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

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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Gene Rank Value Type description Interaction Map Network Comparison Type Filtered red network_comparison green
Results: HTML CSV LaTeX Showing element 1844 to 1893 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
network_comparison
green
922 tubulin-tyrosine ligase. [refseq;acc:nm_153712] Divided 5511.2 1.09862 6054.71
923 eukaryotic translation initiation factor 3 subunit 8 (eif3 p110) (eif3c). [swissprot;acc:q99613] 4057.54 1.09861 4457.66
nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182] Subtracted 3790.11 556.87 4346.98
924 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] 10243.4 556.58 9686.82
opioid binding protein/cell adhesion molecule precursor (obcam) (opioid-binding cell adhesion molecule) (opcml). [swissprot;acc:q14982] Divided 5406.5 1.09857 5939.42
925 grpe protein homolog 2, mitochondrial precursor (mt-grpe#2). [swissprot;acc:q8taa5] Subtracted 4134.77 556.47 4691.24
[pyruvate dehydrogenase [lipoamide]] kinase isozyme 1, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 1). [swissprot;acc:q15118] Divided 5637.43 1.09856 6193.07
926 grpe protein homolog 1, mitochondrial precursor (mt-grpe#1) (hmge). [swissprot;acc:q9hav7] Subtracted 4134.77 556.47 4691.24
[pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 2). [swissprot;acc:q15119] Divided 5637.45 1.09856 6193.08
927 dipeptidylpeptidase 10; dipeptidyl peptidase iv-related protein 3. [refseq;acc:nm_020868] 5638.64 1.09853 6194.22
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] Subtracted 4134.77 556.47 4691.24
928 cytochrome c oxidase assembly protein cox11, mitochondrial precursor. [swissprot;acc:q9y6n1] Divided 5638.46 1.09853 6194.04
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] Subtracted 4134.77 556.47 4691.24
929 surfeit locus protein 1. [swissprot;acc:q15526] Divided 5638.46 1.09853 6194.04
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] Subtracted 4134.77 556.47 4691.24
930 dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [swissprot;acc:p42658] Divided 5638.65 1.09853 6194.23
homeobox protein engrailed-2 (hu-en-2). [swissprot;acc:p19622] Subtracted 6281.21 556.4 6837.61
931 cpg binding protein (protein containing phd finger and cxxc domain 1). [swissprot;acc:q9p0u4]
seprase (ec 3.4.21.-) (fibroblast activation protein alpha) (integral membrane serine protease) (170-kda melanoma membrane-bound gelatinase). [swissprot;acc:q12884] Divided 5638.59 1.09853 6194.17
932 activator of basal transcription 1; tata-binding protein-binding protein; basal transcriptional activator. [refseq;acc:nm_013375] Subtracted 6281.21 556.4 6837.61
cox15 homolog isoform 2 precursor; cytochrome c oxidase subunit 15; cytochrome c oxidase assembly protein. [refseq;acc:nm_004376] Divided 5638.46 1.09853 6194.04
933 cytokine-like nuclear factor n-pac. [refseq;acc:nm_032569] Subtracted 6281.21 556.4 6837.61
protoheme ix farnesyltransferase, mitochondrial precursor (ec 2.5.1.-) (heme o synthase). [swissprot;acc:q12887] Divided 5638.46 1.09853 6194.04
934 hect type e3 ubiquitin ligase. [refseq;acc:nm_015052] Subtracted 6281.21 556.4 6837.61
[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] Divided 5640 1.0985 6195.52
935 homolog of yeast maf1. [refseq;acc:nm_032272] Subtracted 6133.83 556.35 6690.18
neurotrimin precursor (hnt). [swissprot;acc:q9p121] Divided 5413.63 1.09842 5946.46
936 nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] 5628.21 1.09811 6180.37
tumor differentially expressed protein 2. [refseq;acc:nm_178865] Subtracted 6133.83 556.35 6690.18
937 nucleobindin 1 precursor (calnuc). [swissprot;acc:q02818] Divided 5859.25 1.09776 6432.03
tumor differentially expressed protein 1 (transmembrane protein sbbi99). [swissprot;acc:q13530] Subtracted 6133.83 556.35 6690.18
938 dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692] Divided 5859.25 1.09776 6432.03
tumor differentially expressed 1 protein like. [swissprot;acc:q9nrx5] Subtracted 6133.83 556.35 6690.18
939 d-3-phosphoglycerate dehydrogenase (ec 1.1.1.95) (3-pgdh). [swissprot;acc:o43175]
nucleobindin 2 precursor (dna-binding protein nefa). [swissprot;acc:p80303] Divided 5859.25 1.09776 6432.03
940 adenosylhomocysteinase (ec 3.3.1.1) (s-adenosyl-l-homocysteine hydrolase) (adohcyase). [swissprot;acc:p23526] 5568.96 1.09775 6113.35
transducin-like enhancer protein 3 (esg3). [swissprot;acc:q04726] Subtracted 6280.74 556.27 6837.01
941 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] Divided 4970.21 1.09761 5455.34
paraspeckle protein 1. [refseq;acc:nm_018282] Subtracted 10241.3 556.09 9685.21
942 phosphoglycerate kinase, testis specific (ec 2.7.2.3). [swissprot;acc:p07205] Divided 6597.56 1.09747 7240.64
[pyruvate dehydrogenase [lipoamide]] kinase isozyme 1, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 1). [swissprot;acc:q15118] Subtracted 5637.43 555.64 6193.07
943 gamma enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (neural enolase) (nse) (enolase 2). [swissprot;acc:p09104] Divided 6597.98 1.09746 7241
[pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 2). [swissprot;acc:q15119] Subtracted 5637.45 555.63 6193.08
944 beta enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (skeletal muscle enolase) (mse) (enolase 3). [swissprot;acc:p13929] Divided 6597.98 1.09746 7241
dipeptidylpeptidase 10; dipeptidyl peptidase iv-related protein 3. [refseq;acc:nm_020868] Subtracted 5638.64 555.58 6194.22
945 alpha enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (non- neural enolase) (nne) (enolase 1) (phosphopyruvate hydratase). [swissprot;acc:p06733] Divided 6597.98 1.09746 7241
cytochrome c oxidase assembly protein cox11, mitochondrial precursor. [swissprot;acc:q9y6n1] Subtracted 5638.46 555.58 6194.04
946 phosphoglycerate kinase 1 (ec 2.7.2.3) (primer recognition protein 2) (prp 2). [swissprot;acc:p00558] Divided 6598.37 1.09744 7241.32
surfeit locus protein 1. [swissprot;acc:q15526] Subtracted 5638.46 555.58 6194.04
947 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

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/