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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Gene Rank expected description measured Hugo final
Results: HTML CSV LaTeX Showing element 1402 to 1451 of 3206 in total
Rank
expected
description
measured
Hugo
final
1402 0.640129 0.15625 FBXO28 0.244091425
1403 1.19358 EUKARYOTIC TRANSLATION INITIATION FACTOR 2 SUBUNIT 2 (EUKARYOTIC TRANSLATION INITIATION FACTOR 2 BETA SUBUNIT) (EIF-2-BETA). [SWISSPROT;Acc:P20042] 0.291311 EIF2S2 0.244064914
1404 0.191876 EPSIN 3. [RefSeq;Acc:NM_017957] 0.0468234 EPN3 0.244029477
1405 1.45239 FRAGILE X MENTAL RETARDATION 1 PROTEIN (PROTEIN FMR-1) (FMRP). [SWISSPROT;Acc:Q06787] 0.354424 FMR1 0.244028119
1406 0.128904 CYTOCHROME C. [SWISSPROT;Acc:P00001] 0.0314533 CYCS 0.244005617
1407 HEPARAN SULFATE 6-O-SULFOTRANSFERASE; HEPARAN-SULFATE 6-SULFOTRANSFERASE. [RefSeq;Acc:NM_004807] HS6ST1
1408 0.235798 WW DOMAIN BINDING PROTEIN 11; NPW38-BINDING PROTEIN NPWBP; SH3 DOMAIN-BINDING PROTEIN SNP70. [RefSeq;Acc:NM_016312] 0.0575359 WBP11 0.244005038
1409 ELAC HOMOLOG 2; PUTATIVE PROSTATE CANCER SUSCEPTIBILITY PROTEIN; ELAC (E. COLI) HOMOLOG 2. [RefSeq;Acc:NM_018127] ELAC2
1410 0.106604 HEPARAN SULFATE 6-O-SULFOTRANSFERASE 2. [RefSeq;Acc:NM_147174] 0.0260119 HS6ST2 0.244004915
1411 0.369182 RNA-BINDING PROTEIN 10 (RNA BINDING MOTIF PROTEIN 10) (DXS8237E). [SWISSPROT;Acc:P98175] 0.0900822 RBM10 0.244004854
1412 0.303151 RNA-BINDING PROTEIN 5 (RNA BINDING MOTIF PROTEIN 5) (PUTATIVE TUMOR SUPPRESSOR LUCA15) (G15 PROTEIN). [SWISSPROT;Acc:P52756] 0.0739703 RBM5 0.244004803
1413 1.27783 0.311796 PIH1D1 0.244004289
1414 0.108151 FATTY ACID HYDROXYLASE DOMAIN CONTAINING 1. [RefSeq;Acc:NM_024306] 0.0263893 FA2H 0.244004216
1415 0.611499 NUCLEOPORIN NUP43 (P42). [SWISSPROT;Acc:Q8NFH3] 0.149203 NUP43 0.243995493
1416 2.67215 0.651969 NOL10 0.243986677
1417 1.88011 FRAGILE X MENTAL RETARDATION SYNDROME RELATED PROTEIN 1. [SWISSPROT;Acc:P51114] 0.458713 FXR1 0.243982001
1418 FRAGILE X MENTAL RETARDATION SYNDROME RELATED PROTEIN 2. [SWISSPROT;Acc:P51116] FXR2
1419 3.51778 ATP-DEPENDENT RNA HELICASE DDX18 (DEAD-BOX PROTEIN 18) (MYC-REGULATED DEAD-BOX PROTEIN) (MRDB). [SWISSPROT;Acc:Q9NVP1] 0.858096 DDX18 0.243931116
1420 0.125605 "TRANSDUCIN BETA-LIKE 1X PROTEIN (TRANSDUCIN-BETA-LIKE 1, X-LINKED). [SWISSPROT;Acc:O60907]" 0.0306345 TBL1X 0.243895546
1421 0.1246 "TRANSDUCIN BETA-LIKE 1Y PROTEIN (TRANSDUCIN-BETA-LIKE 1, Y-LINKED). [SWISSPROT;Acc:Q9BQ87]" 0.0303893 TBL1Y 0.243894864
1422 0.129562 0.0315995 PCID2 0.243894815
1423 0.129724 NUCLEAR RECEPTOR CO-REPRESSOR/HDAC3 COMPLEX SUBUNIT TBLR1 (TBL1- RELATED PROTEIN 1). [SWISSPROT;Acc:Q9BZK7] 0.031639 no value 0.24389473
1424 1.4749 IMPORTIN BETA-1 SUBUNIT (KARYOPHERIN BETA-1 SUBUNIT) (NUCLEAR FACTOR P97) (IMPORTIN 90). [SWISSPROT;Acc:Q14974] 0.35972 KPNB1 0.243894501
1425 1.44441 0.352259 DCLK2 0.243877431
1426 0.449228 MICROTUBULE-ASSOCIATED PROTEIN RP/EB FAMILY MEMBER 1 (APC-BINDING PROTEIN EB1). [SWISSPROT;Acc:Q15691] 0.109553 MAPRE1 0.243869483
1427 HISTIDINE-RICH MEMBRANE PROTEIN KE4. [SWISSPROT;Acc:Q92504] SLC39A7
1428 0.365289 MICROTUBULE-ASSOCIATED PROTEIN RP/EB FAMILY MEMBER 3 (PROTEIN EB3). [SWISSPROT;Acc:Q9UPY8] 0.0890817 MAPRE3 0.243866363
1429 0.348604 "MICROTUBULE-ASSOCIATED PROTEIN, RP/EB FAMILY, MEMBER 2; T-CELL ACTIVATION PROTEIN, EB1 FAMILY; APC-BINDING PROTEIN EB1. [RefSeq;Acc:NM_014268]" 0.0850122 MAPRE2 0.243864672
1430 5.69292 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 PSMA1 0.243783507
1431 0.355321 ENTHOPROTIN; EPSIN 4; CLATHRIN INTERACTING PROTEIN LOCALIZED IN THE TRANS-GOLGI REGION. [RefSeq;Acc:NM_014666] 0.086609 no value 0.24374861
1432 1.67671 SERINE/THREONINE-PROTEIN KINASE DCAMKL1 (EC 2.7.1.-) (DOUBLECORTIN- LIKE AND CAM KINASE-LIKE 1). [SWISSPROT;Acc:O15075] 0.408607 DCLK1 0.24369569
1433 0.158546 RNA HELICASE-RELATED PROTEIN; RNA HELICASE-LIKE PROTEIN; SF3B125 DEAD-BOX PROTEIN. [RefSeq;Acc:NM_007372] 0.038631 no value 0.243657992
1434 0.476394 SPLICING FACTOR U2AF 35 KDA SUBUNIT (U2 AUXILIARY FACTOR 35 KDA SUBUNIT) (U2 SNRNP AUXILIARY FACTOR SMALL SUBUNIT). [SWISSPROT;Acc:Q01081] 0.116077 U2AF1 0.243657561
1435 0.159183 SPLICING COACTIVATOR SUBUNIT SRM300; RNA BINDING PROTEIN; AT-RICH ELEMENT BINDING FACTOR. [RefSeq;Acc:NM_016333] 0.0387861 SRRM2 0.2436573
1436 1.67604 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 U2AF2 0.243657073
1437 0.0870115 "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 AKT2 0.24352643
1438 0.089649 RAC-ALPHA SERINE/THREONINE KINASE (EC 2.7.1.-) (RAC-PK-ALPHA) (PROTEIN KINASE B) (PKB) (C-AKT). [SWISSPROT;Acc:P31749] 0.0218319 AKT1 0.24352642
1439 0.973079 0.23697 NLE1 0.243525962
1440 0.102427 "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 AKT3 0.243525633
1441 2.21735 0.539944 UTP15 0.243508693
1442 1.26013 TRANSDUCIN BETA-LIKE 3; WD-REPEAT PROTEIN SAZD. [RefSeq;Acc:NM_006453] 0.306804 TBL3 0.243470118
1443 0.105024 0.0255702 COQ2 0.243470064
1444 0.66093 GLUTAMYL TRNA SYNTHETASE. [SPTREMBL;Acc:O14563] 0.16091 EARS2 0.243459973
1445 0.793116 GLUTAMINYL-TRNA SYNTHETASE (EC 6.1.1.18) (GLUTAMINE--TRNA LIGASE) (GLNRS). [SWISSPROT;Acc:P47897] 0.193092 QARS
1446 0.132186 SPERMIDINE SYNTHASE (EC 2.5.1.16) (PUTRESCINE AMINOPROPYLTRANSFERASE) (SPDSY). [SWISSPROT;Acc:P19623] 0.032182 SRM
1447 0.264372 GLYCYL-TRNA SYNTHETASE (EC 6.1.1.14) (GLYCINE--TRNA LIGASE) (GLYRS). [SWISSPROT;Acc:P41250] 0.064364 GARS
1448 0.287741 BASIC PROLINE-RICH PEPTIDE P-E (IB-9). [SWISSPROT;Acc:P02811] 0.0700456 no value 0.243432809
1449 0.316634 SALIVARY PROLINE-RICH PROTEIN PO (ALLELE K) [CONTAINS: PEPTIDE P-D] (FRAGMENT). [SWISSPROT;Acc:P10162] 0.0770791 PRB4 0.243432796
1450 0.296552 PROBABLE CALCIUM-TRANSPORTING ATPASE KIAA0703 (EC 3.6.3.8). [SWISSPROT;Acc:O75185] 0.0721789 ATP2C2 0.243393739
1451 4.367 UPF0202 PROTEIN KIAA1709. [SWISSPROT;Acc:Q9H0A0] 1.06283 NAT10 0.243377605

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/