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 description measured expected final Hugo
Results: HTML CSV LaTeX Showing element 1458 to 1507 of 3206 in total
Rank
description
measured
expected
final
Hugo
1458 MEGF10 PROTEIN. [RefSeq;Acc:NM_032446] 0.0987602 0.406247 0.243103826 MEGF10
1459 BETA ADDUCIN (ERYTHROCYTE ADDUCIN BETA SUBUNIT). [SWISSPROT;Acc:P35612] 0.163578 0.672876 0.243102741 ADD2
1460 ALPHA ADDUCIN (ERYTHROCYTE ADDUCIN ALPHA SUBUNIT). [SWISSPROT;Acc:P35611] 0.183187 0.753661 0.243062862 ADD1
1461 "BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE, CYTOSOLIC (EC 2.6.1.42) (BCAT(C)) (ECA39 PROTEIN). [SWISSPROT;Acc:P54687]" 0.471522 1.94005 0.243046313 BCAT1
1462 MAP/MICROTUBULE AFFINITY-REGULATING KINASE 1. [RefSeq;Acc:NM_018650] 0.021031 0.0865364 0.243030678 MARK1
1463 RIO KINASE 1 ISOFORM 1; AD034 PROTEIN. [RefSeq;Acc:NM_031480] 0.0991443 0.40795 0.243030518 RIOK1
1464 DEFORMED EPIDERMAL AUTOREGULATORY FACTOR 1 HOMOLOG (NUCLEAR DEAF-1 RELATED TRANSCRIPTIONAL REGULATOR) (NUDR) (SUPPRESSIN) (ZINC FINGER MYND DOMAIN CONTAINING PROTEIN 5). [SWISSPROT;Acc:O75398] 0.0656459 0.270114 0.24303035 DEAF1
1465 MEIOTIC RECOMBINATION PROTEIN SPO11. [SWISSPROT;Acc:Q9Y5K1] 0.12393 0.509937 0.243030021 SPO11
1466 MAP/MICROTUBULE AFFINITY-REGULATING KINASE 2 ISOFORM B; ELKL MOTIF KINASE 1; ELKL MOTIF KINASE. [RefSeq;Acc:NM_004954] 0.0198288 0.08159 0.243029783 MARK2
1467 "COPROPORPHYRINOGEN III OXIDASE, MITOCHONDRIAL PRECURSOR (EC 1.3.3.3) (COPROPORPHYRINOGENASE) (COPROGEN OXIDASE) (COX). [SWISSPROT;Acc:P36551]" 0.0753291 0.309975 0.243016695 CPOX
1468 NF-KAPPAB INHIBITOR ALPHA (MAJOR HISTOCOMPATIBILITY COMPLEX ENHANCER- BINDING PROTEIN MAD3) (I-KAPPA-B-ALPHA) (IKAPPABALPHA) (IKB-ALPHA). [SWISSPROT;Acc:P25963] 0.682019 2.80647 0.243016672 NFKBIA
1469 TRANSCRIPTION FACTOR RELB (I-REL). [SWISSPROT;Acc:Q01201] 0.0654684 0.269399 0.243016492 RELB
1470 TRANSCRIPTION FACTOR P65 (NUCLEAR FACTOR NF-KAPPA-B P65 SUBUNIT). [SWISSPROT;Acc:Q04206] 0.0851899 0.350552 0.243016443 RELA
1471 TRANSCRIPTION FACTOR-LIKE PROTEIN MRGX (MORF-RELATED GENE X PROTEIN) (MORTALITY FACTOR 4-LIKE 2) (MSL3-2 PROTEIN). [SWISSPROT;Acc:Q15014] 0.213242 0.877587 0.242986735 MORF4L2
1472 TRANSCRIPTION FACTOR-LIKE PROTEIN MORF4 (MORTALITY FACTOR 4) (CELLULAR SENESCENCE-RELATED PROTEIN 1) (SEN1). [SWISSPROT;Acc:Q9Y690] 0.217383 0.894645 0.242982412 no value
1473 SURVIVAL MOTOR NEURON PROTEIN (COMPONENT OF GEMS 1) (GEMIN1). [SWISSPROT;Acc:Q16637] 0.270547 1.11347 0.242976461
1474 RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 3 (P21-RAC3). [SWISSPROT;Acc:O14658] 0.0569548 0.234405 0.242976046 RAC3
1475 RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1 (P21-RAC1) (RAS-LIKE PROTEIN TC25). [SWISSPROT;Acc:P15154] 0.0733796 0.302004 0.24297559 no value
1476 DNA REPLICATION LICENSING FACTOR MCM5 (CDC46 HOMOLOG) (P1-CDC46). [SWISSPROT;Acc:P33992] 0.0611188 0.251543 0.242975555 MCM5
1477 SURVIVAL OF MOTOR NEURON PROTEIN-INTERACTING PROTEIN 1 (SMN- INTERACTING PROTEIN 1) (COMPONENT OF GEMS 2) (GEMIN2). [SWISSPROT;Acc:O14893] 0.092033 0.378775 0.242975381 SIP1
1478 PROBABLE ATP-DEPENDENT RNA HELICASE DDX20 (DEAD-BOX PROTEIN 20) (DEAD- BOX PROTEIN DP 103) (COMPONENT OF GEMS 3) (GEMIN3). [SWISSPROT;Acc:Q9UHI6] DDX20
1479 RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 2 (P21-RAC2) (SMALL G PROTEIN) (GX). [SWISSPROT;Acc:P15153] 0.0532303 0.219077 0.242975301 RAC2
1480 NUCLEOPORIN 54KDA; NUCLEOPORIN P54. [RefSeq;Acc:NM_017426] 0.114912 0.472937 0.24297528 NUP54
1481 0.0308447 0.126946 0.242974966 no value
1482 TRANSCRIPTION FACTOR-LIKE PROTEIN MRG15 (MORF-RELATED GENE 15 PROTEIN) (MORTALITY FACTOR 4-LIKE 1) (MSL3-1 PROTEIN) (HSPC008/HSPC061). [SWISSPROT;Acc:Q9UBU8] 0.242846 0.999533 0.242959462 MORF4L1
1483 0.54526 2.24437 0.242945682 NOL14
1484 "HIGHLY EXPRESSED IN CANCER, RICH IN LEUCINE HEPTAD REPEATS. [RefSeq;Acc:NM_006101]" 0.0564981 0.23257 0.242929441 NDC80
1485 0.311829 1.28408 0.242842346 VAC14
1486 LIN-7 HOMOLOG A; VERTEBRATE LIN7 HOMOLOG 1; TAX INTERACTION PROTEIN 33; MAMMALIAN LIN-7 1. [RefSeq;Acc:NM_004664] 0.32361 1.33263 0.242835596 LIN7A
1487 U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM2 (SMALL NUCLEAR RIBONUCLEAR PROTEIN D HOMOLOG) (G7B) (SNRNP CORE SM-LIKE PROTEIN SM-X5). [SWISSPROT;Acc:Q9Y333] 0.390142 1.60666 0.242827979 no value
1488 LIN-7 HOMOLOG B; LIN-7B PROTEIN; LIKELY ORTHOLOG OF MOUSE LIN-7B; MAMMALIAN LIN-7 PROTEIN 2; LIKELY ORHOLOG OF MOUSE LIN 7 HOMOLOG B (C. ELEGANS). [RefSeq;Acc:NM_022165] 0.348199 1.43405 0.242808131 LIN7B
1489 RECEPTOR PROTEIN-TYROSINE KINASE ERBB-3 PRECURSOR (EC 2.7.1.112) (C-ERBB3) (TYROSINE KINASE-TYPE CELL SURFACE RECEPTOR HER3). [SWISSPROT;Acc:P21860] 0.0992034 0.408587 0.242796271 ERBB3
1490 RECEPTOR PROTEIN-TYROSINE KINASE ERBB-4 PRECURSOR (EC 2.7.1.112) (P180ERBB4) (TYROSINE KINASE-TYPE CELL SURFACE RECEPTOR HER4). [SWISSPROT;Acc:Q15303] ERBB4
1491 2-HYDROXYPHYTANOYL-COA LYASE (EC 4.1.-.-) (2-HPCL) (HSPC279). [SWISSPROT;Acc:Q9UJ83] 0.0997445 0.410816 0.242796045 HACL1
1492 EPIDERMAL GROWTH FACTOR RECEPTOR PRECURSOR (EC 2.7.1.112) (RECEPTOR PROTEIN-TYROSINE KINASE ERBB-1). [SWISSPROT;Acc:P00533] 0.0818867 0.337266 0.242795598 EGFR
1493 RECEPTOR PROTEIN-TYROSINE KINASE ERBB-2 PRECURSOR (EC 2.7.1.112) (P185ERBB2) (NEU PROTO-ONCOGENE) (C-ERBB-2) (TYROSINE KINASE-TYPE CELL SURFACE RECEPTOR HER2) (MLN 19). [SWISSPROT;Acc:P04626] 0.0803487 0.330932 0.242795197 ERBB2
1494 BREFELDIN A-INHIBITED GUANINE NUCLEOTIDE-EXCHANGE PROTEIN 1 (BREFELDIN A-INHIBITED GEP 1) (P200 ARF-GEP1) (P200 ARF GUANINE NUCLEOTIDE EXCHANGE FACTOR). [SWISSPROT;Acc:Q9Y6D6] 0.0337842 0.139157 0.242777582 ARFGEF1
1495 IMPORTIN 7; RAN-BINDING PROTEIN 7. [RefSeq;Acc:NM_006391] 0.036822 0.15167 0.242777082 no value
1496 BREFELDIN A-INHIBITED GUANINE NUCLEOTIDE-EXCHANGE PROTEIN 2 (BREFELDIN A-INHIBITED GEP 2). [SWISSPROT;Acc:Q9Y6D5] ARFGEF2
1497 T-CELL ACTIVATION WD REPEAT PROTEIN. [RefSeq;Acc:NM_139281] 0.56263 2.31748 0.242776637 WDR36
1498 HSGCN1 (FRAGMENT). [SPTREMBL;Acc:Q99736] 0.287782 1.18538 0.242776156 GCN1L1
1499 IMPORTIN 8; RAN-BINDING PROTEIN 8. [RefSeq;Acc:NM_006390] 0.0330661 0.1362 0.242776065 IPO8
1500 0.536283 2.20914 0.242756457 WDR75
1501 LIN-7 HOMOLOG C; LIN-7 PROTEIN 3. [RefSeq;Acc:NM_018362] 0.410279 1.6901 0.242754275 LIN7C
1502 "CIRHIN; TESTIS EXPRESSED GENE 292; CIRRHOSIS, AUTOSOMAL RECESSIVE 1A. [RefSeq;Acc:NM_032830]" 0.588096 2.42296 0.242717998 CIRH1A
1503 ZUOTIN RELATED FACTOR-1 (M-PHASE PHOSPHOPROTEIN 11). [SWISSPROT;Acc:Q99543] 0.0271819 0.112006 0.242682535 ZRF1
1504 GUANINE NUCLEOTIDE-BINDING PROTEIN BETA SUBUNIT-LIKE PROTEIN 12.3 (P205) (RECEPTOR OF ACTIVATED PROTEIN KINASE C 1) (RACK1) (RECEPTOR FOR ACTIVATED C KINASE). [SWISSPROT;Acc:P25388] 0.112103 0.461933 0.24268238 no value
1505 PBK1 PROTEIN. [SPTREMBL;Acc:O76021] 0.485772 2.00168 0.242682147 RSL1D1
1506 WD-REPEAT PROTEIN BING4. [SWISSPROT;Acc:O15213] 0.562114 2.31688 0.242616795 WDR46
1507 0.511781 2.10953 0.242604277 NOC4L

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/