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 3008 to 3057 of 3206 in total
measured
Hugo
Rank
expected
description
final
0.651969 NOL10 1416 2.67215 0.243986677
0.652807 RPS11 1949 2.82208 40S RIBOSOMAL PROTEIN S11. [SWISSPROT;Acc:P04643] 0.231321224
0.653337 TARDBP 1140 2.60974 TAR DNA-BINDING PROTEIN-43 (TDP-43). [SWISSPROT;Acc:Q13148] 0.250345628
0.659303 CDY2B 2481 3.04797 TESTIS-SPECIFIC CHROMODOMAIN PROTEIN Y PROTEIN 2. [SWISSPROT;Acc:Q9Y6F7] 0.216308888
0.660595 DLSTP 1768 2.79908 "DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE COMPONENT OF 2-OXOGLUTARATE DEHYDROGENASE COMPLEX, MITOCHONDRIAL PRECURSOR (EC 2.3.1.61) (E2) (E2K). [SWISSPROT;Acc:P36957]" 0.23600433
0.661293 GNL3L 1284 2.68731 0.246079909
0.661854 POLR1A 1983 2.86554 DNA-DIRECTED RNA POLYMERASE I LARGEST SUBUNIT (EC 2.7.7.6) (RNA POLYMERASE I 194 KDA SUBUNIT) (RPA194). [SWISSPROT;Acc:O95602] 0.230970079
0.66215 NOL5A 1523 2.73239 NUCLEOLAR PROTEIN NOP56 (NUCLEOLAR PROTEIN 5A). [SWISSPROT;Acc:O00567] 0.242333635
0.663483 ACOX2 2679 3.18084 "ACYL-COENZYME A OXIDASE 2, PEROXISOMAL (EC 1.3.3.6) (BRANCHED-CHAIN ACYL-COA OXIDASE) (BRCACOX) (TRIHYDROXYCOPROSTANOYL-COA OXIDASE) (THCCOX) (THCA-COA OXIDASE). [SWISSPROT;Acc:Q99424]" 0.208587354
0.663698 ACAT1 2604 3.13139 "ACETYL-COA ACETYLTRANSFERASE, MITOCHONDRIAL PRECURSOR (EC 2.3.1.9) (ACETOACETYL-COA THIOLASE) (T2). [SWISSPROT;Acc:P24752]" 0.211949965
0.663776 CDY1B 2482 3.06866 TESTIS-SPECIFIC CHROMODOMAIN Y PROTEIN 1. [SWISSPROT;Acc:Q9Y6F8] 0.216308095
CDYL 2483 "CHROMODOMAIN PROTEIN, Y CHROMOSOME-LIKE ISOFORM A; CDY-LIKE, AUTOSOMAL; TESTIS-SPECIFIC CHROMODOMAIN Y-LIKE PROTEIN. [RefSeq;Acc:NM_004824]"
0.667497 PSMD11 1712 2.81169 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 11 (26S PROTEASOME REGULATORY SUBUNIT S9) (26S PROTEASOME REGULATORY SUBUNIT P44.5). [SWISSPROT;Acc:O00231] 0.237400638
0.667613 RPS4Y2 2041 2.90083 "40S RIBOSOMAL PROTEIN S4, Y ISOFORM 2. [SWISSPROT;Acc:Q8TD47]" 0.23014551
0.66815 SMARCC2 1248 2.69939 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
0.668547 ACAA1 2608 3.15431 "3-KETOACYL-COA THIOLASE, PEROXISOMAL PRECURSOR (EC 2.3.1.16) (BETA- KETOTHIOLASE) (ACETYL-COA ACYLTRANSFERASE) (PEROXISOMAL 3-OXOACYL- COA THIOLASE). [SWISSPROT;Acc:P09110]" 0.211947145
0.669714 FHL3 2763 3.30667 SKELETAL MUSCLE LIM-PROTEIN 2 (SLIM 2) (FOUR AND A HALF LIM DOMAINS PROTEIN 3) (FHL-3). [SWISSPROT;Acc:Q13643] 0.202534272
0.672841 RPS15A 2059 2.92963 40S RIBOSOMAL PROTEIN S15A. [SWISSPROT;Acc:P39027] 0.229667569
0.673422 ATF2 586 2.49889 CYCLIC-AMP-DEPENDENT TRANSCRIPTION FACTOR ATF-2 (ACTIVATING TRANSCRIPTION FACTOR 2) (CAMP RESPONSE ELEMENT BINDING PROTEIN CRE- BP1) (HB16). [SWISSPROT;Acc:P15336] 0.269488453
0.676836 no value 1194 2.7231 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
0.677997 POLR3A 1969 2.9329 DNA-DIRECTED RNA POLYMERASE III LARGEST SUBUNIT (EC 2.7.7.6) (RPC155) (RPC1). [SWISSPROT;Acc:O14802] 0.231169491
0.6803 RRP12 1230 2.74555 0.247782776
0.682019 NFKBIA 1468 2.80647 NF-KAPPAB INHIBITOR ALPHA (MAJOR HISTOCOMPATIBILITY COMPLEX ENHANCER- BINDING PROTEIN MAD3) (I-KAPPA-B-ALPHA) (IKAPPABALPHA) (IKB-ALPHA). [SWISSPROT;Acc:P25963] 0.243016672
0.682678 FHL2 2764 3.37289 SKELETAL MUSCLE LIM-PROTEIN 3 (SLIM 3) (LIM-DOMAIN PROTEIN DRAL) (FOUR AND A HALF LIM DOMAINS PROTEIN 2) (FHL-2). [SWISSPROT;Acc:Q14192] 0.202401501
0.684483 KLC1 895 2.63388 KINESIN LIGHT CHAIN 1 (KLC 1). [SWISSPROT;Acc:Q07866] 0.259876304
0.685788 CASK 1269 2.77992 PERIPHERAL PLASMA MEMBRANE PROTEIN CASK (EC 2.7.1.-) (HCASK) (CALCIUM/CALMODULIN-DEPENDENT SERINE PROTEIN KINASE) (LIN-2 HOMOLOG). [SWISSPROT;Acc:O14936] 0.24669343
0.685868 FTMT 63 1.66819 MITOCHONDRIAL FERRITIN; FERRITIN HEAVY CHAIN-LIKE; FERRITIN H SUBUNIT. [RefSeq;Acc:NM_177478] 0.411145013
0.687281 GFPT2 2240 3.07116 GLUCOSAMINE--FRUCTOSE-6-PHOSPHATE AMINOTRANSFERASE [ISOMERIZING] 2 (EC 2.6.1.16) (HEXOSEPHOSPHATE AMINOTRANSFERASE 2) (D-FRUCTOSE-6- PHOSPHATE AMIDOTRANSFERASE 2) (GFAT 2) (GFAT2). [SWISSPROT;Acc:O94808] 0.223785475
0.687702 HAGH 2602 3.23104 HYDROXYACYLGLUTATHIONE HYDROLASE (EC 3.1.2.6) (GLYOXALASE II) (GLX II). [SWISSPROT;Acc:Q16775] 0.212842305
0.692768 EIF2B1 1583 2.87585 TRANSLATION INITIATION FACTOR EIF-2B ALPHA SUBUNIT (EIF-2B GDP-GTP EXCHANGE FACTOR). [SWISSPROT;Acc:Q14232] 0.240891562
0.694134 no value 522 2.5522 "PRE-MRNA CLEAVAGE FACTOR I, 59 KDA SUBUNIT. [RefSeq;Acc:NM_024811]" 0.271974767
0.696087 SMPD2 2849 3.6375 SPHINGOMYELIN PHOSPHODIESTERASE 2 (EC 3.1.4.12) (NEUTRAL SPHINGOMYELINASE) (NSMASE) (N-SMASE) (LYSO-PLATELET ACTIVATING FACTOR- PHOSPHOLIPASE C) (LYSO-PAF-PLC). [SWISSPROT;Acc:O60906] 0.191364124
0.699473 SESN1 622 2.60745 SESTRIN 1 (P53-REGULATED PROTEIN PA26). [SWISSPROT;Acc:Q9Y6P5] 0.268259411
0.704795 no value 1928 3.04081 0.231778704
0.707942 2040 3.07604 "40S RIBOSOMAL PROTEIN S4, X ISOFORM (SINGLE COPY ABUNDANT MRNA PROTEIN) (SCR10). [SWISSPROT;Acc:P12750]" 0.230147202
0.709304 PLRG1 326 2.4753 "PLEIOTROPIC REGULATOR 1 (PRL1HOMOLOG, ARABIDOPSIS); PLEIOTROPIC REGULATOR 1 (PRL1, ARABIDOPSIS HOMOLOG). [RefSeq;Acc:NM_002669]" 0.286552741
0.712561 ATP6V1A 1698 2.99562 "VACUOLAR ATP SYNTHASE CATALYTIC SUBUNIT A, UBIQUITOUS ISOFORM (EC 3.6.3.14) (V-ATPASE A SUBUNIT 1) (VACUOLAR PROTON PUMP ALPHA SUBUNIT 1) (V-ATPASE 69 KDA SUBUNIT 1) (ISOFORM VA68). [SWISSPROT;Acc:P38606]" 0.23786762
0.714168 NOL1 1565 2.96197 PROLIFERATING-CELL NUCLEOLAR ANTIGEN P120 (PROLIFERATION-ASSOCIATED NUCLEOLAR PROTEIN P120). [SWISSPROT;Acc:P46087] 0.241112503
0.71417 PRPF19 344 2.51546 NUCLEAR MATRIX PROTEIN NMP200 RELATED TO SPLICING FACTOR PRP19. [RefSeq;Acc:NM_014502] 0.283912286
0.716691 SNORA7A 1927 3.09201 60S RIBOSOMAL PROTEIN L32. [SWISSPROT;Acc:P02433] 0.23178806
0.720529 SMARCC1 1227 2.90646 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
0.723587 LUC7L2 183 2.18209 LUC7-LIKE 2; CGI-74 PROTEIN; CGI-59 PROTEIN. [RefSeq;Acc:NM_016019] 0.331602729
0.726532 PSMA8 1815 3.09996 PROTEASOME SUBUNIT ALPHA TYPE 7-LIKE (EC 3.4.25.1). [SWISSPROT;Acc:Q8TAA3] 0.234368185
0.73655 C5orf33 3167 11.3823 0.06471012
0.737493 BTF3 239 2.35516 TRANSCRIPTION FACTOR BTF3 (RNA POLYMERASE B TRANSCRIPTION FACTOR 3). [SWISSPROT;Acc:P20290] 0.313139235
0.743299 no value 251 2.38318 0.311893772
0.745512 2119 3.26763 "PEROXISOMAL 3,2-TRANS-ENOYL-COA ISOMERASE (EC 5.3.3.8) (DODECENOYL-COA DELTA-ISOMERASE) (D3,D2-ENOYL-COA ISOMERASE) (DBI-RELATED PROTEIN 1) (DRS-1) (HEPATOCELLULAR CARCINOMA-ASSOCIATED ANTIGEN 88). [SWISSPROT;Acc:O75521]" 0.228150678
0.745698 TFDP2 81 1.87445 TRANSCRIPTION FACTOR DP-2 (E2F DIMERIZATION PARTNER 2). [SWISSPROT;Acc:Q14188] 0.397822295
0.747794 YME1L1 171 2.19797 YME1-LIKE 1 ISOFORM 3; ATP-DEPENDENT METALLOPROTEASE FTSH1 HOMOLOG. [RefSeq;Acc:NM_014263] 0.340220294
0.750885 PSMD6 1713 3.16322 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 6 (26S PROTEASOME REGULATORY SUBUNIT S10) (P42A) (PROTEASOME REGULATORY PARTICLE SUBUNIT P44S10). [SWISSPROT;Acc:Q15008] 0.237379948

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/