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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Gene Rank measured description final expected Hugo
Results: HTML CSV LaTeX Showing element 1402 to 1451 of 3206 in total
Rank
measured
description
final
expected
Hugo
1402 0.15625 0.244091425 0.640129 FBXO28
1403 0.291311 EUKARYOTIC TRANSLATION INITIATION FACTOR 2 SUBUNIT 2 (EUKARYOTIC TRANSLATION INITIATION FACTOR 2 BETA SUBUNIT) (EIF-2-BETA). [SWISSPROT;Acc:P20042] 0.244064914 1.19358 EIF2S2
1404 0.0468234 EPSIN 3. [RefSeq;Acc:NM_017957] 0.244029477 0.191876 EPN3
1405 0.354424 FRAGILE X MENTAL RETARDATION 1 PROTEIN (PROTEIN FMR-1) (FMRP). [SWISSPROT;Acc:Q06787] 0.244028119 1.45239 FMR1
1406 0.0314533 CYTOCHROME C. [SWISSPROT;Acc:P00001] 0.244005617 0.128904 CYCS
1407 HEPARAN SULFATE 6-O-SULFOTRANSFERASE; HEPARAN-SULFATE 6-SULFOTRANSFERASE. [RefSeq;Acc:NM_004807] HS6ST1
1408 0.0575359 WW DOMAIN BINDING PROTEIN 11; NPW38-BINDING PROTEIN NPWBP; SH3 DOMAIN-BINDING PROTEIN SNP70. [RefSeq;Acc:NM_016312] 0.244005038 0.235798 WBP11
1409 ELAC HOMOLOG 2; PUTATIVE PROSTATE CANCER SUSCEPTIBILITY PROTEIN; ELAC (E. COLI) HOMOLOG 2. [RefSeq;Acc:NM_018127] ELAC2
1410 0.0260119 HEPARAN SULFATE 6-O-SULFOTRANSFERASE 2. [RefSeq;Acc:NM_147174] 0.244004915 0.106604 HS6ST2
1411 0.0900822 RNA-BINDING PROTEIN 10 (RNA BINDING MOTIF PROTEIN 10) (DXS8237E). [SWISSPROT;Acc:P98175] 0.244004854 0.369182 RBM10
1412 0.0739703 RNA-BINDING PROTEIN 5 (RNA BINDING MOTIF PROTEIN 5) (PUTATIVE TUMOR SUPPRESSOR LUCA15) (G15 PROTEIN). [SWISSPROT;Acc:P52756] 0.244004803 0.303151 RBM5
1413 0.311796 0.244004289 1.27783 PIH1D1
1414 0.0263893 FATTY ACID HYDROXYLASE DOMAIN CONTAINING 1. [RefSeq;Acc:NM_024306] 0.244004216 0.108151 FA2H
1415 0.149203 NUCLEOPORIN NUP43 (P42). [SWISSPROT;Acc:Q8NFH3] 0.243995493 0.611499 NUP43
1416 0.651969 0.243986677 2.67215 NOL10
1417 0.458713 FRAGILE X MENTAL RETARDATION SYNDROME RELATED PROTEIN 1. [SWISSPROT;Acc:P51114] 0.243982001 1.88011 FXR1
1418 FRAGILE X MENTAL RETARDATION SYNDROME RELATED PROTEIN 2. [SWISSPROT;Acc:P51116] FXR2
1419 0.858096 ATP-DEPENDENT RNA HELICASE DDX18 (DEAD-BOX PROTEIN 18) (MYC-REGULATED DEAD-BOX PROTEIN) (MRDB). [SWISSPROT;Acc:Q9NVP1] 0.243931116 3.51778 DDX18
1420 0.0306345 "TRANSDUCIN BETA-LIKE 1X PROTEIN (TRANSDUCIN-BETA-LIKE 1, X-LINKED). [SWISSPROT;Acc:O60907]" 0.243895546 0.125605 TBL1X
1421 0.0303893 "TRANSDUCIN BETA-LIKE 1Y PROTEIN (TRANSDUCIN-BETA-LIKE 1, Y-LINKED). [SWISSPROT;Acc:Q9BQ87]" 0.243894864 0.1246 TBL1Y
1422 0.0315995 0.243894815 0.129562 PCID2
1423 0.031639 NUCLEAR RECEPTOR CO-REPRESSOR/HDAC3 COMPLEX SUBUNIT TBLR1 (TBL1- RELATED PROTEIN 1). [SWISSPROT;Acc:Q9BZK7] 0.24389473 0.129724 no value
1424 0.35972 IMPORTIN BETA-1 SUBUNIT (KARYOPHERIN BETA-1 SUBUNIT) (NUCLEAR FACTOR P97) (IMPORTIN 90). [SWISSPROT;Acc:Q14974] 0.243894501 1.4749 KPNB1
1425 0.352259 0.243877431 1.44441 DCLK2
1426 0.109553 MICROTUBULE-ASSOCIATED PROTEIN RP/EB FAMILY MEMBER 1 (APC-BINDING PROTEIN EB1). [SWISSPROT;Acc:Q15691] 0.243869483 0.449228 MAPRE1
1427 HISTIDINE-RICH MEMBRANE PROTEIN KE4. [SWISSPROT;Acc:Q92504] SLC39A7
1428 0.0890817 MICROTUBULE-ASSOCIATED PROTEIN RP/EB FAMILY MEMBER 3 (PROTEIN EB3). [SWISSPROT;Acc:Q9UPY8] 0.243866363 0.365289 MAPRE3
1429 0.0850122 "MICROTUBULE-ASSOCIATED PROTEIN, RP/EB FAMILY, MEMBER 2; T-CELL ACTIVATION PROTEIN, EB1 FAMILY; APC-BINDING PROTEIN EB1. [RefSeq;Acc:NM_014268]" 0.243864672 0.348604 MAPRE2
1430 1.38784 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] 0.243783507 5.69292 PSMA1
1431 0.086609 ENTHOPROTIN; EPSIN 4; CLATHRIN INTERACTING PROTEIN LOCALIZED IN THE TRANS-GOLGI REGION. [RefSeq;Acc:NM_014666] 0.24374861 0.355321 no value
1432 0.408607 SERINE/THREONINE-PROTEIN KINASE DCAMKL1 (EC 2.7.1.-) (DOUBLECORTIN- LIKE AND CAM KINASE-LIKE 1). [SWISSPROT;Acc:O15075] 0.24369569 1.67671 DCLK1
1433 0.038631 RNA HELICASE-RELATED PROTEIN; RNA HELICASE-LIKE PROTEIN; SF3B125 DEAD-BOX PROTEIN. [RefSeq;Acc:NM_007372] 0.243657992 0.158546 no value
1434 0.116077 SPLICING FACTOR U2AF 35 KDA SUBUNIT (U2 AUXILIARY FACTOR 35 KDA SUBUNIT) (U2 SNRNP AUXILIARY FACTOR SMALL SUBUNIT). [SWISSPROT;Acc:Q01081] 0.243657561 0.476394 U2AF1
1435 0.0387861 SPLICING COACTIVATOR SUBUNIT SRM300; RNA BINDING PROTEIN; AT-RICH ELEMENT BINDING FACTOR. [RefSeq;Acc:NM_016333] 0.2436573 0.159183 SRRM2
1436 0.408379 SPLICING FACTOR U2AF 65 KDA SUBUNIT (U2 AUXILIARY FACTOR 65 KDA SUBUNIT) (U2 SNRNP AUXILIARY FACTOR LARGE SUBUNIT) (HU2AF(65)). [SWISSPROT;Acc:P26368] 0.243657073 1.67604 U2AF2
1437 0.0211896 "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]" 0.24352643 0.0870115 AKT2
1438 0.0218319 RAC-ALPHA SERINE/THREONINE KINASE (EC 2.7.1.-) (RAC-PK-ALPHA) (PROTEIN KINASE B) (PKB) (C-AKT). [SWISSPROT;Acc:P31749] 0.24352642 0.089649 AKT1
1439 0.23697 0.243525962 0.973079 NLE1
1440 0.0249436 "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]" 0.243525633 0.102427 AKT3
1441 0.539944 0.243508693 2.21735 UTP15
1442 0.306804 TRANSDUCIN BETA-LIKE 3; WD-REPEAT PROTEIN SAZD. [RefSeq;Acc:NM_006453] 0.243470118 1.26013 TBL3
1443 0.0255702 0.243470064 0.105024 COQ2
1444 0.16091 GLUTAMYL TRNA SYNTHETASE. [SPTREMBL;Acc:O14563] 0.243459973 0.66093 EARS2
1445 0.193092 GLUTAMINYL-TRNA SYNTHETASE (EC 6.1.1.18) (GLUTAMINE--TRNA LIGASE) (GLNRS). [SWISSPROT;Acc:P47897] 0.793116 QARS
1446 0.032182 SPERMIDINE SYNTHASE (EC 2.5.1.16) (PUTRESCINE AMINOPROPYLTRANSFERASE) (SPDSY). [SWISSPROT;Acc:P19623] 0.132186 SRM
1447 0.064364 GLYCYL-TRNA SYNTHETASE (EC 6.1.1.14) (GLYCINE--TRNA LIGASE) (GLYRS). [SWISSPROT;Acc:P41250] 0.264372 GARS
1448 0.0700456 BASIC PROLINE-RICH PEPTIDE P-E (IB-9). [SWISSPROT;Acc:P02811] 0.243432809 0.287741 no value
1449 0.0770791 SALIVARY PROLINE-RICH PROTEIN PO (ALLELE K) [CONTAINS: PEPTIDE P-D] (FRAGMENT). [SWISSPROT;Acc:P10162] 0.243432796 0.316634 PRB4
1450 0.0721789 PROBABLE CALCIUM-TRANSPORTING ATPASE KIAA0703 (EC 3.6.3.8). [SWISSPROT;Acc:O75185] 0.243393739 0.296552 ATP2C2
1451 1.06283 UPF0202 PROTEIN KIAA1709. [SWISSPROT;Acc:Q9H0A0] 0.243377605 4.367 NAT10

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/