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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Rank Gene description measured expected final Hugo
Results: HTML CSV LaTeX Showing element 1558 to 1607 of 3206 in total
Rank
description
measured
expected
final
Hugo
1558 GC-RICH SEQUENCE DNA-BINDING FACTOR HOMOLOG. [SWISSPROT;Acc:Q9Y5B6] 0.037683 0.156176 0.241285473 C21orf66
1559 TOLL-LIKE RECEPTOR 2 PRECURSOR (TOLL/INTERLEUKIN 1 RECEPTOR-LIKE PROTEIN 4). [SWISSPROT;Acc:O60603] TLR2
1560 "THIOREDOXIN INTERACTING PROTEIN; UPREGULATED BY 1,25-DIHYDROXYVITAMIN D-3. [RefSeq;Acc:NM_006472]" 0.0419848 0.174068 0.241197693 TXNIP
1561 0.0442559 0.183485 0.241196283 ARRDC4
1562 0.0467541 0.193844 0.241194466 ARRDC3
1563 U3 SMALL NUCLEOLAR RIBONUCLEOPROTEIN PROTEIN MPP10 (M PHASE PHOSPHOPROTEIN 10). [SWISSPROT;Acc:O00566] 0.63619 2.6381 0.241154619 MPHOSPH10
1564 GCN5-LIKE PROTEIN 1 (RT14 PROTEIN). [SWISSPROT;Acc:P78537] 0.223546 0.927081 0.241128877 BLOC1S1
1565 PROLIFERATING-CELL NUCLEOLAR ANTIGEN P120 (PROLIFERATION-ASSOCIATED NUCLEOLAR PROTEIN P120). [SWISSPROT;Acc:P46087] 0.714168 2.96197 0.241112503 NOL1
1566 ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 1. [SWISSPROT;Acc:P40616] 0.0394801 0.163824 0.240990941 ARL1
1567 NEFA-INTERACTING NUCLEAR PROTEIN NIP30. [RefSeq;Acc:NM_024946] no value
1568 MITOCHONDRIAL 28S RIBOSOMAL PROTEIN S22 (S22MT) (MRP-S22) (GK002). [SWISSPROT;Acc:P82650] 0.070166 0.291157 0.240990256 MRPS22
1569 PROTEASOME SUBUNIT BETA TYPE 2 (EC 3.4.25.1) (PROTEASOME COMPONENT C7-I) (MACROPAIN SUBUNIT C7-I) (MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT C7-I). [SWISSPROT;Acc:P49721] 0.966048 4.00866 PSMB2
1570 LIM HOMEOBOX TRANSCRIPTION FACTOR 1 BETA (LIM/HOMEOBOX PROTEIN LMX1B) (LIM-HOMEOBOX PROTEIN 1.2) (LMX-1.2). [SWISSPROT;Acc:O60663] 0.0789602 0.327649 0.240990206 LMX1B
1571 LIM HOMEOBOX TRANSCRIPTION FACTOR 1 ALPHA (LIM/HOMEOBOX PROTEIN LMX1A) (LIM-HOMEOBOX PROTEIN 1.1) (LMX-1.1). [SWISSPROT;Acc:Q8TE12] LMX1A
1572 MITOCHONDRIAL PRECURSOR PROTEINS IMPORT RECEPTOR (TRANSLOCASE OF OUTER MEMBRANE TOM70). [SWISSPROT;Acc:O94826] 0.11844 0.491473 0.240989841 TOMM70A
1573 BULLOUS PEMPHIGOID ANTIGEN 1 ISOFORMS 1/2/3/4/5/8 (230 KDA BULLOUS PEMPHIGOID ANTIGEN) (BPA) (HEMIDESMOSOMAL PLAQUE PROTEIN) (DYSTONIA MUSCULORUM PROTEIN) (FRAGMENT). [SWISSPROT;Acc:Q03001] 0.0777867 0.322851 0.240936841 DST
1574 "MICROTUBULE-ACTIN CROSSLINKING FACTOR 1, ISOFORM 4. [SWISSPROT;Acc:Q96PK2]" 0.0946162 0.392702 0.240936384 MACF1
1575 "ACTIN, CYTOPLASMIC 2 (GAMMA-ACTIN). [SWISSPROT;Acc:P02571]" 0.228182 0.947072 0.240934163 ACTG1
1576 RIBOKINASE (EC 2.7.1.15). [SWISSPROT;Acc:Q9H477] 0.102962 0.427411 0.240896935 RBKS
1577 SERPIN B12. [SWISSPROT;Acc:Q96P63] 0.0598165 0.248312 0.240892506 SERPINB12
1578 UPF0183 PROTEIN. [SWISSPROT;Acc:Q9BSU1] 0.0385664 0.160098 0.240892453 C16orf70
1579 OXYSTEROLS RECEPTOR LXR-ALPHA (LIVER X RECEPTOR ALPHA) (NUCLEAR ORPHAN RECEPTOR LXR-ALPHA). [SWISSPROT;Acc:Q13133] 0.110811 0.460002 0.240892431 NR1H3
1580 SQUAMOUS CELL CARCINOMA ANTIGEN 1 (SCCA-1) (PROTEIN T4-A). [SWISSPROT;Acc:P29508] 0.0820308 0.340529 0.240892259 SERPINB4
1581 MEGSIN (TP55) (SERPIN B7). [SWISSPROT;Acc:O75635] 0.056548 0.234744 0.240892206 SERPINB7
1582 OXYSTEROLS RECEPTOR LXR-BETA (LIVER X RECEPTOR BETA) (NUCLEAR ORPHAN RECEPTOR LXR-BETA) (UBIQUITOUSLY-EXPRESSED NUCLEAR RECEPTOR) (NUCLEAR RECEPTOR NER). [SWISSPROT;Acc:P55055] 0.0824164 0.34213 0.240892059 NR1H2
1583 TRANSLATION INITIATION FACTOR EIF-2B ALPHA SUBUNIT (EIF-2B GDP-GTP EXCHANGE FACTOR). [SWISSPROT;Acc:Q14232] 0.692768 2.87585 0.240891562 EIF2B1
1584 HURPIN (HACAT UV-REPRESSIBLE SERPIN) (PROTEASE INHIBITOR 13) (HEADPIN) (SERPIN B13). [SWISSPROT;Acc:Q9UIV8] 0.0653411 0.271247 0.240891512 no value
1585 ANTITHROMBIN-III PRECURSOR (ATIII) (PRO0309). [SWISSPROT;Acc:P01008] 0.0555356 0.230542 0.240891464 SERPINC1
1586 EUKARYOTIC TRANSLATION INITIATION FACTOR 5A (EIF-5A) (EIF-4D) (REV- BINDING FACTOR). [SWISSPROT;Acc:P10159] 0.376553 1.56403 0.24075817 EIF5AP1
1587 0.0612982 0.25461 0.240753309 CHAC1
1588 EIF-5A2 PROTEIN. [RefSeq;Acc:NM_020390] 0.326192 1.35491 0.240748094 EIF5A2
1589 HIV-1 REV BINDING PROTEIN 2; REV INTERACTING PROTEIN. [RefSeq;Acc:NM_007043] 0.501293 2.08327 0.240627955 KRR1
1590 EVOLUTIONARILY CONSERVED SIGNALING INTERMEDIATE IN TOLL PATHWAY; ECSIT. [RefSeq;Acc:NM_016581] 0.28028 1.16562 0.240455723 ECSIT
1591 BYSTIN. [SWISSPROT;Acc:Q13895] 0.784986 3.26689 0.240285409 BYSL
1592 LAMIN A/C (70 KDA LAMIN). [SWISSPROT;Acc:P02545] 0.175549 0.730667 0.240258558 LMNA
1593 CENTAURIN BETA 5 (CNT-B5). [SWISSPROT;Acc:Q96P50] 0.0606318 0.252363 0.240256297 CENTB5
1594 CENTAURIN BETA 1 (CNT-B1). [SWISSPROT;Acc:Q15027] 0.058923 0.245251 0.240255901 CENTB1
1595 CENTAURIN BETA 2 (CNT-B2). [SWISSPROT;Acc:Q15057] 0.0726324 0.302313 0.240255629 CENTB2
1596 LAMIN B1. [SWISSPROT;Acc:P20700] 0.210907 0.877854 0.240252935 LMNB1
1597 PUTATIVE EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT (EIF-3) (FRAGMENT). [SWISSPROT;Acc:O75153] 0.275535 1.14705 0.240211848 KIAA0664
1598 SERINE/THREONINE PROTEIN PHOSPHATASE 4 (EC 3.1.3.16) (PP4) (PROTEIN PHOSPHATASE X) (PP-X). [SWISSPROT;Acc:P33172] 0.161804 0.67395 0.240083092 PPP4C
1599 IMMUNOGLOBULIN-BINDING PROTEIN 1 (CD79A-BINDING PROTEIN 1) (B CELL SIGNAL TRANSDUCTION MOLECULE ALPHA 4) (ALPHA 4 PROTEIN). [SWISSPROT;Acc:P78318] 0.0337232 0.140465 0.240082583 IGBP1
1600 TRANSLIN. [SWISSPROT;Acc:Q15631] 0.218752 0.911432 0.240009128 no value
1601 TRANSLIN-ASSOCIATED PROTEIN X (TRANSLIN-ASSOCIATED FACTOR X). [SWISSPROT;Acc:Q99598] 0.0312503 0.130205 0.240008448 TSNAX
1602 POLYGLUTAMINE BINDING PROTEIN 1; NUCLEAR PROTEIN CONTAINING WW DOMAIN 38 KD. [RefSeq;Acc:NM_005710] PQBP1
1603 ADENYLYL CYCLASE-ASSOCIATED PROTEIN 1 (CAP 1). [SWISSPROT;Acc:Q01518] 0.136076 0.567058 0.239968398 CAP1
1604 60S RIBOSOMAL PROTEIN L28. [SWISSPROT;Acc:P46779] 0.0701119 0.292225 0.239924373 RPL28
1605 PROTEIN BAP28. [SWISSPROT;Acc:Q9H583] 0.844333 3.51976 0.239883685 HEATR1
1606 0.232181 0.967917 0.239876973 KATNAL1
1607 ADENYLYL CYCLASE-ASSOCIATED PROTEIN 2 (CAP 2). [SWISSPROT;Acc:P40123] 0.132388 0.551914 0.239870704 CAP2

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/