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 Hugo Gene Rank expected description final
Results: HTML CSV LaTeX Showing element 2858 to 2907 of 3206 in total
measured
Hugo
Rank
expected
description
final
0.481793 no value 1264 1.95026 LAMIN B2. [SWISSPROT;Acc:Q03252] 0.247040395
0.48192 KCTD2 1679 2.02294 0.23822753
0.482398 no value 313 1.63545 BA395L14.12 (NOVEL PROTEIN SIMILAR TO SMALL NUCLEAR RIBONUCLEOPROTEIN POLYPEPTIDE A' (SNRPA1)). [SPTREMBL;Acc:Q9NU36] 0.294963466
0.482651 MPI 826 1.84728 MANNOSE-6-PHOSPHATE ISOMERASE (EC 5.3.1.8) (PHOSPHOMANNOSE ISOMERASE) (PMI) (PHOSPHOHEXOMUTASE). [SWISSPROT;Acc:P34949] 0.26127658
0.483254 C14orf4 579 1.78896 0.270131249
0.483455 FOXA3 473 1.76198 HEPATOCYTE NUCLEAR FACTOR 3-GAMMA (HNF-3G) (FORKHEAD BOX PROTEIN A3) (FORK HEAD-RELATED PROTEIN FKH H3). [SWISSPROT;Acc:P55318] 0.274381662
0.485259 UMPS 2161 2.13541 URIDINE 5'-MONOPHOSPHATE SYNTHASE (UMP SYNTHASE) [INCLUDES: OROTATE PHOSPHORIBOSYLTRANSFERASE (EC 2.4.2.10) (OPRTASE); OROTIDINE 5'- PHOSPHATE DECARBOXYLASE (EC 4.1.1.23) (OMPDECASE)]. [SWISSPROT;Acc:P11172] 0.227243948
0.485772 RSL1D1 1505 2.00168 PBK1 PROTEIN. [SPTREMBL;Acc:O76021] 0.242682147
0.485913 MRPS12 1985 2.1041 "28S RIBOSOMAL PROTEIN S12, MITOCHONDRIAL PRECURSOR (MPR-S12) (MT- RPS12). [SWISSPROT;Acc:O15235]" 0.230936267
RPS23 1986 40S RIBOSOMAL PROTEIN S23. [SWISSPROT;Acc:P39028]
0.486534 SNRPA1 312 1.64947 U2 SMALL NUCLEAR RIBONUCLEOPROTEIN A' (U2 SNRNP-A'). [SWISSPROT;Acc:P09661] 0.294963837
0.487065 KPNA4 167 1.42504 IMPORTIN ALPHA-4 SUBUNIT (KARYOPHERIN ALPHA-4 SUBUNIT) (QIP1 PROTEIN). [SWISSPROT;Acc:O00629] 0.341790406
0.48801 PNKD 2587 2.292 MYOFIBRILLOGENESIS REGULATOR 1; TRANS-ACTIVATED BY HEPATITIS C VIRUS CORE PROTEIN 2; LIKELY ORTHOLOG OF MOUSE BRAIN PROTEIN 17. [RefSeq;Acc:NM_022572] 0.212918848
0.489705 NDUFS4 5 0.74385 "NADH-UBIQUINONE OXIDOREDUCTASE 18 KDA SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 1.6.5.3) (EC 1.6.99.3) (COMPLEX I-18 KDA) (CI-18 KDA) (COMPLEX I- AQDQ) (CI-AQDQ). [SWISSPROT;Acc:O43181]" 0.658338375
0.489733 PHGDH 2418 2.24292 D-3-PHOSPHOGLYCERATE DEHYDROGENASE (EC 1.1.1.95) (3-PGDH). [SWISSPROT;Acc:O43175] 0.218346174
0.491713 HTRA4 2578 2.30709 PROBABLE SERINE PROTEASE HTRA4 PRECURSOR (EC 3.4.21.-). [SWISSPROT;Acc:P83105] 0.213131261
0.492676 no value 772 1.87133 CASEIN KINASE II BETA CHAIN (CK II) (PHOSVITIN) (G5A). [SWISSPROT;Acc:P13862] 0.263275852
0.494361 NME2 2010 2.14316 NUCLEOSIDE DIPHOSPHATE KINASE A (EC 2.7.4.6) (NDK A) (NDP KINASE A) (TUMOR METASTATIC PROCESS-ASSOCIATED PROTEIN) (METASTASIS INHIBITION FACTOR NM23) (NM23-H1). [SWISSPROT;Acc:P15531] 0.230669199
0.494954 SHMT1 1926 2.13521 "SERINE HYDROXYMETHYLTRANSFERASE, CYTOSOLIC (EC 2.1.2.1) (SERINE METHYLASE) (GLYCINE HYDROXYMETHYLTRANSFERASE) (SHMT). [SWISSPROT;Acc:P34896]" 0.231805771
0.495014 LGTN 1920 2.13396 LIGATIN (HEPATOCELLULAR CARCINOMA-ASSOCIATED ANTIGEN 56). [SWISSPROT;Acc:P41214] 0.231969671
0.495507 ELAVL4 572 1.83073 ELAV-LIKE PROTEIN 4 (PARANEOPLASTIC ENCEPHALOMYELITIS ANTIGEN HUD) (HU-ANTIGEN D). [SWISSPROT;Acc:P26378] 0.270660884
0.495602 ELAVL2 574 1.83168 ELAV-LIKE PROTEIN 2 (HU-ANTIGEN B) (HUB) (ELAV-LIKE NEURONAL PROTEIN 1) (NERVOUS SYSTEM-SPECIFIC RNA BINDING PROTEIN HEL-N1). [SWISSPROT;Acc:Q12926] 0.270572371
0.498067 HTRA3 2579 2.33696 PROBABLE SERINE PROTEASE HTRA3 PRECURSOR (EC 3.4.21.-). [SWISSPROT;Acc:P83110] 0.213126027
0.500223 PEX14 815 1.91396 PEROXISOMAL MEMBRANE PROTEIN PEX14 (PEROXIN-14) (PEROXISOMAL MEMBRANE ANCHOR PROTEIN PEX14) (PTS1 RECEPTOR DOCKING PROTEIN). [SWISSPROT;Acc:O75381] 0.261354992
0.501293 KRR1 1589 2.08327 HIV-1 REV BINDING PROTEIN 2; REV INTERACTING PROTEIN. [RefSeq;Acc:NM_007043] 0.240627955
0.502064 CBLB 93 1.32571 SIGNAL TRANSDUCTION PROTEIN CBL-B (SH3-BINDING PROTEIN CBL-B). [SWISSPROT;Acc:Q13191] 0.378713293
0.503361 ACSS2 2609 2.37915 "ACETYL-COENZYME A SYNTHETASE, CYTOPLASMIC (EC 6.2.1.1) (ACETATE--COA LIGASE) (ACYL-ACTIVATING ENZYME) (ACETYL-COA SYNTHETASE) (ACS) (ACECS). [SWISSPROT;Acc:Q9NR19]" 0.21157178
0.50366 DYM 558 1.85853 DYMECLIN. [RefSeq;Acc:NM_017653] 0.270999123
0.504359 RBPMS 521 1.85404 RNA-BINDING PROTEIN WITH MULTIPLE SPLICING (RBP-MS). [SWISSPROT;Acc:Q93062] 0.272032426
0.505323 no value 1989 2.18834 60S RIBOSOMAL PROTEIN L12 LIKE PROTEIN. [SPTREMBL;Acc:O60886] 0.230916128
0.507204 HARS 2440 2.33574 HISTIDYL-TRNA SYNTHETASE (EC 6.1.1.21) (HISTIDINE--TRNA LIGASE) (HISRS). [SWISSPROT;Acc:P12081] 0.217149169
0.508074 POLR2L 1835 2.17246 DNA-DIRECTED RNA POLYMERASE II 7.6 KDA POLYPEPTIDE (EC 2.7.7.6) (RPB10) (RPB7.6) (RPABC5). [SWISSPROT;Acc:P52436] 0.233870359
0.508151 UBQLN1 1384 2.0779 UBIQUILIN 1 ISOFORM 1. [RefSeq;Acc:NM_013438] 0.244550267
0.508993 NR4A1 2777 2.52853 ORPHAN NUCLEAR RECEPTOR HMR (EARLY RESPONSE PROTEIN NAK1) (TR3 ORPHAN RECEPTOR). [SWISSPROT;Acc:P22736] 0.201299965
0.510382 CDC25B 518 1.8743 M-PHASE INDUCER PHOSPHATASE 2 (EC 3.1.3.48) (DUAL SPECIFICITY PHOSPHATASE CDC25B). [SWISSPROT;Acc:P30305] 0.272305394
0.510943 MTFMT 2551 2.38162 "METHIONYL-TRNA FORMYLTRANSFERASE, MITOCHONDRIAL PRECURSOR (EC 2.1.2.9) (MTFMT). [SWISSPROT;Acc:Q96DP5]" 0.214535904
0.51096 DTYMK 1864 2.19044 THYMIDYLATE KINASE (EC 2.7.4.9) (DTMP KINASE). [SWISSPROT;Acc:P23919] 0.233268202
0.511781 EMG1 1508 2.10953 PROBABLE RIBOSOME BIOGENESIS PROTEIN NEP1 (C2F PROTEIN). [SWISSPROT;Acc:Q92979] 0.242604277
NOC4L 1507
0.512064 no value 2566 2.39827 3-HYDROXYISOBUTYRYL-COENZYME A HYDROLASE. [RefSeq;Acc:NM_014362] 0.213513908
0.512921 1988 2.22124 DJ999L4.1 (NOVEL PROTEIN SIMILAR TO RIBOSOMAL PROTEIN L12 (RPL12)). [SPTREMBL;Acc:Q9NQ02] 0.230916515
0.515003 ATG16L1 302 1.71949 0.299509157
0.515195 PRPF31 319 1.77067 PRE-MRNA PROCESSING FACTOR 31 HOMOLOG; PRE-MRNA PROCESSING FACTOR 31 HOMOLOG (YEAST). [RefSeq;Acc:NM_015629] 0.290960484
0.515632 NR4A3 2776 2.56143 NUCLEAR HORMONE RECEPTOR NOR-1 (NEURON-DERIVED ORPHAN RECEPTOR 1) (MITOGEN INDUCED NUCLEAR ORPHAN RECEPTOR). [SWISSPROT;Acc:Q92570] 0.201306302
0.515928 CDS2 2642 2.45712 PHOSPHATIDATE CYTIDYLYLTRANSFERASE 2 (EC 2.7.7.41) (CDP-DIGLYCERIDE SYNTHETASE 2) (CDP-DIGLYCERIDE PYROPHOSPHORYLASE 2) (CDP- DIACYLGLYCEROL SYNTHASE 2) (CDS 2) (CTP:PHOSPHATIDATE CYTIDYLYLTRANSFERASE 2) (CDP-DAG SYNTHASE 2) (CDP-DG SYNTHETASE 2). [Source 0.209972651
0.516861 CRIM1 1282 2.10021 CYSTEINE-RICH MOTOR NEURON 1; CYSTEINE-RICH REPEAT-CONTAINING PROTEIN S52 PRECURSOR. [RefSeq;Acc:NM_016441] 0.246099676
0.516908 SIX2 663 1.93534 HOMEOBOX PROTEIN SIX2 (SINE OCULIS HOMEOBOX HOMOLOG 2). [SWISSPROT;Acc:Q9NPC8] 0.267088987
0.51691 MAT2A 1785 2.19829 S-ADENOSYLMETHIONINE SYNTHETASE GAMMA FORM (EC 2.5.1.6) (METHIONINE ADENOSYLTRANSFERASE) (ADOMET SYNTHETASE) (MAT-II). [SWISSPROT;Acc:P31153] 0.23514186
0.517007 PPP2CA 1827 2.20733 "SERINE/THREONINE PROTEIN PHOSPHATASE 2A, CATALYTIC SUBUNIT, ALPHA ISOFORM (EC 3.1.3.16) (PP2A-ALPHA) (REPLICATION PROTEIN C) (RP-C). [SWISSPROT;Acc:P05323]" 0.234222794
0.517438 RBPJ 1348 2.11039 J KAPPA-RECOMBINATION SIGNAL BINDING PROTEIN (RBP-J KAPPA). [SWISSPROT;Acc:Q06330] 0.245185961

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/