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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Rank Gene description measured expected final Hugo
Results: HTML CSV LaTeX Showing element 1408 to 1457 of 3206 in total
Rank
description
measured
expected
final
Hugo
1408 WW DOMAIN BINDING PROTEIN 11; NPW38-BINDING PROTEIN NPWBP; SH3 DOMAIN-BINDING PROTEIN SNP70. [RefSeq;Acc:NM_016312] 0.0575359 0.235798 0.244005038 WBP11
1409 ELAC HOMOLOG 2; PUTATIVE PROSTATE CANCER SUSCEPTIBILITY PROTEIN; ELAC (E. COLI) HOMOLOG 2. [RefSeq;Acc:NM_018127] ELAC2
1410 HEPARAN SULFATE 6-O-SULFOTRANSFERASE 2. [RefSeq;Acc:NM_147174] 0.0260119 0.106604 0.244004915 HS6ST2
1411 RNA-BINDING PROTEIN 10 (RNA BINDING MOTIF PROTEIN 10) (DXS8237E). [SWISSPROT;Acc:P98175] 0.0900822 0.369182 0.244004854 RBM10
1412 RNA-BINDING PROTEIN 5 (RNA BINDING MOTIF PROTEIN 5) (PUTATIVE TUMOR SUPPRESSOR LUCA15) (G15 PROTEIN). [SWISSPROT;Acc:P52756] 0.0739703 0.303151 0.244004803 RBM5
1413 0.311796 1.27783 0.244004289 PIH1D1
1414 FATTY ACID HYDROXYLASE DOMAIN CONTAINING 1. [RefSeq;Acc:NM_024306] 0.0263893 0.108151 0.244004216 FA2H
1415 NUCLEOPORIN NUP43 (P42). [SWISSPROT;Acc:Q8NFH3] 0.149203 0.611499 0.243995493 NUP43
1416 0.651969 2.67215 0.243986677 NOL10
1417 FRAGILE X MENTAL RETARDATION SYNDROME RELATED PROTEIN 1. [SWISSPROT;Acc:P51114] 0.458713 1.88011 0.243982001 FXR1
1418 FRAGILE X MENTAL RETARDATION SYNDROME RELATED PROTEIN 2. [SWISSPROT;Acc:P51116] FXR2
1419 ATP-DEPENDENT RNA HELICASE DDX18 (DEAD-BOX PROTEIN 18) (MYC-REGULATED DEAD-BOX PROTEIN) (MRDB). [SWISSPROT;Acc:Q9NVP1] 0.858096 3.51778 0.243931116 DDX18
1420 "TRANSDUCIN BETA-LIKE 1X PROTEIN (TRANSDUCIN-BETA-LIKE 1, X-LINKED). [SWISSPROT;Acc:O60907]" 0.0306345 0.125605 0.243895546 TBL1X
1421 "TRANSDUCIN BETA-LIKE 1Y PROTEIN (TRANSDUCIN-BETA-LIKE 1, Y-LINKED). [SWISSPROT;Acc:Q9BQ87]" 0.0303893 0.1246 0.243894864 TBL1Y
1422 0.0315995 0.129562 0.243894815 PCID2
1423 NUCLEAR RECEPTOR CO-REPRESSOR/HDAC3 COMPLEX SUBUNIT TBLR1 (TBL1- RELATED PROTEIN 1). [SWISSPROT;Acc:Q9BZK7] 0.031639 0.129724 0.24389473 no value
1424 IMPORTIN BETA-1 SUBUNIT (KARYOPHERIN BETA-1 SUBUNIT) (NUCLEAR FACTOR P97) (IMPORTIN 90). [SWISSPROT;Acc:Q14974] 0.35972 1.4749 0.243894501 KPNB1
1425 0.352259 1.44441 0.243877431 DCLK2
1426 MICROTUBULE-ASSOCIATED PROTEIN RP/EB FAMILY MEMBER 1 (APC-BINDING PROTEIN EB1). [SWISSPROT;Acc:Q15691] 0.109553 0.449228 0.243869483 MAPRE1
1427 HISTIDINE-RICH MEMBRANE PROTEIN KE4. [SWISSPROT;Acc:Q92504] SLC39A7
1428 MICROTUBULE-ASSOCIATED PROTEIN RP/EB FAMILY MEMBER 3 (PROTEIN EB3). [SWISSPROT;Acc:Q9UPY8] 0.0890817 0.365289 0.243866363 MAPRE3
1429 "MICROTUBULE-ASSOCIATED PROTEIN, RP/EB FAMILY, MEMBER 2; T-CELL ACTIVATION PROTEIN, EB1 FAMILY; APC-BINDING PROTEIN EB1. [RefSeq;Acc:NM_014268]" 0.0850122 0.348604 0.243864672 MAPRE2
1430 PROTEASOME SUBUNIT ALPHA TYPE 1 (EC 3.4.25.1) (PROTEASOME COMPONENT C2) (MACROPAIN SUBUNIT C2) (MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT C2) (PROTEASOME NU CHAIN) (30 KDA PROSOMAL PROTEIN) (PROS-30). [SWISSPROT;Acc:P25786] 1.38784 5.69292 0.243783507 PSMA1
1431 ENTHOPROTIN; EPSIN 4; CLATHRIN INTERACTING PROTEIN LOCALIZED IN THE TRANS-GOLGI REGION. [RefSeq;Acc:NM_014666] 0.086609 0.355321 0.24374861 no value
1432 SERINE/THREONINE-PROTEIN KINASE DCAMKL1 (EC 2.7.1.-) (DOUBLECORTIN- LIKE AND CAM KINASE-LIKE 1). [SWISSPROT;Acc:O15075] 0.408607 1.67671 0.24369569 DCLK1
1433 RNA HELICASE-RELATED PROTEIN; RNA HELICASE-LIKE PROTEIN; SF3B125 DEAD-BOX PROTEIN. [RefSeq;Acc:NM_007372] 0.038631 0.158546 0.243657992 no value
1434 SPLICING FACTOR U2AF 35 KDA SUBUNIT (U2 AUXILIARY FACTOR 35 KDA SUBUNIT) (U2 SNRNP AUXILIARY FACTOR SMALL SUBUNIT). [SWISSPROT;Acc:Q01081] 0.116077 0.476394 0.243657561 U2AF1
1435 SPLICING COACTIVATOR SUBUNIT SRM300; RNA BINDING PROTEIN; AT-RICH ELEMENT BINDING FACTOR. [RefSeq;Acc:NM_016333] 0.0387861 0.159183 0.2436573 SRRM2
1436 SPLICING FACTOR U2AF 65 KDA SUBUNIT (U2 AUXILIARY FACTOR 65 KDA SUBUNIT) (U2 SNRNP AUXILIARY FACTOR LARGE SUBUNIT) (HU2AF(65)). [SWISSPROT;Acc:P26368] 0.408379 1.67604 0.243657073 U2AF2
1437 "RAC-BETA SERINE/THREONINE PROTEIN KINASE (EC 2.7.1.-) (RAC-PK-BETA) (PROTEIN KINASE AKT-2) (PROTEIN KINASE B, BETA) (PKB BETA). [SWISSPROT;Acc:P31751]" 0.0211896 0.0870115 0.24352643 AKT2
1438 RAC-ALPHA SERINE/THREONINE KINASE (EC 2.7.1.-) (RAC-PK-ALPHA) (PROTEIN KINASE B) (PKB) (C-AKT). [SWISSPROT;Acc:P31749] 0.0218319 0.089649 0.24352642 AKT1
1439 0.23697 0.973079 0.243525962 NLE1
1440 "RAC-GAMMA SERINE/THREONINE PROTEIN KINASE (EC 2.7.1.-) (RAC-PK-GAMMA) (PROTEIN KINASE AKT-3) (PROTEIN KINASE B, GAMMA) (PKB GAMMA) (STK-2). [SWISSPROT;Acc:Q9Y243]" 0.0249436 0.102427 0.243525633 AKT3
1441 0.539944 2.21735 0.243508693 UTP15
1442 TRANSDUCIN BETA-LIKE 3; WD-REPEAT PROTEIN SAZD. [RefSeq;Acc:NM_006453] 0.306804 1.26013 0.243470118 TBL3
1443 0.0255702 0.105024 0.243470064 COQ2
1444 GLUTAMYL TRNA SYNTHETASE. [SPTREMBL;Acc:O14563] 0.16091 0.66093 0.243459973 EARS2
1445 GLUTAMINYL-TRNA SYNTHETASE (EC 6.1.1.18) (GLUTAMINE--TRNA LIGASE) (GLNRS). [SWISSPROT;Acc:P47897] 0.193092 0.793116 QARS
1446 SPERMIDINE SYNTHASE (EC 2.5.1.16) (PUTRESCINE AMINOPROPYLTRANSFERASE) (SPDSY). [SWISSPROT;Acc:P19623] 0.032182 0.132186 SRM
1447 GLYCYL-TRNA SYNTHETASE (EC 6.1.1.14) (GLYCINE--TRNA LIGASE) (GLYRS). [SWISSPROT;Acc:P41250] 0.064364 0.264372 GARS
1448 BASIC PROLINE-RICH PEPTIDE P-E (IB-9). [SWISSPROT;Acc:P02811] 0.0700456 0.287741 0.243432809 no value
1449 SALIVARY PROLINE-RICH PROTEIN PO (ALLELE K) [CONTAINS: PEPTIDE P-D] (FRAGMENT). [SWISSPROT;Acc:P10162] 0.0770791 0.316634 0.243432796 PRB4
1450 PROBABLE CALCIUM-TRANSPORTING ATPASE KIAA0703 (EC 3.6.3.8). [SWISSPROT;Acc:O75185] 0.0721789 0.296552 0.243393739 ATP2C2
1451 UPF0202 PROTEIN KIAA1709. [SWISSPROT;Acc:Q9H0A0] 1.06283 4.367 0.243377605 NAT10
1452 "BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE, MITOCHONDRIAL PRECURSOR (EC 2.6.1.42) (BCAT(M)) (PLACENTAL PROTEIN 18) (PP18). [SWISSPROT;Acc:O15382]" 0.384181 1.57878 0.243340427 BCAT2
1453 0.127901 0.525864 0.243220681 UTP18
1454 WD-REPEAT PROTEIN 3. [SWISSPROT;Acc:Q9UNX4] 0.383414 1.57686 0.243150311 WDR3
1455 "CALCIUM-TRANSPORTING ATPASE TYPE 2C, MEMBER 1 (EC 3.6.3.8) (ATPASE 2C1) (ATP-DEPENDENT CA(2+) PUMP PMR1) (HUSSY-28). [SWISSPROT;Acc:P98194]" 0.0944765 0.388558 0.243146454 ATP2C1
1456 GAMMA ADDUCIN (ADDUCIN-LIKE PROTEIN 70). [SWISSPROT;Acc:Q9UEY8] 0.183757 0.755771 0.243138464 ADD3
1457 MEGF11 PROTEIN. [RefSeq;Acc:NM_032445] 0.0835145 0.343534 0.24310403 MEGF11

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/