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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measured Rank Hugo Gene description expected final
Results: HTML CSV LaTeX Showing element 1658 to 1707 of 3206 in total
measured
Rank
Hugo
description
expected
final
0.12721 621 CAPZA1 F-ACTIN CAPPING PROTEIN ALPHA-1 SUBUNIT (CAPZ ALPHA-1). [SWISSPROT;Acc:P52907] 0.47397 0.268392514
0.127536 2616 MAP2K3 DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 3 (EC 2.7.1.-) (MAP KINASE KINASE 3) (MAPKK 3) (MAPK/ERK KINASE 3). [SWISSPROT;Acc:P46734] 0.605166 0.210745481
0.127708 2895 CDC2 CELL DIVISION CONTROL PROTEIN 2 HOMOLOG (EC 2.7.1.-) (P34 PROTEIN KINASE) (CYCLIN-DEPENDENT KINASE 1) (CDK1). [SWISSPROT;Acc:P06493] 0.729117 0.175154331
0.127743 832 ITCH ITCHY HOMOLOG E3 UBIQUITIN PROTEIN LIGASE; ATROPHIN-1 INTERACTING PROTEIN 4; ITCHY (MOUSE HOMOLOG) E3 UBIQUITIN PROTEIN LIGASE; NFE2-ASSOCIATED POLYPEPTIDE 1; UBIQUITIN PROTEIN LIGASE ITCH. [RefSeq;Acc:NM_031483] 0.489392 0.261023883
0.127791 1161 no value ADAPTER-RELATED PROTEIN COMPLEX 1 SIGMA 1B SUBUNIT (SIGMA-ADAPTIN 1B) (ADAPTOR PROTEIN COMPLEX AP-1 SIGMA-1B SUBUNIT) (GOLGI ADAPTOR HA1/AP1 ADAPTIN SIGMA-1B SUBUNIT) (CLATHRIN ASSEMBLY PROTEIN COMPLEX 1 SIGMA- 1B SMALL CHAIN) (SIGMA 1B SUBUNIT OF AP-1 CL 0.512059 0.249563039
0.127824 2039 HIP1R HUNTINGTIN INTERACTING PROTEIN 1 RELATED (HIP1-RELATED) (HIP 12). [SWISSPROT;Acc:O75146] 0.555396 0.230149299
0.127901 1453 UTP18 0.525864 0.243220681
0.12797 2280 MRPS16 "28S RIBOSOMAL PROTEIN S16, MITOCHONDRIAL PRECURSOR (MRP-S16) (CGI- 132). [SWISSPROT;Acc:Q9Y3D3]" 0.575175 0.222488808
0.128098 2049 PPA1 INORGANIC PYROPHOSPHATASE (EC 3.6.1.1) (PYROPHOSPHATE PHOSPHO- HYDROLASE) (PPASE). [SWISSPROT;Acc:Q15181] 0.557073 0.229948319
0.128195 1952 RPIA RIBOSE 5-PHOSPHATE ISOMERASE (EC 5.3.1.6) (PHOSPHORIBOISOMERASE). [SWISSPROT;Acc:P49247] 0.554305 0.231271592
0.128218 1233 PBRM1 POLYBROMO 1. [RefSeq;Acc:NM_018165] 0.517633 0.247700591
0.128228 2209 SLC47A1 0.569623 0.225110292
0.128252 1038 RBL1 RETINOBLASTOMA-LIKE PROTEIN 1 (107 KDA RETINOBLASTOMA-ASSOCIATED PROTEIN) (PRB1) (P107). [SWISSPROT;Acc:P28749] 0.506251 0.253336784
0.128297 2559 CEP164 0.598643 0.214313038
0.128336 902 LSAMP LIMBIC SYSTEM-ASSOCIATED MEMBRANE PROTEIN PRECURSOR (LSAMP). [SWISSPROT;Acc:Q13449] 0.494891 0.25932175
0.128438 661 PFDN1 PREFOLDIN SUBUNIT 1. [SWISSPROT;Acc:O60925] 0.480838 0.267112832
0.128497 697 EPS8L2 EPIDERMAL GROWTH FACTOR RECEPTOR PATHWAY SUBSTRATE 8-LIKE PROTEIN 2; EPS8-RELATED PROTEIN 2; EPIDERMAL GROWTH FACTOR RECEPTOR PATHWAY SUBSTRATE 8-RELATED PROTEIN 2. [RefSeq;Acc:NM_022772] 0.483922 0.265532462
0.128895 3031 PTCD1 1.09557 0.117651086
0.129151 3074 CPEB3 CYTOPLASMIC POLYADENYLATION ELEMENT BINDING PROTEIN 3. [RefSeq;Acc:NM_014912] 1.2515 0.103196964
0.129279 2271 no value GLYCEROL KINASE (EC 2.7.1.30) (ATP:GLYCEROL 3-PHOSPHOTRANSFERASE) (GLYCEROKINASE) (GK). [SWISSPROT;Acc:P32189] 0.58046 0.222718189
0.129493 793 NAPB "BETA-SOLUBLE NSF ATTACHMENT PROTEIN (SNAP-BETA) (N-ETHYLMALEIMIDE- SENSITIVE FACTOR ATTACHMENT PROTEIN, BETA). [SWISSPROT;Acc:Q9H115]" 0.494224 0.262012772
0.129655 1287 no value GUANINE NUCLEOTIDE-BINDING PROTEIN-LIKE 1 (GTP-BINDING PROTEIN HSR1). [SWISSPROT;Acc:P36915] 0.527051 0.246000861
0.129726 3003 GYS2 "GLYCOGEN [STARCH] SYNTHASE, LIVER (EC 2.4.1.11). [SWISSPROT;Acc:P54840]" 1.02722 0.126288429
0.129983 1129 TYR TYROSINASE PRECURSOR (EC 1.14.18.1) (MONOPHENOL MONOOXYGENASE) (TUMOR REJECTION ANTIGEN AB) (SK29-AB) (LB24-AB). [SWISSPROT;Acc:P14679] 0.518618 0.250633414
0.129986 1551 PDRG1 0.53787 0.241668061
0.130061 1861 POLR3G POLYMERASE (RNA) III (DNA DIRECTED) (32KD). [RefSeq;Acc:NM_006467] 0.557208 0.233415529
0.130073 2652 NUMB NUMB PROTEIN HOMOLOG (H-NUMB) (PROTEIN S171). [SWISSPROT;Acc:P49757] 0.619508 0.209961776
0.130242 2109 TTL TUBULIN-TYROSINE LIGASE. [RefSeq;Acc:NM_153712] 0.570434 0.228320893
0.130387 2914 UBE2D2 UBIQUITIN-CONJUGATING ENZYME E2-17 KDA 2 (EC 6.3.2.19) (UBIQUITIN- PROTEIN LIGASE) (UBIQUITIN CARRIER PROTEIN) (E2(17)KB 2). [SWISSPROT;Acc:P51669] 0.751425 0.173519646
0.130458 1234 SMARCA2 POSSIBLE GLOBAL TRANSCRIPTION ACTIVATOR SNF2L2 (SNF2-ALPHA). [SWISSPROT;Acc:P51531] 0.526678 0.247699733
1235 SMARCA4 POSSIBLE GLOBAL TRANSCRIPTION ACTIVATOR SNF2L4 (SNF2-BETA) (BRG-1 PROTEIN) (MITOTIC GROWTH AND TRANSCRIPTION ACTIVATOR) (BRAHMA PROTEIN HOMOLOG 1). [SWISSPROT;Acc:P51532]
0.130459 2057 TKTL2 0.567954 0.22969994
0.130571 1205 ZNF593 ZINC FINGER PROTEIN T86. [SWISSPROT;Acc:O00488] 0.525788 0.248333929
0.130589 2220 no value 60S RIBOSOMAL PROTEIN L21. [SWISSPROT;Acc:P46778] 0.580746 0.224864226
0.130784 2071 AMT "AMINOMETHYLTRANSFERASE, MITOCHONDRIAL PRECURSOR (EC 2.1.2.10) (GLYCINE CLEAVAGE SYSTEM T PROTEIN) (GCVT). [SWISSPROT;Acc:P48728]" 0.569999 0.229446017
0.131004 1925 MTX2 METAXIN 2. [SWISSPROT;Acc:O75431] 0.565103 0.231823225
0.131086 894 KIF5B KINESIN HEAVY CHAIN (UBIQUITOUS KINESIN HEAVY CHAIN) (UKHC). [SWISSPROT;Acc:P33176] 0.504416 0.259876768
0.131317 1002 FH "FUMARATE HYDRATASE, MITOCHONDRIAL PRECURSOR (EC 4.2.1.2) (FUMARASE). [SWISSPROT;Acc:P07954]" 0.51515 0.25491022
0.131576 889 KIF5A NEURONAL KINESIN HEAVY CHAIN (NKHC) (KINESIN HEAVY CHAIN ISOFORM 5A) (KINESIN HEAVY CHAIN NEURON-SPECIFIC 1). [SWISSPROT;Acc:Q12840] 0.5063 0.259877543
0.131587 3157 PYCR2 PYRROLINE 5-CARBOXYLATE REDUCTASE ISOFORM. [RefSeq;Acc:NM_013328] 2.02325 0.06503744
0.131623 364 C16orf42 "C316G12.2 (NOVEL PROTEIN SIMILAR TO PREDICTED YEAST, WORM AND ARCHAE- BACTERIAL PROTEINS) (SIMILAR TO UND313) (S. CERVISIAE) (HYPOTHETICAL PROTEIN). [SPTREMBL;Acc:Q9UJK0]" 0.469919 0.280097208
0.131761 2396 SQLE SQUALENE MONOOXYGENASE (EC 1.14.99.7) (SQUALENE EPOXIDASE) (SE). [SWISSPROT;Acc:Q14534] 0.60095 0.219254514
0.131767 2272 no value "GLYCEROL KINASE, TESTIS SPECIFIC 1 (EC 2.7.1.30) (ATP:GLYCEROL 3- PHOSPHOTRANSFERASE) (GLYCEROKINASE) (GK). [SWISSPROT;Acc:Q14409]" 0.591632 0.222717838
0.131799 1391 GART TRIFUNCTIONAL PURINE BIOSYNTHETIC PROTEIN ADENOSINE-3 [INCLUDES: PHOSPHORIBOSYLAMINE--GLYCINE LIGASE (EC 6.3.4.13) (GARS) (GLYCINAMIDE RIBONUCLEOTIDE SYNTHETASE) (PHOSPHORIBOSYLGLYCINAMIDE SYNTHETASE); PHOSPHORIBOSYLFORMYLGLYCINAMIDINE CYCLO-LIGASE (EC 6. 0.53927 0.244402618
0.131908 1806 TP53RK P53-RELATED PROTEIN KINASE (EC 2.7.1.-) (NORI-2). [SWISSPROT;Acc:Q96S44] 0.562339 0.23457025
0.131932 511 CLK2 PROTEIN KINASE CLK2 (EC 2.7.1.-) (CDC-LIKE KINASE 2). [SWISSPROT;Acc:P49760] 0.482648 0.273350351
0.132014 598 CREB5 CAMP RESPONSE ELEMENT-BINDING PROTEIN CRE-BPA. [RefSeq;Acc:NM_004904] 0.490424 0.2691834
0.132038 1630 PHLPPL 0.551746 0.239309392
0.13204 948 RABAC1 RAB ACCEPTOR 1 (PRENYLATED); PRENYLATED RAB ACCEPTOR 1. [RefSeq;Acc:NM_006423] 0.514965 0.256405775
0.132041 454 TBL2 TRANSDUCIN BETA-LIKE 2 PROTEIN (WS BETA-TRANSDUCIN REPEATS PROTEIN) (WS-BETATRP) (WILLIAMS-BEUREN SYNDROME CHROMOSOME REGION 13 PROTEIN). [SWISSPROT;Acc:Q9Y4P3] 0.478695 0.275835344

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/