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 Rank Gene expected description final
Results: HTML CSV LaTeX Showing element 902 to 951 of 3206 in total
measured
Hugo
Rank
expected
description
final
0.0586001 DNASE2B 3085 0.589168 DEOXYRIBONUCLEASE II BETA ISOFORM 1 PRECURSOR; DEOXYRIBONUCLEASE II BETA; ENDONUCLEASE DLAD. [RefSeq;Acc:NM_021233] 0.099462462
0.0586077 KCNAB2 946 0.228574 VOLTAGE-GATED POTASSIUM CHANNEL BETA-2 SUBUNIT (K+ CHANNEL BETA-2 SUBUNIT) (KV-BETA-2) (HKVBETA2). [SWISSPROT;Acc:Q13303] 0.256405803
0.0586202 LSM14A 2476 0.270652 0.21658883
0.0586244 CSMD1 610 0.21806 DJ947L8.1.6 (NOVEL CUB AND SUSHI (SCR REPEAT) DOMAIN PROTEIN) (FRAGMENT). [SPTREMBL;Acc:Q9H4W2] 0.268845272
0.0586323 IDH3B 2236 0.261755 "ISOCITRATE DEHYDROGENASE [NAD] SUBUNIT BETA, MITOCHONDRIAL PRECURSOR (EC 1.1.1.41) (ISOCITRIC DEHYDROGENASE) (NAD+-SPECIFIC ICDH). [SWISSPROT;Acc:O43837]" 0.223996867
0.0586994 CRBN 2170 0.25856 PROTEIN X 0001. [RefSeq;Acc:NM_016302] 0.227024288
0.0588477 no value 127 0.165745 ERO1-LIKE. [RefSeq;Acc:NM_014584] 0.355049624
0.0588972 SF4 2944 0.382047 SPLICING FACTOR 4 ISOFORM B; RNA-BINDING PROTEIN. [RefSeq;Acc:NM_021164] 0.154162184
0.058923 CENTB1 1594 0.245251 CENTAURIN BETA 1 (CNT-B1). [SWISSPROT;Acc:Q15027] 0.240255901
0.0589414 no value 1940 0.254478 "ISOLEUCYL-TRNA SYNTHETASE, CYTOPLASMIC (EC 6.1.1.5) (ISOLEUCINE--TRNA LIGASE) (ILERS) (IRS). [SWISSPROT;Acc:P41252]" 0.231616878
IARS2 1941
0.0589602 LMBR1 2364 0.26764 LIMB REGION 1 PROTEIN; LIMB REGION 1. [RefSeq;Acc:NM_022458] 0.220296667
0.0593799 PIK3R1 2256 0.266211 PHOSPHATIDYLINOSITOL 3-KINASE REGULATORY ALPHA SUBUNIT (PI3-KINASE P85-ALPHA SUBUNIT) (PTDINS-3-KINASE P85-ALPHA) (PI3K). [SWISSPROT;Acc:P27986] 0.223055772
0.0593831 C16orf35 1018 0.233925 CGTHBA PROTEIN (-14 GENE PROTEIN). [SWISSPROT;Acc:Q12980] 0.253855296
0.0595157 SPTLC1 2167 0.262124 SERINE PALMITOYLTRANSFERASE 1 (EC 2.3.1.50) (LONG CHAIN BASE BIOSYNTHESIS PROTEIN 1) (LCB 1) (SERINE-PALMITOYL-COA TRANSFERASE 1) (SPT 1) (SPT1). [SWISSPROT;Acc:O15269] 0.227051701
0.0597214 DNAJB1 972 0.23369 DNAJ HOMOLOG SUBFAMILY B MEMBER 1 (HEAT SHOCK 40 KDA PROTEIN 1) (HEAT SHOCK PROTEIN 40) (HSP40) (DNAJ PROTEIN HOMOLOG 1) (HDJ-1). [SWISSPROT;Acc:P25685] 0.255558218
0.0597428 PSCD1 3112 0.650054 CYTOHESIN 1 (SEC7 HOMOLOG B2-1). [SWISSPROT;Acc:Q15438] 0.091904365
0.0597741 PIK3R3 2253 0.267978 PHOSPHATIDYLINOSITOL 3-KINASE REGULATORY GAMMA SUBUNIT (PI3-KINASE P85-GAMMA SUBUNIT) (PTDINS-3-KINASE P85-GAMMA) (P55PIK). [SWISSPROT;Acc:Q92569] 0.223055997
0.0598165 SERPINB12 1577 0.248312 SERPIN B12. [SWISSPROT;Acc:Q96P63] 0.240892506
0.0598238 C11orf46 2517 0.278552 0.214767081
G3BP2 2518 RAS-GTPASE-ACTIVATING PROTEIN BINDING PROTEIN 2 (GAP SH3-DOMAIN BINDING PROTEIN 2) (G3BP-2). [SWISSPROT;Acc:Q9UN86]
STARD5 2516 STAR-RELATED LIPID TRANSFER PROTEIN 5 (STARD5) (START DOMAIN- CONTAINING PROTEIN 5). [SWISSPROT;Acc:Q9NSY2]
0.0598365 TRIOBP 935 0.233092 PROTEIN TARA (TRIO-ASSOCIATED REPEAT ON ACTIN) (HRIHFB2122). [SWISSPROT;Acc:Q9H2D6] 0.256707652
0.0599642 AQP4 2843 0.311107 AQUAPORIN 4 (WCH4) (MERCURIAL-INSENSITIVE WATER CHANNEL) (MIWC). [SWISSPROT;Acc:P55087] 0.192744618
0.0600275 MED28 1900 0.258242 ENDOTHELIAL-DERIVED GENE 1. [RefSeq;Acc:NM_025205] 0.232446697
0.0601271 FDXR 2092 0.262913 "NADPH:ADRENODOXIN OXIDOREDUCTASE, MITOCHONDRIAL PRECURSOR (EC 1.18.1.2) (ADRENODOXIN REDUCTASE) (AR) (FERREDOXIN-NADP(+) REDUCTASE). [SWISSPROT;Acc:P22570]" 0.228695804
0.0601277 ESPNP 2515 0.279967 ESPIN. [RefSeq;Acc:NM_031475] 0.214767098
0.0601623 SGPL1 2114 0.263668 SPHINGOSINE-1-PHOSPHATE LYASE 1; SPHINGOSINE-1-PHOSPHATE LYASE. [RefSeq;Acc:NM_003901] 0.228174447
0.0602832 ATPIF1 441 0.217862 "ATPASE INHIBITOR, MITOCHONDRIAL PRECURSOR. [SWISSPROT;Acc:Q9UII2]" 0.276703601
SMOX 442 POLYAMINE OXIDASE ISOFORM 1; POLYAMINE OXIDASE; FLAVIN-CONTAINING SPERMINE OXIDASE; PUTATIVE CYCLIN G1 INTERACTING PROTEIN; FLAVIN CONTAINING AMINE OXIDASE. [RefSeq;Acc:NM_019025]
0.0604093 no value 2366 0.274218 PEPSIN A PRECURSOR (EC 3.4.23.1). [SWISSPROT;Acc:P00790] 0.220296625
0.0604602 AQP5 2842 0.313678 AQUAPORIN 5. [SWISSPROT;Acc:P55064] 0.192746064
0.0606318 CENTB5 1593 0.252363 CENTAURIN BETA 5 (CNT-B5). [SWISSPROT;Acc:Q96P50] 0.240256297
0.0607427 no value 1764 0.257167 0.236199435
0.0608484 AQP2 2841 0.315691 AQUAPORIN-CD (AQP-CD) (WATER CHANNEL PROTEIN FOR RENAL COLLECTING DUCT) (ADH WATER CHANNEL) (AQUAPORIN 2) (COLLECTING DUCT WATER CHANNEL PROTEIN) (WCH-CD). [SWISSPROT;Acc:P41181] 0.192746705
0.06101 TPT1 2147 0.268263 TRANSLATIONALLY CONTROLLED TUMOR PROTEIN (TCTP) (P23) (HISTAMINE- RELEASING FACTOR) (HRF). [SWISSPROT;Acc:P13693] 0.227426071
0.0610425 MIP 2840 0.316697 LENS FIBER MAJOR INTRINSIC PROTEIN (MIP26) (MP26) (AQUAPORIN 0). [SWISSPROT;Acc:P30301] 0.192747326
0.0611188 MCM5 1476 0.251543 DNA REPLICATION LICENSING FACTOR MCM5 (CDC46 HOMOLOG) (P1-CDC46). [SWISSPROT;Acc:P33992] 0.242975555
0.0612127 PPP1R2P9 2340 0.27731 TYPE 1 PROTEIN PHOSPHATASE INHIBITOR. [RefSeq;Acc:NM_025210] 0.220737442
0.0612982 CHAC1 1587 0.25461 0.240753309
0.0613805 CSDA 2189 0.271164 DNA-BINDING PROTEIN A (COLD SHOCK DOMAIN PROTEIN A) (SINGLE-STRAND DNA BINDING PROTEIN NF-GMB). [SWISSPROT;Acc:P16989] 0.226359325
0.0614057 SMAD9 1171 0.246217 MOTHERS AGAINST DECAPENTAPLEGIC HOMOLOG 9 (SMAD 9) (MOTHERS AGAINST DPP HOMOLOG 9) (SMAD9) (MADH6). [SWISSPROT;Acc:O15198] 0.24939667
0.0614814 no value 960 0.240043 "ACYL-COA DEHYDROGENASE, SHORT/BRANCHED CHAIN SPECIFIC, MITOCHONDRIAL PRECURSOR (EC 1.3.99.-) (SBCAD) (2-METHYL BRANCHED CHAIN ACYL-COA DEHYDROGENASE) (2-MEBCAD) (2-METHYLBUTYRYL-COENZYME A DEHYDROGENASE) (2-METHYLBUTYRYL-COA DEHYDROGENASE). [SWISSP" 0.256126611
0.0616259 ING4 616 0.229333 P29ING4; CANDIDATE TUMOR SUPPRESSOR P33 ING1 HOMOLOG. [RefSeq;Acc:NM_016162] 0.268717978
0.0617004 HEYL 70 0.151924 HAIRY/ENHANCER-OF-SPLIT RELATED WITH YRPW MOTIF-LIKE. [RefSeq;Acc:NM_014571] 0.406126748
0.061947 no value 2565 0.290115 TETRATRICOPEPTIDE REPEAT PROTEIN 4 (MY044 PROTEIN). [SWISSPROT;Acc:O95801] 0.213525671
0.0619579 INPP4A 100 0.165754 "INOSITOL POLYPHOSPHATE-4-PHOSPHATASE, TYPE 1 ISOFORM B; INOSITOL POLYPHOSPHATE-4-PHOSPHATASE, TYPE I, 107KD; 4-PHOSPHATASE I; INOSITOL POLYPHOSPHATE-4-PHOSPHATASE I. [RefSeq;Acc:NM_001566]" 0.373794298
0.0620387 ABLIM2 71 0.152757 ACTIN BINDING LIM PROTEIN 2. [RefSeq;Acc:NM_032432] 0.406126724
0.0620748 SEPHS1 102 0.166067 "SELENIDE,WATER DIKINASE 1 (EC 2.7.9.3) (SELENOPHOSPHATE SYNTHETASE 1) (SELENIUM DONOR PROTEIN 1). [SWISSPROT;Acc:P49903]" 0.37379371
0.0621046 UTRN 1217 0.250362 UTROPHIN (DYSTROPHIN-RELATED PROTEIN 1) (DRP1) (DRP). [SWISSPROT;Acc:P46939] 0.24805921

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/