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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Network Comparison Type Value Type Gene Rank Interaction Map green network_comparison description red Filtered
Results: HTML CSV LaTeX Showing element 3180 to 3229 of 77072 in total
Network Comparison Type  : Divided
Value Type  : Measured
Filtered  : 1
Rank
Interaction Map
green
network_comparison
description
red
918 High confidence 8001.64 1.09888 scratch; scratch 1. [refseq;acc:nm_031309] 7281.6
Low confidence 8609.86 1.03924 nadp-dependent malic enzyme (ec 1.1.1.40) (nadp-me) (malic enzyme 1). [swissprot;acc:p48163] 8284.79
919 High confidence 5929.41 1.09878 limbic system-associated membrane protein precursor (lsamp). [swissprot;acc:q13449] 5396.36
Low confidence 7652.4 1.03922 proto-oncogene tyrosine-protein kinase fer (ec 2.7.1.112) (p94-fer) (c-fer). [swissprot;acc:p16591] 7363.63
920 High confidence 7991.72 1.0987 dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03] 7273.78
Low confidence 7652.73 1.03921 proto-oncogene tyrosine-protein kinase fes/fps (ec 2.7.1.112) (c-fes). [swissprot;acc:p07332] 7363.99
921 High confidence 6948.5 1.0987 translation initiation factor if-2, mitochondrial precursor (if-2mt) (if-2(mt)). [swissprot;acc:p46199] 6324.31
Low confidence 7652.55 1.03921 60s ribosomal protein l29 (cell surface heparin binding protein hip). [swissprot;acc:p47914] 7363.79
922 High confidence 6054.71 1.09862 tubulin-tyrosine ligase. [refseq;acc:nm_153712] 5511.2
Low confidence 8300.91 1.03918 xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7] 7987.95
923 High confidence 4457.66 1.09861 eukaryotic translation initiation factor 3 subunit 8 (eif3 p110) (eif3c). [swissprot;acc:q99613] 4057.54
Low confidence 8506.98 1.03915 glycogenin-1 (ec 2.4.1.186). [swissprot;acc:p46976] 8186.49
924 High confidence 5939.42 1.09857 opioid binding protein/cell adhesion molecule precursor (obcam) (opioid-binding cell adhesion molecule) (opcml). [swissprot;acc:q14982] 5406.5
Low confidence 9404.18 1.03912 syndecan-3 (synd3). [swissprot;acc:o75056] 9050.12
925 High confidence 6193.07 1.09856 [pyruvate dehydrogenase [lipoamide]] kinase isozyme 1, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 1). [swissprot;acc:q15118] 5637.43
Low confidence 8726.39 1.03909 my016 protein. [sptrembl;acc:q9h3k6] 8398.07
926 High confidence 6193.08 1.09856 [pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 2). [swissprot;acc:q15119] 5637.45
Low confidence 8366.23 1.03905 tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685] 8051.79
927 High confidence 6194.22 1.09853 dipeptidylpeptidase 10; dipeptidyl peptidase iv-related protein 3. [refseq;acc:nm_020868] 5638.64
Low confidence 8318.27 1.03902 apurinic/apyrimidinic endonuclease 2; apurinic/apyrimidinic endonuclease-like 2; apex nuclease-like 2. [refseq;acc:nm_014481] 8005.86
928 High confidence 6194.04 1.09853 cytochrome c oxidase assembly protein cox11, mitochondrial precursor. [swissprot;acc:q9y6n1] 5638.46
Low confidence 8610.75 1.03902 junctional adhesion molecule 1 precursor (jam) (platelet adhesion molecule 1) (pam-1) (platelet f11 receptor). [swissprot;acc:q9y624] 8287.37
929 High confidence 6194.04 1.09853 surfeit locus protein 1. [swissprot;acc:q15526] 5638.46
Low confidence 8385.43 1.03902 citrate synthase, mitochondrial precursor (ec 2.3.3.1). [swissprot;acc:o75390] 8070.54
930 High confidence 6194.23 1.09853 dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [swissprot;acc:p42658] 5638.65
Low confidence 8237.48 1.039 elongation factor ts, mitochondrial precursor (ef-ts) (ef-tsmt). [swissprot;acc:p43897] 7928.24
931 High confidence 6194.17 1.09853 seprase (ec 3.4.21.-) (fibroblast activation protein alpha) (integral membrane serine protease) (170-kda melanoma membrane-bound gelatinase). [swissprot;acc:q12884] 5638.59
Low confidence 7935.35 1.03899 acidic leucine-rich nuclear phosphoprotein 32 family member c (tumorigenic protein pp32r1). [swissprot;acc:o43423] 7637.56
932 High confidence 6194.04 1.09853 cox15 homolog isoform 2 precursor; cytochrome c oxidase subunit 15; cytochrome c oxidase assembly protein. [refseq;acc:nm_004376] 5638.46
Low confidence 7935.35 1.03899 acidic leucine-rich nuclear phosphoprotein 32 family member a (potent heat-stable protein phosphatase 2a inhibitor i1pp2a) (hla-dr associated protein i) (phapi) (acidic nuclear phosphoprotein pp32) (cerebellar leucine rich acidic nuclear protein). [swissprot;acc:p39687] 7637.56
933 High confidence 6194.04 1.09853 protoheme ix farnesyltransferase, mitochondrial precursor (ec 2.5.1.-) (heme o synthase). [swissprot;acc:q12887] 5638.46
Low confidence 7935.35 1.03899 acidic leucine-rich nuclear phosphoprotein 32 family member d (tumorigenic protein pp32r2). [swissprot;acc:o95626] 7637.56
934 High confidence 6195.52 1.0985 [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
Low confidence 7935.35 1.03899 general vesicular transport factor p115 (transcytosis associated protein) (tap) (vesicle docking protein). [swissprot;acc:o60763] 7637.56
935 High confidence 5946.46 1.09842 neurotrimin precursor (hnt). [swissprot;acc:q9p121] 5413.63
Low confidence 7935.35 1.03899 acidic leucine-rich nuclear phosphoprotein 32 family member b (phapi2 protein) (silver-stainable protein ssp29) (acidic protein rich in leucines). [swissprot;acc:q92688] 7637.56
936 High confidence 6180.37 1.09811 nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] 5628.21
Low confidence 7935.35 1.03899 bromodomain containing 8; thyroid hormone receptor coactivating protein; skeletal muscle abundant protein. [refseq;acc:nm_006696] 7637.56
937 High confidence 6432.03 1.09776 nucleobindin 1 precursor (calnuc). [swissprot;acc:q02818] 5859.25
Low confidence 8534.22 1.03895 protein x 0001. [refseq;acc:nm_016302] 8214.28
938 High confidence 6432.03 1.09776 dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692] 5859.25
Low confidence 8053.37 1.03891 hiv tat specific factor 1; cofactor required for tat activation of hiv-1 transcription. [refseq;acc:nm_014500] 7751.77
939 High confidence 6432.03 1.09776 nucleobindin 2 precursor (dna-binding protein nefa). [swissprot;acc:p80303] 5859.25
Low confidence 8783.33 1.0389 mannose-6-phosphate isomerase (ec 5.3.1.8) (phosphomannose isomerase) (pmi) (phosphohexomutase). [swissprot;acc:p34949] 8454.45
940 High confidence 6113.35 1.09775 adenosylhomocysteinase (ec 3.3.1.1) (s-adenosyl-l-homocysteine hydrolase) (adohcyase). [swissprot;acc:p23526] 5568.96
Low confidence 7863.85 1.0389 nocturnin (ccr4 protein homolog). [swissprot;acc:q9uk39] 7569.42
941 High confidence 5455.34 1.09761 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
Low confidence 8332.09 1.0389 transcription factor ap-2 alpha (ap2-alpha) (activating enhancer- binding protein 2 alpha) (ap-2 transcription factor) (activator protein-2) (ap-2). [swissprot;acc:p05549] 8020.09
942 High confidence 7240.64 1.09747 phosphoglycerate kinase, testis specific (ec 2.7.2.3). [swissprot;acc:p07205] 6597.56
Low confidence 8783.33 1.0389 mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 8454.45

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/