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 Gene measured final Rank description Hugo
Results: HTML CSV LaTeX Showing element 1652 to 1701 of 3206 in total
expected
measured
final
Rank
description
Hugo
0.554305 0.128195 0.231271592 1952 RIBOSE 5-PHOSPHATE ISOMERASE (EC 5.3.1.6) (PHOSPHORIBOISOMERASE). [SWISSPROT;Acc:P49247] RPIA
0.555396 0.127824 0.230149299 2039 HUNTINGTIN INTERACTING PROTEIN 1 RELATED (HIP1-RELATED) (HIP 12). [SWISSPROT;Acc:O75146] HIP1R
0.556039 0.138619 0.249297262 1178 PROTEIN PHOSPHATASE 2C BETA ISOFORM (EC 3.1.3.16) (PP2C-BETA). [SWISSPROT;Acc:O75688] PPM1B
0.557073 0.128098 0.229948319 2049 INORGANIC PYROPHOSPHATASE (EC 3.6.1.1) (PYROPHOSPHATE PHOSPHO- HYDROLASE) (PPASE). [SWISSPROT;Acc:Q15181] PPA1
0.557208 0.130061 0.233415529 1861 POLYMERASE (RNA) III (DNA DIRECTED) (32KD). [RefSeq;Acc:NM_006467] POLR3G
0.558604 0.0558136 0.09991622 3082 UBIQUINONE BIOSYNTHESIS PROTEIN COQ7 HOMOLOG (COENZYME Q BIOSYNTHESIS PROTEIN 7 HOMOLOG) (TIMING PROTEIN CLK-1 HOMOLOG). [SWISSPROT;Acc:Q99807] COQ7
0.559309 0.153744 0.274882042 470 "PALLIDIN; PALLID (MOUSE) HOMOLOG, PALLIDIN. [RefSeq;Acc:NM_012388]" PLDN
0.560999 0.145116 0.258674258 903 OPIOID BINDING PROTEIN/CELL ADHESION MOLECULE PRECURSOR (OBCAM) (OPIOID-BINDING CELL ADHESION MOLECULE) (OPCML). [SWISSPROT;Acc:Q14982] OPCML
0.561582 0.185143 0.329681151 186 KCTD9
0.561935 0.152328 0.271077616 542 PROTEIN REGULATOR OF CYTOKINESIS 1; PROTEIN REGULATING CYTOKINESIS 1. [RefSeq;Acc:NM_003981] no value
0.562331 0.147338 0.262012943 791 SYNTAXIN 1A (NEURON-SPECIFIC ANTIGEN HPC-1). [SWISSPROT;Acc:Q16623] STX1A
0.562339 0.131908 0.23457025 1806 P53-RELATED PROTEIN KINASE (EC 2.7.1.-) (NORI-2). [SWISSPROT;Acc:Q96S44] TP53RK
0.562729 0.231369 0.411155281 55 no value
0.56322 0.143571 0.254911047 1000 ISOC2
0.563416 0.181398 0.321961038 202 HSKIN17 PROTEIN. [RefSeq;Acc:NM_012311] KIN
0.563645 0.12244 0.21722893 2438 MY016 PROTEIN. [SPTREMBL;Acc:Q9H3K6] BOLA2B
0.563754 0.139566 0.247565427 1246 DNA-DIRECTED RNA POLYMERASE II 16 KDA POLYPEPTIDE (EC 2.7.7.6) (RPB4). [SWISSPROT;Acc:O15514] POLR2D
0.563976 0.0518319 0.091904443 3110 CYTOHESIN 3 (ARF NUCLEOTIDE-BINDING SITE OPENER 3) (ARNO3 PROTEIN) (GENERAL RECEPTOR OF PHOSPHOINOSITIDES 1) (GRP1). [SWISSPROT;Acc:O43739] PSCD3
0.564193 0.140708 0.249396926 1167 "THIOREDOXIN, MITOCHONDRIAL PRECURSOR (MT-TRX) (THIOREDOXIN 2). [SWISSPROT;Acc:Q99757]" TXN2
0.564523 0.139096 0.24639563 1278 MYB PROTO-ONCOGENE PROTEIN (C-MYB). [SWISSPROT;Acc:P10242] MYB
0.565103 0.131004 0.231823225 1925 METAXIN 2. [SWISSPROT;Acc:O75431] MTX2
0.565408 0.0519635 0.09190443 3111 CYTOHESIN 2 (ARF NUCLEOTIDE-BINDING SITE OPENER) (ARNO PROTEIN) (ARF EXCHANGE FACTOR). [SWISSPROT;Acc:Q99418] PSCD2
0.566199 0.134029 0.236717126 1746 YEAST SEC31P HOMOLOG. [RefSeq;Acc:NM_014933] SEC31A
0.567058 0.136076 0.239968398 1603 ADENYLYL CYCLASE-ASSOCIATED PROTEIN 1 (CAP 1). [SWISSPROT;Acc:Q01518] CAP1
0.567061 0.177169 0.312433759 243 "5'-AMP-ACTIVATED PROTEIN KINASE, GAMMA-3 SUBUNIT (AMPK GAMMA-3 CHAIN) (AMPK GAMMA3). [SWISSPROT;Acc:Q9UGI9]" PRKAG3
0.567583 0.116023 0.204415918 2747 UBIQUITIN-SPECIFIC PROTEASE OTUBAIN 2. [RefSeq;Acc:NM_023112] OTUB2
0.567954 0.130459 0.22969994 2057 TKTL2
0.569623 0.128228 0.225110292 2209 SLC47A1
0.569999 0.130784 0.229446017 2071 "AMINOMETHYLTRANSFERASE, MITOCHONDRIAL PRECURSOR (EC 2.1.2.10) (GLYCINE CLEAVAGE SYSTEM T PROTEIN) (GCVT). [SWISSPROT;Acc:P48728]" AMT
0.570026 0.132484 0.232417469 1901 RRP5 PROTEIN HOMOLOG (PROGRAMMED CELL DEATH PROTEIN 11). [SWISSPROT;Acc:Q14690] PDCD11
0.570423 0.183967 0.322509787 198 PAXILLIN. [SWISSPROT;Acc:P49023] PXN
0.570434 0.130242 0.228320893 2109 TUBULIN-TYROSINE LIGASE. [RefSeq;Acc:NM_153712] TTL
0.571608 0.148259 0.259371807 901 SPLICING FACTOR ARGININE/SERINE-RICH 11 (ARGININE-RICH 54 KDA NUCLEAR PROTEIN) (P54). [SWISSPROT;Acc:Q05519] SFRS11
0.573002 0.150787 0.263152659 781 "NUCLEAR FACTOR, INTERLEUKIN 3 REGULATED. [RefSeq;Acc:NM_005384]" NFIL3
0.573028 0.15014 0.262011629 804 ANKYRIN-REPEAT FAMILY A PROTEIN 2 (RFXANK-LIKE 2). [SWISSPROT;Acc:Q9H9E1] ANKRA2
0.573452 0.133589 0.232955853 1867 NICOTINATE-NUCLEOTIDE PYROPHOSPHORYLASE [CARBOXYLATING] (EC 2.4.2.19) (QUINOLINATE PHOSPHORIBOSYLTRANSFERASE [DECARBOXYLATING]) (QAPRTASE) (QPRTASE). [SWISSPROT;Acc:Q15274] QPRT
0.574482 0.157432 0.274041658 506 INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE 2 (EC 1.1.1.205) (IMP DEHYDROGENASE 2) (IMPDH-II) (IMPD 2). [SWISSPROT;Acc:P12268] IMPDH2
0.574873 0.119287 0.207501483 2705 ABHD14B
0.575175 0.12797 0.222488808 2280 "28S RIBOSOMAL PROTEIN S16, MITOCHONDRIAL PRECURSOR (MRP-S16) (CGI- 132). [SWISSPROT;Acc:Q9Y3D3]" MRPS16
0.576375 0.117541 0.203931468 2751 NARS2
2752 "ASPARAGINYL-TRNA SYNTHETASE, CYTOPLASMIC (EC 6.1.1.22) (ASPARAGINE-- TRNA LIGASE) (ASNRS). [SWISSPROT;Acc:O43776]" NARS
0.576477 0.12372 0.214613939 2542 SURFEIT LOCUS PROTEIN 1. [SWISSPROT;Acc:Q15526] SURF1
0.577362 0.237385 0.411154527 62 CELLULAR REPRESSOR OF E1A-STIMULATED GENES 2. [RefSeq;Acc:NM_153836] CREG2
0.577642 0.180475 0.312433999 242 "5'-AMP-ACTIVATED PROTEIN KINASE, GAMMA-1 SUBUNIT (AMPK GAMMA-1 CHAIN) (AMPKG). [SWISSPROT;Acc:P54619]" PRKAG1
0.577812 0.145632 0.252040456 1084 PROTEIN C20ORF4 (PROTEIN CGI-23) (PRO0225). [SWISSPROT;Acc:Q9Y312] C20orf4
0.579965 0.144652 0.249415051 1165 "SH2 DOMAIN BINDING PROTEIN 1; TPR-CONTAINING, SH2-BINDING PHOSPHOPROTEIN. [RefSeq;Acc:NM_014633]" no value
0.580323 0.116337 0.200469394 2783 CA2+-DEPENDENT ENDOPLASMIC RETICULUM NUCLEOSIDE DIPHOSPHATASE; APYRASE; SOLUBLE CALCIUM-ACTIVATED NUCLEOTIDASE SCAN-1. [RefSeq;Acc:NM_138793] CANT1
0.58046 0.129279 0.222718189 2271 GLYCEROL KINASE (EC 2.7.1.30) (ATP:GLYCEROL 3-PHOSPHOTRANSFERASE) (GLYCEROKINASE) (GK). [SWISSPROT;Acc:P32189] no value
0.580746 0.130589 0.224864226 2220 60S RIBOSOMAL PROTEIN L21. [SWISSPROT;Acc:P46778]
0.580932 0.121 0.208285996 2686 EH-DOMAIN CONTAINING PROTEIN 1 (TESTILIN) (HPAST1). [SWISSPROT;Acc:Q9H4M9] EHD1

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/