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 description Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 3180 to 3229 of 9634 in total
Network Comparison Type  : Divided
Value Type  : Measured
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
918 nadp-dependent malic enzyme (ec 1.1.1.40) (nadp-me) (malic enzyme 1). [swissprot;acc:p48163] Low confidence 8284.79 8609.86 1.03924
scratch; scratch 1. [refseq;acc:nm_031309] High confidence 7281.6 8001.64 1.09888
919 limbic system-associated membrane protein precursor (lsamp). [swissprot;acc:q13449] 5396.36 5929.41 1.09878
proto-oncogene tyrosine-protein kinase fer (ec 2.7.1.112) (p94-fer) (c-fer). [swissprot;acc:p16591] Low confidence 7363.63 7652.4 1.03922
920 dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03] High confidence 7273.78 7991.72 1.0987
proto-oncogene tyrosine-protein kinase fes/fps (ec 2.7.1.112) (c-fes). [swissprot;acc:p07332] Low confidence 7363.99 7652.73 1.03921
921 60s ribosomal protein l29 (cell surface heparin binding protein hip). [swissprot;acc:p47914] 7363.79 7652.55
translation initiation factor if-2, mitochondrial precursor (if-2mt) (if-2(mt)). [swissprot;acc:p46199] High confidence 6324.31 6948.5 1.0987
922 tubulin-tyrosine ligase. [refseq;acc:nm_153712] 5511.2 6054.71 1.09862
xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7] Low confidence 7987.95 8300.91 1.03918
923 eukaryotic translation initiation factor 3 subunit 8 (eif3 p110) (eif3c). [swissprot;acc:q99613] High confidence 4057.54 4457.66 1.09861
glycogenin-1 (ec 2.4.1.186). [swissprot;acc:p46976] Low confidence 8186.49 8506.98 1.03915
924 opioid binding protein/cell adhesion molecule precursor (obcam) (opioid-binding cell adhesion molecule) (opcml). [swissprot;acc:q14982] High confidence 5406.5 5939.42 1.09857
syndecan-3 (synd3). [swissprot;acc:o75056] Low confidence 9050.12 9404.18 1.03912
925 my016 protein. [sptrembl;acc:q9h3k6] 8398.07 8726.39 1.03909
[pyruvate dehydrogenase [lipoamide]] kinase isozyme 1, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 1). [swissprot;acc:q15118] High confidence 5637.43 6193.07 1.09856
926 tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685] Low confidence 8051.79 8366.23 1.03905
[pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 2). [swissprot;acc:q15119] High confidence 5637.45 6193.08 1.09856
927 apurinic/apyrimidinic endonuclease 2; apurinic/apyrimidinic endonuclease-like 2; apex nuclease-like 2. [refseq;acc:nm_014481] Low confidence 8005.86 8318.27 1.03902
dipeptidylpeptidase 10; dipeptidyl peptidase iv-related protein 3. [refseq;acc:nm_020868] High confidence 5638.64 6194.22 1.09853
928 cytochrome c oxidase assembly protein cox11, mitochondrial precursor. [swissprot;acc:q9y6n1] 5638.46 6194.04
junctional adhesion molecule 1 precursor (jam) (platelet adhesion molecule 1) (pam-1) (platelet f11 receptor). [swissprot;acc:q9y624] Low confidence 8287.37 8610.75 1.03902
929 citrate synthase, mitochondrial precursor (ec 2.3.3.1). [swissprot;acc:o75390] 8070.54 8385.43
surfeit locus protein 1. [swissprot;acc:q15526] High confidence 5638.46 6194.04 1.09853
930 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
elongation factor ts, mitochondrial precursor (ef-ts) (ef-tsmt). [swissprot;acc:p43897] Low confidence 7928.24 8237.48 1.039
931 acidic leucine-rich nuclear phosphoprotein 32 family member c (tumorigenic protein pp32r1). [swissprot;acc:o43423] 7637.56 7935.35 1.03899
seprase (ec 3.4.21.-) (fibroblast activation protein alpha) (integral membrane serine protease) (170-kda melanoma membrane-bound gelatinase). [swissprot;acc:q12884] High confidence 5638.59 6194.17 1.09853
932 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] Low confidence 7637.56 7935.35 1.03899
cox15 homolog isoform 2 precursor; cytochrome c oxidase subunit 15; cytochrome c oxidase assembly protein. [refseq;acc:nm_004376] High confidence 5638.46 6194.04 1.09853
933 acidic leucine-rich nuclear phosphoprotein 32 family member d (tumorigenic protein pp32r2). [swissprot;acc:o95626] Low confidence 7637.56 7935.35 1.03899
protoheme ix farnesyltransferase, mitochondrial precursor (ec 2.5.1.-) (heme o synthase). [swissprot;acc:q12887] High confidence 5638.46 6194.04 1.09853
934 general vesicular transport factor p115 (transcytosis associated protein) (tap) (vesicle docking protein). [swissprot;acc:o60763] Low confidence 7637.56 7935.35 1.03899
[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] High confidence 5640 6195.52 1.0985
935 acidic leucine-rich nuclear phosphoprotein 32 family member b (phapi2 protein) (silver-stainable protein ssp29) (acidic protein rich in leucines). [swissprot;acc:q92688] Low confidence 7637.56 7935.35 1.03899
neurotrimin precursor (hnt). [swissprot;acc:q9p121] High confidence 5413.63 5946.46 1.09842
936 bromodomain containing 8; thyroid hormone receptor coactivating protein; skeletal muscle abundant protein. [refseq;acc:nm_006696] Low confidence 7637.56 7935.35 1.03899
nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] High confidence 5628.21 6180.37 1.09811
937 nucleobindin 1 precursor (calnuc). [swissprot;acc:q02818] 5859.25 6432.03 1.09776
protein x 0001. [refseq;acc:nm_016302] Low confidence 8214.28 8534.22 1.03895
938 dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692] High confidence 5859.25 6432.03 1.09776
hiv tat specific factor 1; cofactor required for tat activation of hiv-1 transcription. [refseq;acc:nm_014500] Low confidence 7751.77 8053.37 1.03891
939 mannose-6-phosphate isomerase (ec 5.3.1.8) (phosphomannose isomerase) (pmi) (phosphohexomutase). [swissprot;acc:p34949] 8454.45 8783.33 1.0389
nucleobindin 2 precursor (dna-binding protein nefa). [swissprot;acc:p80303] High confidence 5859.25 6432.03 1.09776
940 adenosylhomocysteinase (ec 3.3.1.1) (s-adenosyl-l-homocysteine hydrolase) (adohcyase). [swissprot;acc:p23526] 5568.96 6113.35 1.09775
nocturnin (ccr4 protein homolog). [swissprot;acc:q9uk39] Low confidence 7569.42 7863.85 1.0389
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] High confidence 4970.21 5455.34 1.09761
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] Low confidence 8020.09 8332.09 1.0389
942 mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 8454.45 8783.33
phosphoglycerate kinase, testis specific (ec 2.7.2.3). [swissprot;acc:p07205] High confidence 6597.56 7240.64 1.09747

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/