PP2A, B SUBUNIT, R5 EPSILON ISOFORM). [SWISSPR" 0.497941 0.147674925
0.0735677 1034 ATP1A3 SODIUM/POTASSIUM-TRANSPORTING ATPASE ALPHA-3 CHAIN (EC 3.6.3.9) (SODIUM PUMP 3) (NA+/K+ ATPASE 3) (ALPHA(III)). [SWISSPROT;Acc:P13637] 0.290389 0.253341897
0.0736246 2354 USF2 UPSTREAM STIMULATORY FACTOR 2 (UPSTREAM TRANSCRIPTION FACTOR 2) (FOS-INTERACTING PROTEIN) (FIP) (MAJOR LATE TRANSCRIPTION FACTOR 2). [SWISSPROT;Acc:Q15853] 0.334101 0.220366296
0.0736571 3165 MYH4 "MYOSIN HEAVY CHAIN, SKELETAL MUSCLE, FETAL (MYOSIN HEAVY CHAIN IIB) (MYHC-IIB). [SWISSPROT;Acc:Q9Y623]" 1.13826 0.06471026
0.0736608 1921 FLAD1 FAD SYNTHETASE. [RefSeq;Acc:NM_025207] 0.317545 0.231969642
0.0736761 1014 HRBL HIV-1 REV BINDING PROTEIN-LIKE; REV/REX ACTIVATION DOMAIN BINDING PROTEIN-RELATED. [RefSeq;Acc:NM_006076] 0.290228 0.253855934
0.0736775 3159 MYH8 "MYOSIN HEAVY CHAIN, SKELETAL MUSCLE, PERINATAL (MYHC-PERINATAL). [SWISSPROT;Acc:P13535]" 1.13857 0.064710558
0.0737619 2468 SDF4 45 KDA CALCIUM-BINDING PROTEIN PRECURSOR (CAB45) (STROMAL CELL-DERIVED FACTOR 4) (SDF-4). [SWISSPROT;Acc:Q9BRK5] 0.340556 0.216592572
2469 SPTBN5 "SPECTRIN BETA CHAIN, BRAIN 4 (SPECTRIN, NON-ERYTHROID BETA CHAIN 4) (BETA-V SPECTRIN) (BSPECV). [SWISSPROT;Acc:Q9NRC6]"
2470 LSM14B
0.0737653 3118 SHCBP1 LIKELY ORTHOLOG OF MOUSE SHC SH2-DOMAIN BINDING PROTEIN 1. [RefSeq;Acc:NM_024745] 0.836397 0.088194123
0.0739703 1412 RBM5 RNA-BINDING PROTEIN 5 (RNA BINDING MOTIF PROTEIN 5) (PUTATIVE TUMOR SUPPRESSOR LUCA15) (G15 PROTEIN). [SWISSPROT;Acc:P52756] 0.303151 0.244004803
0.0739754 936 no value RHO INTERACTING PROTEIN 3. [RefSeq;Acc:NM_015134] 0.28817 0.256707499
0.0739839 3164 MYH2 "MYOSIN HEAVY CHAIN, SKELETAL MUSCLE, ADULT 2 (MYOSIN HEAVY CHAIN IIA) (MYHC-IIA). [SWISSPROT;Acc:Q9UKX2]" 1.14331 0.064710271
0.0741473 3158 MYH1 "MYOSIN HEAVY CHAIN, SKELETAL MUSCLE, ADULT 1 (MYOSIN HEAVY CHAIN IIX/D) (MYHC-IIX/D). [SWISSPROT;Acc:P12882]" 1.14583 0.064710559
0.0741822 362 OSTF1 OSTEOCLAST STIMULATING FACTOR 1. [SWISSPROT;Acc:Q92882] 0.264688 0.2802628
0.0742746 1335 PPAN-P2RY11 SUPPRESSOR OF SWI4 1 HOMOLOG (SSF-1) (PETER PAN HOMOLOG). [SWISSPROT;Acc:Q9NQ55] 0.302799 0.245293412
0.0742909 1071 CTRL 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] 0.294313 0.252421402
0.0744045 2868 RPL8 60S RIBOSOMAL PROTEIN L8. [SWISSPROT;Acc:P25120] 0.393799 0.188940297
0.0744051 2910 RRN3 RNA POLYMERASE I TRANSCRIPTION FACTOR RRN3. [RefSeq;Acc:NM_018427] 0.427267 0.17414193
0.0744175 1170 TNFSF5IP1 HEPATOCELLULAR CARCINOMA SUSCEPTIBILITY PROTEIN; X 003 PROTEIN; HDCMC29P; HSPC260; LIKELY ORTHOLOG OF MOUSE CD40 LIGAND-ACTIVATED SPECIFIC TRANSCRIPT 3 (CLAST3). [RefSeq;Acc:NM_020232] 0.29839 0.249396763
0.0744186 992 IPMK INOSITOL POLYPHOSPHATE MULTIKINASE. [RefSeq;Acc:NM_152230] 0.291777 0.255053003
0.0744473 3105 NEUROD6 NEUROGENIC DIFFERENTIATION FACTOR 6 (NEUROD6) (MY051 PROTEIN). [SWISSPROT;Acc:Q96NK8] 0.807248 0.092223579
0.0745937 988 HECW1 HECT TYPE E3 UBIQUITIN LIGASE. [RefSeq;Acc:NM_015052] 0.292332 0.255167754
0.0746316 2960 no value RAL GUANINE NUCLEOTIDE DISSOCIATION STIMULATOR-LIKE 2 (RALGDS-LIKE FACTOR) (RAS-ASSOCIATED PROTEIN RAB2L). [SWISSPROT;Acc:O15211] 0.510598 0.146165085
0.0746521 1041 RAD17 RAD17 HOMOLOG ISOFORM 1; RAD17-LIKE PROTEIN; CELL CYCLE CHECKPOINT PROTEIN (RAD17); RF-C ACTIVATOR 1 HOMOLOG. [RefSeq;Acc:NM_002873] 0.294737 0.253283775
0.0746561 898 WTAP WILMS' TUMOR 1-ASSOCIATING PROTEIN (WT1-ASSOCIATED PROTEIN). [SWISSPROT;Acc:Q15007] 0.287738 0.259458605
0.0746708 1399 LSG1 0.305803 0.244179423
0.0749538 3104 CHD3 CHROMODOMAIN HELICASE-DNA-BINDING PROTEIN 3 (CHD-3) (MI-2 AUTOANTIGEN 240 KDA PROTEIN) (MI2-ALPHA). [SWISSPROT;Acc:Q12873] 0.81274 0.092223589
0.0750119 2449 PGLS 6-PHOSPHOGLUCONOLACTONASE (EC 3.1.1.31) (6PGL). [SWISSPROT;Acc:O95336] 0.345603 0.217046438
0.0750554 718 HYAL3 INTERFERON-RELATED DEVELOPMENTAL REGULATOR 2 (SKMC15 PROTEIN). [SWISSPROT;Acc:Q12894] 0.28346 0.264783038
0.0750779 317 SRP9 SIGNAL RECOGNITION PARTICLE 9 KDA PROTEIN (SRP9). [SWISSPROT;Acc:P49458] 0.257511 0.291552206
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]" 0.354697 0.211948508
0.0752577 3102 NEUROD1 NEUROGENIC DIFFERENTIATION FACTOR 1 (NEUROD1) (NEUROD). [SWISSPROT;Acc:Q13562] 0.816035 0.092223618
0.0752905 2190 YBX1 NUCLEASE SENSITIVE ELEMENT BINDING PROTEIN 1 (Y BOX BINDING PROTEIN-1) (Y-BOX TRANSCRIPTION FACTOR) (YB-1) (CCAAT-BINDING TRANSCRIPTION FACTOR I SUBUNIT A) (CBF-A) (ENHANCER FACTOR I SUBUNIT A) (EFI-A) (DNA-BINDING PROTEIN B) (DBPB). [SWISSPROT;Acc 0.332615 0.226359304
0.0753031 28 no value DOK-LIKE PROTEIN. [RefSeq;Acc:NM_024872] 0.176719 0.426117735
0.0753291 1467 CPOX "COPROPORPHYRINOGEN III OXIDASE, MITOCHONDRIAL PRECURSOR (EC 1.3.3.3) (COPROPORPHYRINOGENASE) (COPROGEN OXIDASE) (COX). [SWISSPROT;Acc:P36551]" 0.309975 0.243016695

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/