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:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene expected description measured Hugo final
Results: HTML CSV LaTeX Showing element 1452 to 1501 of 3206 in total
Rank
expected
description
measured
Hugo
final
1452 1.57878 "BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE, MITOCHONDRIAL PRECURSOR (EC 2.6.1.42) (BCAT(M)) (PLACENTAL PROTEIN 18) (PP18). [SWISSPROT;Acc:O15382]" 0.384181 BCAT2 0.243340427
1453 0.525864 0.127901 UTP18 0.243220681
1454 1.57686 WD-REPEAT PROTEIN 3. [SWISSPROT;Acc:Q9UNX4] 0.383414 WDR3 0.243150311
1455 0.388558 "CALCIUM-TRANSPORTING ATPASE TYPE 2C, MEMBER 1 (EC 3.6.3.8) (ATPASE 2C1) (ATP-DEPENDENT CA(2+) PUMP PMR1) (HUSSY-28). [SWISSPROT;Acc:P98194]" 0.0944765 ATP2C1 0.243146454
1456 0.755771 GAMMA ADDUCIN (ADDUCIN-LIKE PROTEIN 70). [SWISSPROT;Acc:Q9UEY8] 0.183757 ADD3 0.243138464
1457 0.343534 MEGF11 PROTEIN. [RefSeq;Acc:NM_032445] 0.0835145 MEGF11 0.24310403
1458 0.406247 MEGF10 PROTEIN. [RefSeq;Acc:NM_032446] 0.0987602 MEGF10 0.243103826
1459 0.672876 BETA ADDUCIN (ERYTHROCYTE ADDUCIN BETA SUBUNIT). [SWISSPROT;Acc:P35612] 0.163578 ADD2 0.243102741
1460 0.753661 ALPHA ADDUCIN (ERYTHROCYTE ADDUCIN ALPHA SUBUNIT). [SWISSPROT;Acc:P35611] 0.183187 ADD1 0.243062862
1461 1.94005 "BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE, CYTOSOLIC (EC 2.6.1.42) (BCAT(C)) (ECA39 PROTEIN). [SWISSPROT;Acc:P54687]" 0.471522 BCAT1 0.243046313
1462 0.0865364 MAP/MICROTUBULE AFFINITY-REGULATING KINASE 1. [RefSeq;Acc:NM_018650] 0.021031 MARK1 0.243030678
1463 0.40795 RIO KINASE 1 ISOFORM 1; AD034 PROTEIN. [RefSeq;Acc:NM_031480] 0.0991443 RIOK1 0.243030518
1464 0.270114 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 DEAF1 0.24303035
1465 0.509937 MEIOTIC RECOMBINATION PROTEIN SPO11. [SWISSPROT;Acc:Q9Y5K1] 0.12393 SPO11 0.243030021
1466 0.08159 MAP/MICROTUBULE AFFINITY-REGULATING KINASE 2 ISOFORM B; ELKL MOTIF KINASE 1; ELKL MOTIF KINASE. [RefSeq;Acc:NM_004954] 0.0198288 MARK2 0.243029783
1467 0.309975 "COPROPORPHYRINOGEN III OXIDASE, MITOCHONDRIAL PRECURSOR (EC 1.3.3.3) (COPROPORPHYRINOGENASE) (COPROGEN OXIDASE) (COX). [SWISSPROT;Acc:P36551]" 0.0753291 CPOX 0.243016695
1468 2.80647 NF-KAPPAB INHIBITOR ALPHA (MAJOR HISTOCOMPATIBILITY COMPLEX ENHANCER- BINDING PROTEIN MAD3) (I-KAPPA-B-ALPHA) (IKAPPABALPHA) (IKB-ALPHA). [SWISSPROT;Acc:P25963] 0.682019 NFKBIA 0.243016672
1469 0.269399 TRANSCRIPTION FACTOR RELB (I-REL). [SWISSPROT;Acc:Q01201] 0.0654684 RELB 0.243016492
1470 0.350552 TRANSCRIPTION FACTOR P65 (NUCLEAR FACTOR NF-KAPPA-B P65 SUBUNIT). [SWISSPROT;Acc:Q04206] 0.0851899 RELA 0.243016443
1471 0.877587 TRANSCRIPTION FACTOR-LIKE PROTEIN MRGX (MORF-RELATED GENE X PROTEIN) (MORTALITY FACTOR 4-LIKE 2) (MSL3-2 PROTEIN). [SWISSPROT;Acc:Q15014] 0.213242 MORF4L2 0.242986735
1472 0.894645 TRANSCRIPTION FACTOR-LIKE PROTEIN MORF4 (MORTALITY FACTOR 4) (CELLULAR SENESCENCE-RELATED PROTEIN 1) (SEN1). [SWISSPROT;Acc:Q9Y690] 0.217383 no value 0.242982412
1473 1.11347 SURVIVAL MOTOR NEURON PROTEIN (COMPONENT OF GEMS 1) (GEMIN1). [SWISSPROT;Acc:Q16637] 0.270547 0.242976461
1474 0.234405 RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 3 (P21-RAC3). [SWISSPROT;Acc:O14658] 0.0569548 RAC3 0.242976046
1475 0.302004 RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1 (P21-RAC1) (RAS-LIKE PROTEIN TC25). [SWISSPROT;Acc:P15154] 0.0733796 no value 0.24297559
1476 0.251543 DNA REPLICATION LICENSING FACTOR MCM5 (CDC46 HOMOLOG) (P1-CDC46). [SWISSPROT;Acc:P33992] 0.0611188 MCM5 0.242975555
1477 0.378775 SURVIVAL OF MOTOR NEURON PROTEIN-INTERACTING PROTEIN 1 (SMN- INTERACTING PROTEIN 1) (COMPONENT OF GEMS 2) (GEMIN2). [SWISSPROT;Acc:O14893] 0.092033 SIP1 0.242975381
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 0.219077 RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 2 (P21-RAC2) (SMALL G PROTEIN) (GX). [SWISSPROT;Acc:P15153] 0.0532303 RAC2 0.242975301
1480 0.472937 NUCLEOPORIN 54KDA; NUCLEOPORIN P54. [RefSeq;Acc:NM_017426] 0.114912 NUP54 0.24297528
1481 0.126946 0.0308447 no value 0.242974966
1482 0.999533 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 MORF4L1 0.242959462
1483 2.24437 0.54526 NOL14 0.242945682
1484 0.23257 "HIGHLY EXPRESSED IN CANCER, RICH IN LEUCINE HEPTAD REPEATS. [RefSeq;Acc:NM_006101]" 0.0564981 NDC80 0.242929441
1485 1.28408 0.311829 VAC14 0.242842346
1486 1.33263 LIN-7 HOMOLOG A; VERTEBRATE LIN7 HOMOLOG 1; TAX INTERACTION PROTEIN 33; MAMMALIAN LIN-7 1. [RefSeq;Acc:NM_004664] 0.32361 LIN7A 0.242835596
1487 1.60666 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 no value 0.242827979
1488 1.43405 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 LIN7B 0.242808131
1489 0.408587 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 ERBB3 0.242796271
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 0.410816 2-HYDROXYPHYTANOYL-COA LYASE (EC 4.1.-.-) (2-HPCL) (HSPC279). [SWISSPROT;Acc:Q9UJ83] 0.0997445 HACL1 0.242796045
1492 0.337266 EPIDERMAL GROWTH FACTOR RECEPTOR PRECURSOR (EC 2.7.1.112) (RECEPTOR PROTEIN-TYROSINE KINASE ERBB-1). [SWISSPROT;Acc:P00533] 0.0818867 EGFR 0.242795598
1493 0.330932 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 ERBB2 0.242795197
1494 0.139157 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 ARFGEF1 0.242777582
1495 0.15167 IMPORTIN 7; RAN-BINDING PROTEIN 7. [RefSeq;Acc:NM_006391] 0.036822 no value 0.242777082
1496 BREFELDIN A-INHIBITED GUANINE NUCLEOTIDE-EXCHANGE PROTEIN 2 (BREFELDIN A-INHIBITED GEP 2). [SWISSPROT;Acc:Q9Y6D5] ARFGEF2
1497 2.31748 T-CELL ACTIVATION WD REPEAT PROTEIN. [RefSeq;Acc:NM_139281] 0.56263 WDR36 0.242776637
1498 1.18538 HSGCN1 (FRAGMENT). [SPTREMBL;Acc:Q99736] 0.287782 GCN1L1 0.242776156
1499 0.1362 IMPORTIN 8; RAN-BINDING PROTEIN 8. [RefSeq;Acc:NM_006390] 0.0330661 IPO8 0.242776065
1500 2.20914 0.536283 WDR75 0.242756457
1501 1.6901 LIN-7 HOMOLOG C; LIN-7 PROTEIN 3. [RefSeq;Acc:NM_018362] 0.410279 LIN7C 0.242754275

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/