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 measured description expected final Hugo
Results: HTML CSV LaTeX Showing element 1551 to 1600 of 3206 in total
Rank
measured
description
expected
final
Hugo
1551 0.129986 0.53787 0.241668061 PDRG1
1552 0.415409 TRANSLATION INITIATION FACTOR EIF-2B BETA SUBUNIT (EIF-2B GDP-GTP EXCHANGE FACTOR) (S20I15) (S20III15). [SWISSPROT;Acc:P49770] 1.71958 0.24157585 EIF2B2
1553 0.100408 BIFUNCTIONAL PURINE BIOSYNTHESIS PROTEIN PURH [INCLUDES: PHOSPHORIBOSYLAMINOIMIDAZOLECARBOXAMIDE FORMYLTRANSFERASE (EC 2.1.2.3) (AICAR TRANSFORMYLASE); IMP CYCLOHYDROLASE (EC 3.5.4.10) (INOSINICASE) (IMP SYNTHETASE) (ATIC)]. [SWISSPROT;Acc:P31939] 0.416 0.241365385 ATIC
1554 PHOSPHORIBOSYLFORMYLGLYCINAMIDINE SYNTHASE (EC 6.3.5.3) (FGAM SYNTHASE) (FGAMS) (FORMYLGLYCINAMIDE RIBOTIDE AMIDOTRANSFERASE) (FGARAT) (FORMYLGLYCINAMIDE RIBOTIDE SYNTHETASE). [SWISSPROT;Acc:O15067] PFAS
1555 0.200816 MULTIFUNCTIONAL PROTEIN ADE2 [INCLUDES: PHOSPHORIBOSYLAMINOIMIDAZOLE- SUCCINOCARBOXAMIDE SYNTHASE (EC 6.3.2.6) (SAICAR SYNTHETASE); PHOSPHORIBOSYLAMINOIMIDAZOLE CARBOXYLASE (EC 4.1.1.21) (AIR CARBOXYLASE) (AIRC)]. [SWISSPROT;Acc:P22234] 0.832 PAICS
1556 0.184977 0.766628 0.241286517 no value
1557 0.0753661 0.312352 0.241285793
1558 0.037683 GC-RICH SEQUENCE DNA-BINDING FACTOR HOMOLOG. [SWISSPROT;Acc:Q9Y5B6] 0.156176 0.241285473 C21orf66
1559 TOLL-LIKE RECEPTOR 2 PRECURSOR (TOLL/INTERLEUKIN 1 RECEPTOR-LIKE PROTEIN 4). [SWISSPROT;Acc:O60603] TLR2
1560 0.0419848 "THIOREDOXIN INTERACTING PROTEIN; UPREGULATED BY 1,25-DIHYDROXYVITAMIN D-3. [RefSeq;Acc:NM_006472]" 0.174068 0.241197693 TXNIP
1561 0.0442559 0.183485 0.241196283 ARRDC4
1562 0.0467541 0.193844 0.241194466 ARRDC3
1563 0.63619 U3 SMALL NUCLEOLAR RIBONUCLEOPROTEIN PROTEIN MPP10 (M PHASE PHOSPHOPROTEIN 10). [SWISSPROT;Acc:O00566] 2.6381 0.241154619 MPHOSPH10
1564 0.223546 GCN5-LIKE PROTEIN 1 (RT14 PROTEIN). [SWISSPROT;Acc:P78537] 0.927081 0.241128877 BLOC1S1
1565 0.714168 PROLIFERATING-CELL NUCLEOLAR ANTIGEN P120 (PROLIFERATION-ASSOCIATED NUCLEOLAR PROTEIN P120). [SWISSPROT;Acc:P46087] 2.96197 0.241112503 NOL1
1566 0.0394801 ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 1. [SWISSPROT;Acc:P40616] 0.163824 0.240990941 ARL1
1567 NEFA-INTERACTING NUCLEAR PROTEIN NIP30. [RefSeq;Acc:NM_024946] no value
1568 0.070166 MITOCHONDRIAL 28S RIBOSOMAL PROTEIN S22 (S22MT) (MRP-S22) (GK002). [SWISSPROT;Acc:P82650] 0.291157 0.240990256 MRPS22
1569 0.966048 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] 4.00866 PSMB2
1570 0.0789602 LIM HOMEOBOX TRANSCRIPTION FACTOR 1 BETA (LIM/HOMEOBOX PROTEIN LMX1B) (LIM-HOMEOBOX PROTEIN 1.2) (LMX-1.2). [SWISSPROT;Acc:O60663] 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 0.11844 MITOCHONDRIAL PRECURSOR PROTEINS IMPORT RECEPTOR (TRANSLOCASE OF OUTER MEMBRANE TOM70). [SWISSPROT;Acc:O94826] 0.491473 0.240989841 TOMM70A
1573 0.0777867 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] 0.322851 0.240936841 DST
1574 0.0946162 "MICROTUBULE-ACTIN CROSSLINKING FACTOR 1, ISOFORM 4. [SWISSPROT;Acc:Q96PK2]" 0.392702 0.240936384 MACF1
1575 0.228182 "ACTIN, CYTOPLASMIC 2 (GAMMA-ACTIN). [SWISSPROT;Acc:P02571]" 0.947072 0.240934163 ACTG1
1576 0.102962 RIBOKINASE (EC 2.7.1.15). [SWISSPROT;Acc:Q9H477] 0.427411 0.240896935 RBKS
1577 0.0598165 SERPIN B12. [SWISSPROT;Acc:Q96P63] 0.248312 0.240892506 SERPINB12
1578 0.0385664 UPF0183 PROTEIN. [SWISSPROT;Acc:Q9BSU1] 0.160098 0.240892453 C16orf70
1579 0.110811 OXYSTEROLS RECEPTOR LXR-ALPHA (LIVER X RECEPTOR ALPHA) (NUCLEAR ORPHAN RECEPTOR LXR-ALPHA). [SWISSPROT;Acc:Q13133] 0.460002 0.240892431 NR1H3
1580 0.0820308 SQUAMOUS CELL CARCINOMA ANTIGEN 1 (SCCA-1) (PROTEIN T4-A). [SWISSPROT;Acc:P29508] 0.340529 0.240892259 SERPINB4
1581 0.056548 MEGSIN (TP55) (SERPIN B7). [SWISSPROT;Acc:O75635] 0.234744 0.240892206 SERPINB7
1582 0.0824164 OXYSTEROLS RECEPTOR LXR-BETA (LIVER X RECEPTOR BETA) (NUCLEAR ORPHAN RECEPTOR LXR-BETA) (UBIQUITOUSLY-EXPRESSED NUCLEAR RECEPTOR) (NUCLEAR RECEPTOR NER). [SWISSPROT;Acc:P55055] 0.34213 0.240892059 NR1H2
1583 0.692768 TRANSLATION INITIATION FACTOR EIF-2B ALPHA SUBUNIT (EIF-2B GDP-GTP EXCHANGE FACTOR). [SWISSPROT;Acc:Q14232] 2.87585 0.240891562 EIF2B1
1584 0.0653411 HURPIN (HACAT UV-REPRESSIBLE SERPIN) (PROTEASE INHIBITOR 13) (HEADPIN) (SERPIN B13). [SWISSPROT;Acc:Q9UIV8] 0.271247 0.240891512 no value
1585 0.0555356 ANTITHROMBIN-III PRECURSOR (ATIII) (PRO0309). [SWISSPROT;Acc:P01008] 0.230542 0.240891464 SERPINC1
1586 0.376553 EUKARYOTIC TRANSLATION INITIATION FACTOR 5A (EIF-5A) (EIF-4D) (REV- BINDING FACTOR). [SWISSPROT;Acc:P10159] 1.56403 0.24075817 EIF5AP1
1587 0.0612982 0.25461 0.240753309 CHAC1
1588 0.326192 EIF-5A2 PROTEIN. [RefSeq;Acc:NM_020390] 1.35491 0.240748094 EIF5A2
1589 0.501293 HIV-1 REV BINDING PROTEIN 2; REV INTERACTING PROTEIN. [RefSeq;Acc:NM_007043] 2.08327 0.240627955 KRR1
1590 0.28028 EVOLUTIONARILY CONSERVED SIGNALING INTERMEDIATE IN TOLL PATHWAY; ECSIT. [RefSeq;Acc:NM_016581] 1.16562 0.240455723 ECSIT
1591 0.784986 BYSTIN. [SWISSPROT;Acc:Q13895] 3.26689 0.240285409 BYSL
1592 0.175549 LAMIN A/C (70 KDA LAMIN). [SWISSPROT;Acc:P02545] 0.730667 0.240258558 LMNA
1593 0.0606318 CENTAURIN BETA 5 (CNT-B5). [SWISSPROT;Acc:Q96P50] 0.252363 0.240256297 CENTB5
1594 0.058923 CENTAURIN BETA 1 (CNT-B1). [SWISSPROT;Acc:Q15027] 0.245251 0.240255901 CENTB1
1595 0.0726324 CENTAURIN BETA 2 (CNT-B2). [SWISSPROT;Acc:Q15057] 0.302313 0.240255629 CENTB2
1596 0.210907 LAMIN B1. [SWISSPROT;Acc:P20700] 0.877854 0.240252935 LMNB1
1597 0.275535 PUTATIVE EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT (EIF-3) (FRAGMENT). [SWISSPROT;Acc:O75153] 1.14705 0.240211848 KIAA0664
1598 0.161804 SERINE/THREONINE PROTEIN PHOSPHATASE 4 (EC 3.1.3.16) (PP4) (PROTEIN PHOSPHATASE X) (PP-X). [SWISSPROT;Acc:P33172] 0.67395 0.240083092 PPP4C
1599 0.0337232 IMMUNOGLOBULIN-BINDING PROTEIN 1 (CD79A-BINDING PROTEIN 1) (B CELL SIGNAL TRANSDUCTION MOLECULE ALPHA 4) (ALPHA 4 PROTEIN). [SWISSPROT;Acc:P78318] 0.140465 0.240082583 IGBP1
1600 0.218752 TRANSLIN. [SWISSPROT;Acc:Q15631] 0.911432 0.240009128 no value

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/