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 Value Type Network Comparison Type description Interaction Map red Filtered green network_comparison
Results: HTML CSV LaTeX Showing element 1844 to 1893 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
Network Comparison Type
description
red
green
network_comparison
922 Subtracted eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [swissprot;acc:p56537] 3893.85 4450.98 557.13
923 Divided eukaryotic translation initiation factor 3 subunit 8 (eif3 p110) (eif3c). [swissprot;acc:q99613] 4057.54 4457.66 1.09861
Subtracted nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182] 3790.11 4346.98 556.87
924 Divided opioid binding protein/cell adhesion molecule precursor (obcam) (opioid-binding cell adhesion molecule) (opcml). [swissprot;acc:q14982] 5406.5 5939.42 1.09857
Subtracted 54 kda nuclear rna- and dna-binding protein (p54(nrb)) (p54nrb) (55 kda nuclear protein) (nmt55) (non-pou domain-containing octamer- binding protein) (dna-binding p52/p100 complex, 52 kda subunit). [swissprot;acc:q15233] 10243.4 9686.82 556.58
925 Divided [pyruvate dehydrogenase [lipoamide]] kinase isozyme 1, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 1). [swissprot;acc:q15118] 5637.43 6193.07 1.09856
Subtracted grpe protein homolog 2, mitochondrial precursor (mt-grpe#2). [swissprot;acc:q8taa5] 4134.77 4691.24 556.47
926 Divided [pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 2). [swissprot;acc:q15119] 5637.45 6193.08 1.09856
Subtracted grpe protein homolog 1, mitochondrial precursor (mt-grpe#1) (hmge). [swissprot;acc:q9hav7] 4134.77 4691.24 556.47
927 Divided dipeptidylpeptidase 10; dipeptidyl peptidase iv-related protein 3. [refseq;acc:nm_020868] 5638.64 6194.22 1.09853
Subtracted swi/snf-related matrix-associated actin-dependent regulator of chromatin d2; rsc6p; mammalian chromatin remodeling complex brg1-associated factor 60b; swp73-like protein; chromatin remodeling complex baf60b subunit; swi/snf complex 60 kda subunit b. [refseq;acc:nm_003077] 4134.77 4691.24 556.47
928 Divided cytochrome c oxidase assembly protein cox11, mitochondrial precursor. [swissprot;acc:q9y6n1] 5638.46 6194.04 1.09853
Subtracted swi/snf-related matrix-associated actin-dependent regulator of chromatin d3; rsc6p; mammalian chromatin remodeling complex brg1-associated factor 60c; swp73-like protein; chromatin remodeling complex baf60c subunit; swi/snf complex 60 kda subunit c. [refseq;acc:nm_003078] 4134.77 4691.24 556.47
929 Divided surfeit locus protein 1. [swissprot;acc:q15526] 5638.46 6194.04 1.09853
Subtracted swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily d member 1 (swi/snf complex 60 kda subunit) (brg1- associated factor 60a). [swissprot;acc:q96gm5] 4134.77 4691.24 556.47
930 Divided dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [swissprot;acc:p42658] 5638.65 6194.23 1.09853
Subtracted homeobox protein engrailed-2 (hu-en-2). [swissprot;acc:p19622] 6281.21 6837.61 556.4
931 Divided seprase (ec 3.4.21.-) (fibroblast activation protein alpha) (integral membrane serine protease) (170-kda melanoma membrane-bound gelatinase). [swissprot;acc:q12884] 5638.59 6194.17 1.09853
Subtracted cpg binding protein (protein containing phd finger and cxxc domain 1). [swissprot;acc:q9p0u4] 6281.21 6837.61 556.4
932 Divided cox15 homolog isoform 2 precursor; cytochrome c oxidase subunit 15; cytochrome c oxidase assembly protein. [refseq;acc:nm_004376] 5638.46 6194.04 1.09853
Subtracted activator of basal transcription 1; tata-binding protein-binding protein; basal transcriptional activator. [refseq;acc:nm_013375] 6281.21 6837.61 556.4
933 Divided protoheme ix farnesyltransferase, mitochondrial precursor (ec 2.5.1.-) (heme o synthase). [swissprot;acc:q12887] 5638.46 6194.04 1.09853
Subtracted cytokine-like nuclear factor n-pac. [refseq;acc:nm_032569] 6281.21 6837.61 556.4
934 Divided [3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial precursor (ec 2.7.1.115) (branched-chain alpha-ketoacid dehydrogenase kinase) (bckdhkin) (bckd-kinase). [swissprot;acc:o14874] 5640 6195.52 1.0985
Subtracted hect type e3 ubiquitin ligase. [refseq;acc:nm_015052] 6281.21 6837.61 556.4
935 Divided neurotrimin precursor (hnt). [swissprot;acc:q9p121] 5413.63 5946.46 1.09842
Subtracted homolog of yeast maf1. [refseq;acc:nm_032272] 6133.83 6690.18 556.35
936 Divided nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] 5628.21 6180.37 1.09811
Subtracted tumor differentially expressed protein 2. [refseq;acc:nm_178865] 6133.83 6690.18 556.35
937 Divided nucleobindin 1 precursor (calnuc). [swissprot;acc:q02818] 5859.25 6432.03 1.09776
Subtracted tumor differentially expressed protein 1 (transmembrane protein sbbi99). [swissprot;acc:q13530] 6133.83 6690.18 556.35
938 Divided dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692] 5859.25 6432.03 1.09776
Subtracted tumor differentially expressed 1 protein like. [swissprot;acc:q9nrx5] 6133.83 6690.18 556.35
939 Divided nucleobindin 2 precursor (dna-binding protein nefa). [swissprot;acc:p80303] 5859.25 6432.03 1.09776
Subtracted d-3-phosphoglycerate dehydrogenase (ec 1.1.1.95) (3-pgdh). [swissprot;acc:o43175] 6133.83 6690.18 556.35
940 Divided adenosylhomocysteinase (ec 3.3.1.1) (s-adenosyl-l-homocysteine hydrolase) (adohcyase). [swissprot;acc:p23526] 5568.96 6113.35 1.09775
Subtracted transducin-like enhancer protein 3 (esg3). [swissprot;acc:q04726] 6280.74 6837.01 556.27
941 Divided caax prenyl protease 1 homolog (ec 3.4.24.-) (prenyl protein-specific endoprotease 1) (farnesylated-proteins converting enzyme 1) (face-1) (zinc metalloproteinase ste24 homolog). [swissprot;acc:o75844] 4970.21 5455.34 1.09761
Subtracted paraspeckle protein 1. [refseq;acc:nm_018282] 10241.3 9685.21 556.09
942 Divided phosphoglycerate kinase, testis specific (ec 2.7.2.3). [swissprot;acc:p07205] 6597.56 7240.64 1.09747
Subtracted [pyruvate dehydrogenase [lipoamide]] kinase isozyme 1, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 1). [swissprot;acc:q15118] 5637.43 6193.07 555.64
943 Divided gamma enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (neural enolase) (nse) (enolase 2). [swissprot;acc:p09104] 6597.98 7241 1.09746
Subtracted [pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 2). [swissprot;acc:q15119] 5637.45 6193.08 555.63
944 Divided beta enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (skeletal muscle enolase) (mse) (enolase 3). [swissprot;acc:p13929] 6597.98 7241 1.09746
Subtracted dipeptidylpeptidase 10; dipeptidyl peptidase iv-related protein 3. [refseq;acc:nm_020868] 5638.64 6194.22 555.58
945 Divided alpha enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (non- neural enolase) (nne) (enolase 1) (phosphopyruvate hydratase). [swissprot;acc:p06733] 6597.98 7241 1.09746
Subtracted cytochrome c oxidase assembly protein cox11, mitochondrial precursor. [swissprot;acc:q9y6n1] 5638.46 6194.04 555.58
946 Divided phosphoglycerate kinase 1 (ec 2.7.2.3) (primer recognition protein 2) (prp 2). [swissprot;acc:p00558] 6598.37 7241.32 1.09744
Subtracted surfeit locus protein 1. [swissprot;acc:q15526] 5638.46 6194.04 555.58
947 Divided signal transducing adaptor molecule 1; signal transducing adaptor molecule. [refseq;acc:nm_003473] 11797.1 10750.2 1.09738

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
- 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/