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 [...,...].
measured Hugo Gene Rank expected description final
Results: HTML CSV LaTeX Showing element 2558 to 2607 of 3206 in total
measured
Hugo
Rank
expected
description
final
0.312681 no value 61 0.760495 PUTATIVE ADENOSYLHOMOCYSTEINASE 3 (EC 3.3.1.1) (S-ADENOSYL-L- HOMOCYSTEINE HYDROLASE) (ADOHCYASE). [SWISSPROT;Acc:Q96HN2] 0.411154577
CREG1 60 CELLULAR REPRESSOR OF E1A-STIMULATED GENES. [RefSeq;Acc:NM_003851]
0.31296 ECH1 72 0.770597 "DELTA3,5-DELTA2,4-DIENOYL-COA ISOMERASE, MITOCHONDRIAL PRECURSOR (EC 5.3.3.-). [SWISSPROT;Acc:Q13011]" 0.406126678
0.313086 AP1B1 1164 1.25482 ADAPTER-RELATED PROTEIN COMPLEX 1 BETA 1 SUBUNIT (BETA-ADAPTIN 1) (ADAPTOR PROTEIN COMPLEX AP-1 BETA-1 SUBUNIT) (GOLGI ADAPTOR HA1/AP1 ADAPTIN BETA SUBUNIT) (CLATHRIN ASSEMBLY PROTEIN COMPLEX 1 BETA LARGE CHAIN). [SWISSPROT;Acc:Q10567] 0.249506702
0.313207 OGDH 2093 1.36954 "2-OXOGLUTARATE DEHYDROGENASE E1 COMPONENT, MITOCHONDRIAL PRECURSOR (EC 1.2.4.2) (ALPHA-KETOGLUTARATE DEHYDROGENASE). [SWISSPROT;Acc:Q02218]" 0.228695036
0.313715 UBAP2L 517 1.15171 0.272390619
0.314149 PFKM 2948 2.07226 "6-PHOSPHOFRUCTOKINASE, MUSCLE TYPE (EC 2.7.1.11) (PHOSPHOFRUCTOKINASE 1) (PHOSPHOHEXOKINASE) (PHOSPHOFRUCTO-1-KINASE ISOZYME A) (PFK-A) (PHOSPHOFRUCTOKINASE-M). [SWISSPROT;Acc:P08237]" 0.15159729
0.314489 DHODH 2269 1.41191 "DIHYDROOROTATE DEHYDROGENASE, MITOCHONDRIAL PRECURSOR (EC 1.3.3.1) (DIHYDROOROTATE OXIDASE) (DHODEHASE) (FRAGMENT). [SWISSPROT;Acc:Q02127]" 0.222740118
0.314497 GPKOW 877 1.20911 T54 PROTEIN. [SWISSPROT;Acc:Q92917] 0.260106194
0.3145 CCDC53 358 1.11741 PROTEIN AD-016 (PROTEIN CGI-116) (X0009). [SWISSPROT;Acc:Q9Y3C0] 0.281454435
0.314547 SNX6 982 1.23231 SORTING NEXIN 6 (TRAF4-ASSOCIATED FACTOR 2). [SWISSPROT;Acc:Q9UNH7] 0.255249897
0.315262 ABI2 500 1.14976 ABL-INTERACTOR 2; ABL-INTERACTING PROTEIN 1 (SH3-CONTAINING PROTEIN); ABL BINDING PROTEIN 3; ARG PROTEIN TYROSINE KINASE-BINDING PROTEIN; ABL-INTERACTOR PROTEIN 2B; SIMILAR TO SPECTRIN SH3 DOMAIN BINDING PROTEIN 1. [RefSeq;Acc:NM_005759] 0.274198094
0.316686 TRIT1 2332 1.4315 TRNA ISOPENTENYLPYROPHOSPHATE TRANSFERASE. [RefSeq;Acc:NM_017646] 0.221226685
0.316909 C14orf172 274 1.03903 0.305004668
0.317455 CNNM2 1657 1.3291 CYCLIN M2; ANCIENT CONSERVED DOMAIN PROTEIN 2. [RefSeq;Acc:NM_017649] 0.238849597
0.317621 SNX5 1011 1.24807 SORTING NEXIN 5. [SWISSPROT;Acc:Q9Y5X3] 0.254489732
0.317947 ARPC1B 732 1.20127 ARP2/3 COMPLEX 41 KDA SUBUNIT (P41-ARC) (ACTIN-RELATED PROTEIN 2/3 COMPLEX SUBUNIT 1B). [SWISSPROT;Acc:O15143] 0.264675718
0.318597 KARS 1206 1.28364 LYSYL-TRNA SYNTHETASE (EC 6.1.1.6) (LYSINE--TRNA LIGASE) (LYSRS). [SWISSPROT;Acc:Q15046] 0.248198093
0.318787 PEF1 172 0.941277 PEF PROTEIN WITH A LONG N-TERMINAL HYDROPHOBIC DOMAIN (PEFLIN). [RefSeq;Acc:NM_012392] 0.338675013
0.318849 no value 53 0.775495 DISKS LARGE-ASSOCIATED PROTEIN 2 (DAP-2) (SAP90/PSD-95-ASSOCIATED PROTEIN 2) (SAPAP2) (PSD-95/SAP90 BINDING PROTEIN 2) (FRAGMENT). [SWISSPROT;Acc:Q9P1A6] 0.411155456
0.319576 GIT1 1182 1.28396 ARF GTPASE-ACTIVATING PROTEIN GIT1 (G PROTEIN-COUPLED RECEPTOR KINASE- INTERACTOR 1). [SWISSPROT;Acc:Q9Y2X7] 0.24889872
0.320357 TNS1 779 1.21727 TENSIN. [RefSeq;Acc:NM_022648] 0.263176617
0.321031 MDN1 1720 1.35288 MIDASIN (MIDAS-CONTAINING PROTEIN). [SWISSPROT;Acc:Q9NU22] 0.237294512
0.321097 RNASEH2A 2467 1.48248 RIBONUCLEASE HI LARGE SUBUNIT (EC 3.1.26.-) (RNASE HI LARGE SUBUNIT) (RNASE H(35)) (RIBONUCLEASE H2) (RNASE H2). [SWISSPROT;Acc:O75792] 0.21659449
0.321507 AARS 1862 1.37786 ALANYL-TRNA SYNTHETASE (EC 6.1.1.7) (ALANINE--TRNA LIGASE) (ALARS). [SWISSPROT;Acc:P49588] 0.23333793
0.32192 no value 980 1.26105 0.255279331
0.322293 NDUFB10 1533 1.3313 NADH-UBIQUINONE OXIDOREDUCTASE PDSW SUBUNIT (EC 1.6.5.3) (EC 1.6.99.3) (COMPLEX I-PDSW) (CI-PDSW). [SWISSPROT;Acc:O96000] 0.242088936
0.322726 ACTR3B 722 1.21932 SIMILAR TO ACTIN-RELATED PROTEIN 3-BETA. [SPTREMBL;Acc:Q96BT2] 0.264677033
0.322756 DPH1 2329 1.45734 CANDIDATE TUMOR SUPPRESSOR IN OVARIAN CANCER 2. [RefSeq;Acc:NM_080822] 0.221469252
0.322799 MEIS2 1068 1.27773 HOMEOBOX PROTEIN MEIS2 (MEIS1-RELATED PROTEIN 1). [SWISSPROT;Acc:O14770] 0.252634751
0.322861 no value 1775 1.36866 SCRATCH; SCRATCH 1. [RefSeq;Acc:NM_031309] 0.235895694
0.32361 LIN7A 1486 1.33263 LIN-7 HOMOLOG A; VERTEBRATE LIN7 HOMOLOG 1; TAX INTERACTION PROTEIN 33; MAMMALIAN LIN-7 1. [RefSeq;Acc:NM_004664] 0.242835596
0.324046 no value 2767 1.60341 HELICASE (FRAGMENT). [SPTREMBL;Acc:Q92771] 0.202098029
0.326192 EIF5A2 1588 1.35491 EIF-5A2 PROTEIN. [RefSeq;Acc:NM_020390] 0.240748094
0.327115 SNX1 2300 1.47133 SORTING NEXIN 1. [SWISSPROT;Acc:Q13596] 0.222326059
0.327497 no value 2372 1.48829 RIBULOSE-5-PHOSPHATE-3-EPIMERASE; RIBULOSE 5-PHOSPHATE 3-EPIMERASE. [RefSeq;Acc:NM_006916] 0.220049184
0.329144 COPB1 3029 2.79482 COATOMER BETA SUBUNIT (BETA-COAT PROTEIN) (BETA-COP). [SWISSPROT;Acc:P53618] 0.117769302
0.329649 ATG16L2 305 1.10466 0.298416707
0.329852 COPA 3006 2.63087 COATOMER ALPHA SUBUNIT (ALPHA-COAT PROTEIN) (ALPHA-COP) (HEPCOP) (HEP-COP) [CONTAINS: XENIN (XENOPSIN-RELATED PEPTIDE); PROXENIN]. [SWISSPROT;Acc:P53621] 0.125377537
0.330618 FUBP3 835 1.26685 FUSE BINDING PROTEIN 3 (FRAGMENT). [SPTREMBL;Acc:Q92946] 0.260976438
0.331362 TAF5 2368 1.50518 TRANSCRIPTION INITIATION FACTOR TFIID 100 KDA SUBUNIT (TAFII-100) (TAFII100). [SWISSPROT;Acc:Q15542] 0.220147756
0.331603 KIF2B 227 1.04653 KINESIN PROTEIN. [RefSeq;Acc:NM_032559] 0.316859526
0.331884 STAT1 858 1.2742 SIGNAL TRANSDUCER AND ACTIVATOR OF TRANSCRIPTION 1-ALPHA/BETA (TRANSCRIPTION FACTOR ISGF-3 COMPONENTS P91/P84). [SWISSPROT;Acc:P42224] 0.260464605
0.332106 WDSOF1 1514 1.37021 0.242375986
0.33278 ATP6V0D2 1763 1.40872 "ATPASE, H+ TRANSPORTING, LYSOSOMAL 38KDA, V0 SUBUNIT D ISOFORM 2. [RefSeq;Acc:NM_152565]" 0.236228633
0.333006 STAT4 857 1.2785 SIGNAL TRANSDUCER AND ACTIVATOR OF TRANSCRIPTION 4. [SWISSPROT;Acc:Q14765] 0.260466171
0.333016 CDC5L 520 1.2232 "CDC5-LIKE; CDC5 (CELL DIVISION CYCLE 5, S. POMBE, HOMOLOG)-LIKE; CELL DIVISION CYCLE 5, S. POMBE, HOMOLOG-LIKE; CDC5-RELATED PROTEIN. [RefSeq;Acc:NM_001253]" 0.272249836
0.333664 TLE3 984 1.30756 TRANSDUCIN-LIKE ENHANCER PROTEIN 3 (ESG3). [SWISSPROT;Acc:Q04726] 0.255180642
0.333707 STAT3 856 1.28119 SIGNAL TRANSDUCER AND ACTIVATOR OF TRANSCRIPTION 3 (ACUTE-PHASE RESPONSE FACTOR). [SWISSPROT;Acc:P40763] 0.260466441
0.334139 ADSS 2179 1.47327 ADENYLOSUCCINATE SYNTHETASE (EC 6.3.4.4) (IMP--ASPARTATE LIGASE) (ADSS) (AMPSASE). [SWISSPROT;Acc:P30520] 0.226800926

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/