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 Analysis - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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 [...,...].
Rank Gene Network Comparison Type Hugo description Value Type Interaction Map Filtered network_comparison red green
Results: HTML CSV LaTeX Showing element 3708 to 3757 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
Network Comparison Type
Hugo
description
network_comparison
red
green
1854 Subtracted BBOX1 gamma-butyrobetaine,2-oxoglutarate dioxygenase (ec 1.14.11.1) (gamma-butyrobetaine hydroxylase) (gamma-bbh). [swissprot;acc:o75936] 2.342 212.455 210.113
1855 Divided GRSF1 g-rich sequence factor-1 (grsf-1). [swissprot;acc:q12849] 1.0109 217.891 215.542
Subtracted ATP11A potential phospholipid-transporting atpase ih (ec 3.6.3.1) (atpase class i type 11a) (atpase is). [swissprot;acc:p98196] 2.342 212.455 210.113
1856 Divided HNRPH3 heterogeneous nuclear ribonucleoprotein h3 (hnrnp h3) (hnrnp 2h9). [swissprot;acc:p31942] 1.0109 217.892 215.543
Subtracted APEX1 dna-(apurinic or apyrimidinic site) lyase (ec 4.2.99.18) (ap endonuclease 1) (apex nuclease) (apen) (ref-1 protein). [swissprot;acc:p27695] 2.338 211.882 209.544
1857 Divided EIF2B3 translation initiation factor eif-2b gamma subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q9nr50] 1.0109 222.215 224.637
Subtracted GMPPB gdp-mannose pyrophosphorylase b isoform 1; mannose-1-phosphate guanylyltransferase; amphoterin induced gene 3. [refseq;acc:nm_013334] 2.328 222.842 225.17
1858 Divided HNRPF heterogeneous nuclear ribonucleoprotein f (hnrnp f). [swissprot;acc:p52597] 1.01089 217.893 215.545
Subtracted GMPPA gdp-mannose pyrophosphorylase a; mannose-1-phosphate guanylyltransferase (gdp). [refseq;acc:nm_013335] 2.328 222.842 225.17
1859 Divided HNRPH1 heterogeneous nuclear ribonucleoprotein h (hnrnp h). [swissprot;acc:p31943] 1.01089 217.895 215.547
Subtracted SARM1 sterile alpha and tir motif containing 1; sterile alpha and heat/armadillo motif protein, ortholog of drosophila. [refseq;acc:nm_015077] 2.319 220.896 218.577
1860 Divided HNRPH2 heterogeneous nuclear ribonucleoprotein h' (hnrnp h') (ftp-3). [swissprot;acc:p55795] 1.01089 217.895 215.547
Subtracted FXR2 fragile x mental retardation syndrome related protein 2. [swissprot;acc:p51116] 2.3 202.386 200.086
1861 Divided CYB5R2 cytochrome b5 reductase b5r.2. [refseq;acc:nm_016229] 1.01087 210.856 213.147
Subtracted FXR1 fragile x mental retardation syndrome related protein 1. [swissprot;acc:p51114] 2.3 202.386 200.086
1862 Divided CYB5R1 cytochrome b5 reductase 1 (b5r.1). [refseq;acc:nm_016243] 1.01087 210.856 213.147
Subtracted NUP43 nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] 2.299 202.393 200.094
1863 Divided CYB5R3 nadh-cytochrome b5 reductase (ec 1.6.2.2) (b5r). [swissprot;acc:p00387] 1.01087 210.856 213.147
Subtracted FMR1 fragile x mental retardation 1 protein (protein fmr-1) (fmrp). [swissprot;acc:q06787] 2.295 202.41 200.115
1864 Divided PUF60 fuse-binding protein-interacting repressor isoform b; siah binding protein 1; pyrimidine tract binding splicing factor; ro ribonucleoprotein-binding protein 1; poly-u binding splicing factor puf60. [refseq;acc:nm_014281] 1.01086 203.071 200.89
Subtracted OLA1 putative gtp-binding protein ptd004 (pro2455). [swissprot;acc:q9ntk5] 2.292 215.081 217.373
1865 Divided EIF2S3 eukaryotic translation initiation factor 2 subunit 3 (eukaryotic translation initiation factor 2 gamma subunit) (eif-2-gamma). [swissprot;acc:p41091] 1.01086 221.639 224.046
Subtracted CYB5R2 cytochrome b5 reductase b5r.2. [refseq;acc:nm_016229] 2.291 210.856 213.147
1866 Divided EIF2B4 translation initiation factor eif-2b delta subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q9ui10] 1.01086 221.725 224.133
Subtracted CYB5R1 cytochrome b5 reductase 1 (b5r.1). [refseq;acc:nm_016243] 2.291 210.856 213.147
1867 Divided no value multisynthetase complex auxiliary component p38 (jtv-1 protein) (pro0992). [swissprot;acc:q13155] 1.01086 203.071 200.89
Subtracted CYB5R3 nadh-cytochrome b5 reductase (ec 1.6.2.2) (b5r). [swissprot;acc:p00387] 2.291 210.856 213.147
1868 Divided TPD52L3 protein kinase nyd-sp25. [refseq;acc:nm_033516] 1.01085 207.642 209.895
Subtracted RPL28 60s ribosomal protein l28. [swissprot;acc:p46779] 2.286 215.896 213.61
1869 Divided LANCL2 lanc lantibiotic synthetase component c-like 2; testis-specific adriamycin sensitivity protein; lanc (bacterial lantibiotic synthetase component c)-like 2; g protein-coupled receptor 69b. [refseq;acc:nm_018697] 1.01082 220.107 217.75
Subtracted ICT1 immature colon carcinoma transcript 1 (digestion substraction 1) (ds- 1). [swissprot;acc:q14197] 2.283 218.414 216.131
1870 Divided LANCL1 lanthionine synthetase c-like protein 1; g protein-coupled receptor 69a; lanc (bacterial lantibiotic synthetase component c)-like 1; lanc (bacterial lantibiotic synthetase component). [refseq;acc:nm_006055] 1.01082 220.107 217.75
Subtracted NUCB1 nucleobindin 1 precursor (calnuc). [swissprot;acc:q02818] 2.281 212.186 214.467
1871 Divided CLPX atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [swissprot;acc:o76031] 1.01081 222.819 225.228
Subtracted MLH1 dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692] 2.281 212.186 214.467
1872 Divided POLDIP2 dna polymerase delta p38 subunit. [refseq;acc:nm_015584] 1.01081 222.819 225.228
Subtracted NUCB2 nucleobindin 2 precursor (dna-binding protein nefa). [swissprot;acc:p80303] 2.281 212.186 214.467
1873 Divided no value scratch; scratch 1. [refseq;acc:nm_031309] 1.01078 210.55 208.305
Subtracted NME2P1 putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361] 2.277 193.1 190.823
1874 Divided no value williams-beuren syndrome critical region protein 20 copy b. [refseq;acc:nm_145645] 1.01076 223.862 226.271
Subtracted nucleoside diphosphate kinase b (ec 2.7.4.6) (ndk b) (ndp kinase b) (nm23-h2) (c-myc purine-binding transcription factor puf). [swissprot;acc:p22392] 2.277 193.138 190.861
1875 Divided NSUN5 williams beuren syndrome critical region 20a isoform 2; nol1/nop2/sun gene family member; williams-beuren syndrome critical region protein 20 copy a; williams beuren syndrome chromosome region 20. [refseq;acc:nm_018044] 1.01076 223.862 226.271
Subtracted NME2 nucleoside diphosphate kinase a (ec 2.7.4.6) (ndk a) (ndp kinase a) (tumor metastatic process-associated protein) (metastasis inhibition factor nm23) (nm23-h1). [swissprot;acc:p15531] 2.277 193.111 190.834
1876 Divided NSUN5B williams beuren syndrome chromosome region 20c isoform 1. [refseq;acc:nm_032158] 1.01076 223.862 226.271
Subtracted HSD17B4 estradiol 17 beta-dehydrogenase 4 (ec 1.1.1.62) (17-beta-hsd 4) (17-beta-hydroxysteroid dehydrogenase 4). [swissprot;acc:p51659] 2.258 185.276 187.534
1877 Divided NUCB1 nucleobindin 1 precursor (calnuc). [swissprot;acc:q02818] 1.01075 212.186 214.467
Subtracted TPD52L3 protein kinase nyd-sp25. [refseq;acc:nm_033516] 2.253 207.642 209.895
1878 Divided MLH1 dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692] 1.01075 212.186 214.467
Subtracted no value scratch; scratch 1. [refseq;acc:nm_031309] 2.245 210.55 208.305
1879 Divided NUCB2 nucleobindin 2 precursor (dna-binding protein nefa). [swissprot;acc:p80303] 1.01075 212.186 214.467

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 HGNC identifier if it exists
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.
- http://analysis.yellowcouch.org/