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 Gene Rank description Hugo expected final
Results: HTML CSV LaTeX Showing element 2608 to 2657 of 3206 in total
measured
Rank
description
Hugo
expected
final
0.334146 2748 WD-REPEAT PROTEIN WDC146. [SWISSPROT;Acc:Q9C0J8] WDR33 1.63634 0.204203283
2749 "CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR, 160 KDA SUBUNIT (CPSF 160 KDA SUBUNIT). [SWISSPROT;Acc:Q10570]" CPSF1
0.33474 278 "OLIGOPEPTIDE TRANSPORTER, KIDNEY ISOFORM (PEPTIDE TRANSPORTER 2) (KIDNEY H+/PEPTIDE COTRANSPORTER) (SOLUTE CARRIER FAMILY 15, MEMBER 2). [SWISSPROT;Acc:Q16348]" SLC15A2 1.10122 0.303971958
0.334862 581 UBIQUITIN-LIKE PROTEIN SUMO-1 CONJUGATING ENZYME (EC 6.3.2.19) (SUMO- 1-PROTEIN LIGASE) (UBIQUITIN CARRIER PROTEIN) (UBIQUITIN-CONJUGATING ENZYME UBCE2A) (P18). [SWISSPROT;Acc:P50550] UBE2I 1.23982 0.270089206
0.334917 2365 FARNESYL PYROPHOSPHATE SYNTHETASE (FPP SYNTHETASE) (FPS) (FARNESYL DIPHOSPHATE SYNTHETASE) [INCLUDES: DIMETHYLALLYLTRANSFERASE (EC 2.5.1.1); GERANYLTRANSTRANSFERASE (EC 2.5.1.10)]. [SWISSPROT;Acc:P14324] FDPS 1.5203 0.220296652
0.335885 1098 CCDC42 1.33654 0.251309351
0.336304 1393 ABCF3 1.37608 0.244392768
0.336662 181 EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT 2 (EIF-3 BETA) (EIF3 P36) (EIF3I) (TGF-BETA RECEPTOR INTERACTING PROTEIN 1) (TRIP-1). [SWISSPROT;Acc:Q13347] EIF3I 0.99966 0.336776504
0.337171 2096 SIGNAL TRANSDUCING ADAPTOR MOLECULE 2; STAM-LIKE PROTEIN CONTAINING SH3 AND ITAM DOMAINS 2. [RefSeq;Acc:NM_005843] STAM2 1.47582 0.228463498
0.337407 1624 CAMP-DEPENDENT PROTEIN KINASE TYPE II-BETA REGULATORY CHAIN. [SWISSPROT;Acc:P31323] PRKAR2B 1.40952 0.239377235
0.337714 2353 BIFUNCTIONAL AMINOACYL-TRNA SYNTHETASE [INCLUDES: GLUTAMYL-TRNA SYNTHETASE (EC 6.1.1.17) (GLUTAMATE--TRNA LIGASE); PROLYL-TRNA SYNTHETASE (EC 6.1.1.15) (PROLINE--TRNA LIGASE)]. [SWISSPROT;Acc:P07814] EPRS 1.5325 0.220368026
0.339171 2766 DEAD/H (ASP-GLU-ALA-ASP/HIS) BOX POLYPEPTIDE 11; DEAD/H BOX-11 (CHL1-RELATED HELICASE GENE-1); YEAST CHL1 HOMOLOG. [RefSeq;Acc:NM_030655] DDX12 1.6782 0.20210404
0.339248 205 TRANSCRIPTION FACTOR JUN-B. [SWISSPROT;Acc:P17275] JUNB 1.0574 0.32083223
0.341129 1039 HEAT SHOCK PROTEIN HSP 90-BETA (HSP 84) (HSP 90). [SWISSPROT;Acc:P08238] HSP90AB1 1.34662 0.253322392
0.341137 1825 RFK 1.45621 0.234263602
0.341608 1116 DENDRITIC CELL PROTEIN. [RefSeq;Acc:NM_006360] EIF3M 1.36198 0.250817193
0.341867 2083 CAD PROTEIN [INCLUDES: GLUTAMINE-DEPENDENT CARBAMOYL-PHOSPHATE SYNTHASE (EC 6.3.5.5); ASPARTATE CARBAMOYLTRANSFERASE (EC 2.1.3.2); DIHYDROOROTASE (EC 3.5.2.3)]. [SWISSPROT;Acc:P27708] CAD 1.49271 0.229024392
0.342509 122 SON OF SEVENLESS PROTEIN HOMOLOG 2 (SOS-2). [SWISSPROT;Acc:Q07890] SOS2 0.955286 0.358540793
0.343318 1013 TRANSCRIPTION INITIATION FACTOR TFIID 28 KDA SUBUNIT (TAFII-28) (TAFII28) (TFIID SUBUNIT P30-BETA). [SWISSPROT;Acc:Q15544] TAF11 1.35164 0.254001065
0.343832 1044 ASCC1 1.3576 0.253264585
0.34395 609 HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE (EC 2.4.2.8) (HGPRT) (HGPRTASE). [SWISSPROT;Acc:P00492] HPRT1 1.27889 0.268944163
0.343973 2484 HEMK PROTEIN HOMOLOG (EC 2.1.1.-) (M.HSAHEMKP). [SWISSPROT;Acc:Q9Y5R4] HEMK1 1.59051 0.216265852
0.345566 438 TRANSFORMER-2 PROTEIN HOMOLOG (TRA-2 ALPHA). [SWISSPROT;Acc:Q13595] no value 1.24774 0.276953532
0.345751 1541 "DNA-DIRECTED RNA POLYMERASES I, II, AND III 17.1 KDA POLYPEPTIDE (EC 2.7.7.6) (RPB17) (RPB8) (RPABC3). [SWISSPROT;Acc:P52434]" POLR2H 1.42971 0.241832959
0.345758 1229 ARF GTPASE-ACTIVATING PROTEIN GIT2 (G PROTEIN-COUPLED RECEPTOR KINASE- INTERACTOR 2). [SWISSPROT;Acc:Q14161] GIT2 1.39492 0.247869412
0.346601 1761 O-SIALOGLYCOPROTEIN ENDOPEPTIDASE. [RefSeq;Acc:NM_017807] OSGEP 1.46589 0.236444072
0.346654 611 CALCIPRESSIN 1 (DOWN SYNDROME CRITICAL REGION PROTEIN 1) (MYOCYTE- ENRICHED CALCINEURIN INTERACTING PROTEIN 1) (MCIP1) (ADAPT78). [SWISSPROT;Acc:P53805] RCAN1 1.28942 0.268844907
0.346955 2278 DIPHTHAMIDE BIOSYNTHESIS-LIKE PROTEIN 2. [RefSeq;Acc:NM_001384] DPH2 1.55897 0.222553994
0.3472 1897 40S RIBOSOMAL PROTEIN S13. [SWISSPROT;Acc:Q02546] RPS13 1.49288 0.232570602
0.347203 1139 MSTP028 PROTEIN. [RefSeq;Acc:NM_031954] KCTD10 1.38684 0.250355484
0.347585 855 SIGNAL TRANSDUCER AND ACTIVATOR OF TRANSCRIPTION 6 (IL-4 STAT). [SWISSPROT;Acc:P42226] STAT6 1.3344 0.260480366
0.347798 2139 PEPTIDYL-PROLYL CIS-TRANS ISOMERASE NIMA-INTERACTING 1 (EC 5.2.1.8) (ROTAMASE PIN1) (PPIASE PIN1). [SWISSPROT;Acc:Q13526] PIN1 1.52661 0.22782374
0.348199 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] LIN7B 1.43405 0.242808131
0.3486 768 DPY-30-LIKE PROTEIN. [SWISSPROT;Acc:Q9C005] no value 1.32226 0.263639526
0.348668 507 GMP SYNTHASE [GLUTAMINE-HYDROLYZING] (EC 6.3.5.2) (GLUTAMINE AMIDOTRANSFERASE) (GMP SYNTHETASE). [SWISSPROT;Acc:P49915] GMPS 1.27232 0.274041122
0.349158 780 RNA-BINDING REGION CONTAINING PROTEIN 2 (HEPATOCELLULAR CARCINOMA PROTEIN 1) (SPLICING FACTOR HCC1). [SWISSPROT;Acc:Q14498] RBM39 1.32674 0.263169875
0.349374 733 C-TERMINAL BINDING PROTEIN 1 (CTBP1). [SWISSPROT;Acc:Q13363] CTBP1 1.32007 0.264663238
0.349731 2829 DOLICHOL-PHOSPHATE MANNOSYLTRANSFERASE (EC 2.4.1.83) (DOLICHOL- PHOSPHATE MANNOSE SYNTHASE) (DOLICHYL-PHOSPHATE BETA-D- MANNOSYLTRANSFERASE) (MANNOSE-P-DOLICHOL SYNTHASE) (MPD SYNTHASE) (DPM SYNTHASE). [SWISSPROT;Acc:O60762] DPM1 1.80836 0.193396779
0.351386 754 U4/U6-ASSOCIATED RNA SPLICING FACTOR. [RefSeq;Acc:NM_004698] PRPF3 1.32896 0.264406754
0.352259 1425 DCLK2 1.44441 0.243877431
0.352414 1067 HOMEOBOX PROTEIN MEIS1. [SWISSPROT;Acc:O00470] MEIS1 1.39495 0.252635578
0.352885 1649 COQ5 1.47667 0.238973501
0.353001 834 FAR UPSTREAM ELEMENT-BINDING PROTEIN; FAR UPSTREAM ELEMENT BINDING PROTEIN; FUSE-BINDING PROTEIN. [RefSeq;Acc:NM_003902] FUBP1 1.35261 0.260977665
0.353795 2030 "PYRUVATE DEHYDROGENASE E1 COMPONENT ALPHA SUBUNIT, TESTIS-SPECIFIC FORM, MITOCHONDRIAL PRECURSOR (EC 1.2.4.1) (PDHE1-A TYPE II). [SWISSPROT;Acc:P29803]" PDHA2 1.53626 0.230296304
0.353823 2392 GUANYLATE KINASE (EC 2.7.4.8) (GMP KINASE). [SWISSPROT;Acc:Q16774] GUK1 1.61155 0.219554466
0.354332 2731 CRLS1 1.72277 0.205675743
0.354424 1405 FRAGILE X MENTAL RETARDATION 1 PROTEIN (PROTEIN FMR-1) (FMRP). [SWISSPROT;Acc:Q06787] FMR1 1.45239 0.244028119
0.354694 2576 14-3-3 PROTEIN ZETA/DELTA (PROTEIN KINASE C INHIBITOR PROTEIN-1) (KCIP-1) (FACTOR ACTIVATING EXOENZYME S) (FAS). [SWISSPROT;Acc:P29312] YWHAZ 1.66376 0.2131882
0.35482 2132 60S RIBOSOMAL PROTEIN L18. [SWISSPROT;Acc:Q07020] RPL18 1.55638 0.227977743
0.354858 974 TRANSDUCIN-LIKE ENHANCER PROTEIN 4. [SWISSPROT;Acc:Q04727] TLE4 1.38936 0.255411125

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/