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 Rank Hugo Gene measured description final
Results: HTML CSV LaTeX Showing element 3008 to 3057 of 3206 in total
expected
Rank
Hugo
measured
description
final
2.61855 2707 no value 0.542979 0.207358653
2.62976 2307 GORASP2 0.584026 "GOLGI REASSEMBLY STACKING PROTEIN 2; GOLGI REASSEMBLY STACKING PROTEIN 2, 55 KDA. [RefSeq;Acc:NM_015530]" 0.222083384
2.63087 3006 COPA 0.329852 COATOMER ALPHA SUBUNIT (ALPHA-COAT PROTEIN) (ALPHA-COP) (HEPCOP) (HEP-COP) [CONTAINS: XENIN (XENOPSIN-RELATED PEPTIDE); PROXENIN]. [SWISSPROT;Acc:P53621] 0.125377537
2.63388 895 KLC1 0.684483 KINESIN LIGHT CHAIN 1 (KLC 1). [SWISSPROT;Acc:Q07866] 0.259876304
2.6381 1563 MPHOSPH10 0.63619 U3 SMALL NUCLEOLAR RIBONUCLEOPROTEIN PROTEIN MPP10 (M PHASE PHOSPHOPROTEIN 10). [SWISSPROT;Acc:O00566] 0.241154619
2.65323 2058 RPL11 0.609415 60S RIBOSOMAL PROTEIN L11. [SWISSPROT;Acc:P39026] 0.229687965
2.66089 2661 CDS1 0.558539 PHOSPHATIDATE CYTIDYLYLTRANSFERASE 1 (EC 2.7.7.41) (CDP-DIGLYCERIDE SYNTHETASE 1) (CDP-DIGLYCERIDE PYROPHOSPHORYLASE 1) (CDP- DIACYLGLYCEROL SYNTHASE 1) (CDS 1) (CTP:PHOSPHATIDATE CYTIDYLYLTRANSFERASE 1) (CDP-DAG SYNTHASE 1) (CDP-DG SYNTHETASE 1). [Source 0.209906836
2.66198 1736 ATPBD3 0.630807 0.236969098
2.66667 2798 WDFY2 0.533046 WD REPEAT- AND FYVE DOMAIN-CONTAINING PROTEIN 2; WD40 AND FYVE DOMAIN CONTAINING 2. [RefSeq;Acc:NM_052950] 0.199892
2.66927 2708 SLC27A2 0.553489 VERY-LONG-CHAIN ACYL-COA SYNTHETASE (EC 6.2.1.-) (VERY-LONG-CHAIN- FATTY-ACID-COA LIGASE). [SWISSPROT;Acc:O14975] 0.207355944
2.67215 1416 NOL10 0.651969 0.243986677
2.67998 3101 CDK2AP2 0.247158 DOC-1 RELATED PROTEIN (DOC-1R). [SWISSPROT;Acc:O75956] 0.092223823
2.68731 1284 GNL3L 0.661293 0.246079909
2.68753 2194 DLAT 0.607431 "DIHYDROLIPOAMIDE ACETYLTRANSFERASE COMPONENT OF PYRUVATE DEHYDROGENASE COMPLEX, MITOCHONDRIAL PRECURSOR (EC 2.3.1.12) (E2) (PDC-E2) (70 KDA MITOCHONDRIAL AUTOANTIGEN OF PRIMARY BILIARY CIRRHOSIS) (PBC) (M2 ANTIGEN COMPLEX 70 KDA SUBUNIT). [SWISSPRO" 0.226018314
2.69828 2586 HTRA1 0.574918 SERINE PROTEASE HTRA1 PRECURSOR (EC 3.4.21.-) (L56). [SWISSPROT;Acc:Q92743] 0.213068325
2.69939 1248 SMARCC2 0.66815 SWI/SNF-RELATED MATRIX-ASSOCIATED ACTIN-DEPENDENT REGULATOR OF CHROMATIN C2 ISOFORM A; MAMMALIAN CHROMATIN REMODELING COMPLEX BRG1-ASSOCIATED FACTOR 170; CHROMATIN REMODELING COMPLEX BAF170 SUBUNIT; SWI3-LIKE PROTEIN; SWI/SNF COMPLEX 170 KDA SUBUNIT. [Sou 0.247518884
2.72155 2231 no value 0.61026 GLUCOSAMINE--FRUCTOSE-6-PHOSPHATE AMINOTRANSFERASE [ISOMERIZING] 1 (EC 2.6.1.16) (HEXOSEPHOSPHATE AMINOTRANSFERASE 1) (D-FRUCTOSE-6- PHOSPHATE AMIDOTRANSFERASE 1) (GFAT 1) (GFAT1). [SWISSPROT;Acc:Q06210] 0.224232515
2.72242 1899 0.63284 60S RIBOSOMAL PROTEIN L17 (L23). [SWISSPROT;Acc:P18621] 0.232454948
2.7231 1194 0.676836 PROTEASOME SUBUNIT BETA TYPE 8 PRECURSOR (EC 3.4.25.1) (PROTEASOME COMPONENT C13) (MACROPAIN SUBUNIT C13) (MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT C13). [SWISSPROT;Acc:P28062] 0.248553487
2.73239 1523 NOL5A 0.66215 NUCLEOLAR PROTEIN NOP56 (NUCLEOLAR PROTEIN 5A). [SWISSPROT;Acc:O00567] 0.242333635
2.7378 259 EIF4G3 0.84511 "EUKARYOTIC TRANSLATION INITIATION FACTOR 4 GAMMA, 3. [RefSeq;Acc:NM_003760]" 0.308682154
2.74555 1230 RRP12 0.6803 0.247782776
2.77604 265 EIF4G1 0.856237 EUKARYOTIC TRANSLATION INITIATION FACTOR 4 GAMMA (EIF-4-GAMMA) (EIF- 4G) (EIF4G) (P220). [SWISSPROT;Acc:Q04637] 0.308438279
2.77992 1269 CASK 0.685788 PERIPHERAL PLASMA MEMBRANE PROTEIN CASK (EC 2.7.1.-) (HCASK) (CALCIUM/CALMODULIN-DEPENDENT SERINE PROTEIN KINASE) (LIN-2 HOMOLOG). [SWISSPROT;Acc:O14936] 0.24669343
2.79016 2014 no value 0.64348 60S RIBOSOMAL PROTEIN L23 (L17). [SWISSPROT;Acc:P23131] 0.230624767
2.79379 2072 MRPS9 0.640883 "28S RIBOSOMAL PROTEIN S9, MITOCHONDRIAL PRECURSOR (MRP-S9). [SWISSPROT;Acc:P82933]" 0.229395552
2.79482 3029 COPB1 0.329144 COATOMER BETA SUBUNIT (BETA-COAT PROTEIN) (BETA-COP). [SWISSPROT;Acc:P53618] 0.117769302
2.79908 1768 DLSTP 0.660595 "DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE COMPONENT OF 2-OXOGLUTARATE DEHYDROGENASE COMPLEX, MITOCHONDRIAL PRECURSOR (EC 2.3.1.61) (E2) (E2K). [SWISSPROT;Acc:P36957]" 0.23600433
2.80647 1468 NFKBIA 0.682019 NF-KAPPAB INHIBITOR ALPHA (MAJOR HISTOCOMPATIBILITY COMPLEX ENHANCER- BINDING PROTEIN MAD3) (I-KAPPA-B-ALPHA) (IKAPPABALPHA) (IKB-ALPHA). [SWISSPROT;Acc:P25963] 0.243016672
2.81057 1947 MRPL4 0.650404 MITOCHONDRIAL RIBOSOMAL PROTEIN L4 ISOFORM A. [RefSeq;Acc:NM_015956] 0.231413557
2.81169 1712 PSMD11 0.667497 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 11 (26S PROTEASOME REGULATORY SUBUNIT S9) (26S PROTEASOME REGULATORY SUBUNIT P44.5). [SWISSPROT;Acc:O00231] 0.237400638
2.82208 1949 RPS11 0.652807 40S RIBOSOMAL PROTEIN S11. [SWISSPROT;Acc:P04643] 0.231321224
2.82668 238 BTF3L4 0.887185 0.313861137
2.83362 2770 GLO1 0.570693 LACTOYLGLUTATHIONE LYASE (EC 4.4.1.5) (METHYLGLYOXALASE) (ALDOKETOMUTASE) (GLYOXALASE I) (GLX I) (KETONE-ALDEHYDE MUTASE) (S-D-LACTOYLGLUTATHIONE METHYLGLYOXAL LYASE). [SWISSPROT;Acc:Q04760] 0.201400682
2.86352 130 HOXB9 1.00641 HOMEOBOX PROTEIN HOX-B9 (HOX-2E) (HOX-2.5). [SWISSPROT;Acc:P17482] 0.351459043
2.86554 1983 POLR1A 0.661854 DNA-DIRECTED RNA POLYMERASE I LARGEST SUBUNIT (EC 2.7.7.6) (RNA POLYMERASE I 194 KDA SUBUNIT) (RPA194). [SWISSPROT;Acc:O95602] 0.230970079
2.86607 2333 PPP1CA 0.634044 SERINE/THREONINE PROTEIN PHOSPHATASE PP1-ALPHA 1 CATALYTIC SUBUNIT (EC 3.1.3.16) (PP-1A). [SWISSPROT;Acc:P08129] 0.221224185
2.87585 1583 EIF2B1 0.692768 TRANSLATION INITIATION FACTOR EIF-2B ALPHA SUBUNIT (EIF-2B GDP-GTP EXCHANGE FACTOR). [SWISSPROT;Acc:Q14232] 0.240891562
2.8765 379 CRNKL1 0.802935 CROOKED NECK-LIKE PROTEIN 1 (CROOKED NECK HOMOLOG) (HCRN) (CGI-201) (MSTP021). [SWISSPROT;Acc:Q9BZJ0] 0.279136103
2.89146 218 SNRPD3 0.923366 SMALL NUCLEAR RIBONUCLEOPROTEIN SM D3 (SNRNP CORE PROTEIN D3) (SM-D3). [SWISSPROT;Acc:P43331] 0.319342478
2.90083 2041 RPS4Y2 0.667613 "40S RIBOSOMAL PROTEIN S4, Y ISOFORM 2. [SWISSPROT;Acc:Q8TD47]" 0.23014551
2.90646 1227 SMARCC1 0.720529 SWI/SNF-RELATED MATRIX-ASSOCIATED ACTIN-DEPENDENT REGULATOR OF CHROMATIN C1; MAMMALIAN CHROMATIN REMODELING COMPLEX BRG1-ASSOCIATED FACTOR 155; SWI/SNF COMPLEX 155 KDA SUBUNIT; CHROMATIN REMODELING COMPLEX BAF155 SUBUNIT. [RefSeq;Acc:NM_003074] 0.247906044
2.91316 3178 SKP1A 0.145007 S-PHASE KINASE-ASSOCIATED PROTEIN 1A (CYCLIN A/CDK2-ASSOCIATED PROTEIN P19) (P19A) (P19SKP1) (RNA POLYMERASE II ELONGATION FACTOR-LIKE PROTEIN) (ORGAN OF CORTI PROTEIN 2) (OCP-II PROTEIN) (OCP-2) (TRANSCRIPTION ELONGATION FACTOR B) (SIII). [SWISSPR 0.049776531
2.9151 131 HOXA9 1.02451 HOMEOBOX PROTEIN HOX-A9 (HOX-1G). [SWISSPROT;Acc:P31269] 0.35144935
2.92963 2059 RPS15A 0.672841 40S RIBOSOMAL PROTEIN S15A. [SWISSPROT;Acc:P39027] 0.229667569
2.93235 132 HOXC9 1.0305 HOMEOBOX PROTEIN HOX-C9 (HOX-3B). [SWISSPROT;Acc:P31274] 0.351424625
2.9329 1969 POLR3A 0.677997 DNA-DIRECTED RNA POLYMERASE III LARGEST SUBUNIT (EC 2.7.7.6) (RPC155) (RPC1). [SWISSPROT;Acc:O14802] 0.231169491
2.95595 994 PSMB4 0.753893 PROTEASOME SUBUNIT BETA TYPE 4 PRECURSOR (EC 3.4.25.1) (PROTEASOME BETA CHAIN) (MACROPAIN BETA CHAIN) (MULTICATALYTIC ENDOPEPTIDASE COMPLEX BETA CHAIN) (PROTEASOME CHAIN 3) (HSN3) (HSBPROS26). [SWISSPROT;Acc:P28070] 0.255042541
2.95928 2669 TAF9 0.61918 TRANSCRIPTION INITIATION FACTOR TFIID 31 KDA SUBUNIT (TAFII-31) (TAFII-32) (TAFII32). [SWISSPROT;Acc:Q16594] 0.209233327
2.96197 1565 NOL1 0.714168 PROLIFERATING-CELL NUCLEOLAR ANTIGEN P120 (PROLIFERATION-ASSOCIATED NUCLEOLAR PROTEIN P120). [SWISSPROT;Acc:P46087] 0.241112503

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/