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 description expected Rank final
Results: HTML CSV LaTeX Showing element 2608 to 2657 of 3206 in total
measured
Hugo
description
expected
Rank
final
0.334146 CPSF1 "CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR, 160 KDA SUBUNIT (CPSF 160 KDA SUBUNIT). [SWISSPROT;Acc:Q10570]" 1.63634 2749 0.204203283
WDR33 WD-REPEAT PROTEIN WDC146. [SWISSPROT;Acc:Q9C0J8] 2748
0.33474 SLC15A2 "OLIGOPEPTIDE TRANSPORTER, KIDNEY ISOFORM (PEPTIDE TRANSPORTER 2) (KIDNEY H+/PEPTIDE COTRANSPORTER) (SOLUTE CARRIER FAMILY 15, MEMBER 2). [SWISSPROT;Acc:Q16348]" 1.10122 278 0.303971958
0.334862 UBE2I 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] 1.23982 581 0.270089206
0.334917 FDPS 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] 1.5203 2365 0.220296652
0.335885 CCDC42 1.33654 1098 0.251309351
0.336304 ABCF3 1.37608 1393 0.244392768
0.336662 EIF3I EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT 2 (EIF-3 BETA) (EIF3 P36) (EIF3I) (TGF-BETA RECEPTOR INTERACTING PROTEIN 1) (TRIP-1). [SWISSPROT;Acc:Q13347] 0.99966 181 0.336776504
0.337171 STAM2 SIGNAL TRANSDUCING ADAPTOR MOLECULE 2; STAM-LIKE PROTEIN CONTAINING SH3 AND ITAM DOMAINS 2. [RefSeq;Acc:NM_005843] 1.47582 2096 0.228463498
0.337407 PRKAR2B CAMP-DEPENDENT PROTEIN KINASE TYPE II-BETA REGULATORY CHAIN. [SWISSPROT;Acc:P31323] 1.40952 1624 0.239377235
0.337714 EPRS 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] 1.5325 2353 0.220368026
0.339171 DDX12 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] 1.6782 2766 0.20210404
0.339248 JUNB TRANSCRIPTION FACTOR JUN-B. [SWISSPROT;Acc:P17275] 1.0574 205 0.32083223
0.341129 HSP90AB1 HEAT SHOCK PROTEIN HSP 90-BETA (HSP 84) (HSP 90). [SWISSPROT;Acc:P08238] 1.34662 1039 0.253322392
0.341137 RFK 1.45621 1825 0.234263602
0.341608 EIF3M DENDRITIC CELL PROTEIN. [RefSeq;Acc:NM_006360] 1.36198 1116 0.250817193
0.341867 CAD 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] 1.49271 2083 0.229024392
0.342509 SOS2 SON OF SEVENLESS PROTEIN HOMOLOG 2 (SOS-2). [SWISSPROT;Acc:Q07890] 0.955286 122 0.358540793
0.343318 TAF11 TRANSCRIPTION INITIATION FACTOR TFIID 28 KDA SUBUNIT (TAFII-28) (TAFII28) (TFIID SUBUNIT P30-BETA). [SWISSPROT;Acc:Q15544] 1.35164 1013 0.254001065
0.343832 ASCC1 1.3576 1044 0.253264585
0.34395 HPRT1 HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE (EC 2.4.2.8) (HGPRT) (HGPRTASE). [SWISSPROT;Acc:P00492] 1.27889 609 0.268944163
0.343973 HEMK1 HEMK PROTEIN HOMOLOG (EC 2.1.1.-) (M.HSAHEMKP). [SWISSPROT;Acc:Q9Y5R4] 1.59051 2484 0.216265852
0.345566 no value TRANSFORMER-2 PROTEIN HOMOLOG (TRA-2 ALPHA). [SWISSPROT;Acc:Q13595] 1.24774 438 0.276953532
0.345751 POLR2H "DNA-DIRECTED RNA POLYMERASES I, II, AND III 17.1 KDA POLYPEPTIDE (EC 2.7.7.6) (RPB17) (RPB8) (RPABC3). [SWISSPROT;Acc:P52434]" 1.42971 1541 0.241832959
0.345758 GIT2 ARF GTPASE-ACTIVATING PROTEIN GIT2 (G PROTEIN-COUPLED RECEPTOR KINASE- INTERACTOR 2). [SWISSPROT;Acc:Q14161] 1.39492 1229 0.247869412
0.346601 OSGEP O-SIALOGLYCOPROTEIN ENDOPEPTIDASE. [RefSeq;Acc:NM_017807] 1.46589 1761 0.236444072
0.346654 RCAN1 CALCIPRESSIN 1 (DOWN SYNDROME CRITICAL REGION PROTEIN 1) (MYOCYTE- ENRICHED CALCINEURIN INTERACTING PROTEIN 1) (MCIP1) (ADAPT78). [SWISSPROT;Acc:P53805] 1.28942 611 0.268844907
0.346955 DPH2 DIPHTHAMIDE BIOSYNTHESIS-LIKE PROTEIN 2. [RefSeq;Acc:NM_001384] 1.55897 2278 0.222553994
0.3472 RPS13 40S RIBOSOMAL PROTEIN S13. [SWISSPROT;Acc:Q02546] 1.49288 1897 0.232570602
0.347203 KCTD10 MSTP028 PROTEIN. [RefSeq;Acc:NM_031954] 1.38684 1139 0.250355484
0.347585 STAT6 SIGNAL TRANSDUCER AND ACTIVATOR OF TRANSCRIPTION 6 (IL-4 STAT). [SWISSPROT;Acc:P42226] 1.3344 855 0.260480366
0.347798 PIN1 PEPTIDYL-PROLYL CIS-TRANS ISOMERASE NIMA-INTERACTING 1 (EC 5.2.1.8) (ROTAMASE PIN1) (PPIASE PIN1). [SWISSPROT;Acc:Q13526] 1.52661 2139 0.22782374
0.348199 LIN7B 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] 1.43405 1488 0.242808131
0.3486 no value DPY-30-LIKE PROTEIN. [SWISSPROT;Acc:Q9C005] 1.32226 768 0.263639526
0.348668 GMPS GMP SYNTHASE [GLUTAMINE-HYDROLYZING] (EC 6.3.5.2) (GLUTAMINE AMIDOTRANSFERASE) (GMP SYNTHETASE). [SWISSPROT;Acc:P49915] 1.27232 507 0.274041122
0.349158 RBM39 RNA-BINDING REGION CONTAINING PROTEIN 2 (HEPATOCELLULAR CARCINOMA PROTEIN 1) (SPLICING FACTOR HCC1). [SWISSPROT;Acc:Q14498] 1.32674 780 0.263169875
0.349374 CTBP1 C-TERMINAL BINDING PROTEIN 1 (CTBP1). [SWISSPROT;Acc:Q13363] 1.32007 733 0.264663238
0.349731 DPM1 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] 1.80836 2829 0.193396779
0.351386 PRPF3 U4/U6-ASSOCIATED RNA SPLICING FACTOR. [RefSeq;Acc:NM_004698] 1.32896 754 0.264406754
0.352259 DCLK2 1.44441 1425 0.243877431
0.352414 MEIS1 HOMEOBOX PROTEIN MEIS1. [SWISSPROT;Acc:O00470] 1.39495 1067 0.252635578
0.352885 COQ5 1.47667 1649 0.238973501
0.353001 FUBP1 FAR UPSTREAM ELEMENT-BINDING PROTEIN; FAR UPSTREAM ELEMENT BINDING PROTEIN; FUSE-BINDING PROTEIN. [RefSeq;Acc:NM_003902] 1.35261 834 0.260977665
0.353795 PDHA2 "PYRUVATE DEHYDROGENASE E1 COMPONENT ALPHA SUBUNIT, TESTIS-SPECIFIC FORM, MITOCHONDRIAL PRECURSOR (EC 1.2.4.1) (PDHE1-A TYPE II). [SWISSPROT;Acc:P29803]" 1.53626 2030 0.230296304
0.353823 GUK1 GUANYLATE KINASE (EC 2.7.4.8) (GMP KINASE). [SWISSPROT;Acc:Q16774] 1.61155 2392 0.219554466
0.354332 CRLS1 1.72277 2731 0.205675743
0.354424 FMR1 FRAGILE X MENTAL RETARDATION 1 PROTEIN (PROTEIN FMR-1) (FMRP). [SWISSPROT;Acc:Q06787] 1.45239 1405 0.244028119
0.354694 YWHAZ 14-3-3 PROTEIN ZETA/DELTA (PROTEIN KINASE C INHIBITOR PROTEIN-1) (KCIP-1) (FACTOR ACTIVATING EXOENZYME S) (FAS). [SWISSPROT;Acc:P29312] 1.66376 2576 0.2131882
0.35482 RPL18 60S RIBOSOMAL PROTEIN L18. [SWISSPROT;Acc:Q07020] 1.55638 2132 0.227977743
0.354858 TLE4 TRANSDUCIN-LIKE ENHANCER PROTEIN 4. [SWISSPROT;Acc:Q04727] 1.38936 974 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/