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