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 Value Type Rank green Filtered Network Comparison Type description network_comparison Interaction Map red
Results: HTML CSV LaTeX Showing element 3180 to 3229 of 38536 in total
Value Type  : Measured
Filtered  : 1
Network Comparison Type  : Divided
Rank
green
description
network_comparison
Interaction Map
red
918 8001.64 scratch; scratch 1. [refseq;acc:nm_031309] 1.09888 High confidence 7281.6
8609.86 nadp-dependent malic enzyme (ec 1.1.1.40) (nadp-me) (malic enzyme 1). [swissprot;acc:p48163] 1.03924 Low confidence 8284.79
919 5929.41 limbic system-associated membrane protein precursor (lsamp). [swissprot;acc:q13449] 1.09878 High confidence 5396.36
7652.4 proto-oncogene tyrosine-protein kinase fer (ec 2.7.1.112) (p94-fer) (c-fer). [swissprot;acc:p16591] 1.03922 Low confidence 7363.63
920 7652.73 proto-oncogene tyrosine-protein kinase fes/fps (ec 2.7.1.112) (c-fes). [swissprot;acc:p07332] 1.03921 7363.99
7991.72 dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03] 1.0987 High confidence 7273.78
921 6948.5 translation initiation factor if-2, mitochondrial precursor (if-2mt) (if-2(mt)). [swissprot;acc:p46199] 6324.31
7652.55 60s ribosomal protein l29 (cell surface heparin binding protein hip). [swissprot;acc:p47914] 1.03921 Low confidence 7363.79
922 6054.71 tubulin-tyrosine ligase. [refseq;acc:nm_153712] 1.09862 High confidence 5511.2
8300.91 xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7] 1.03918 Low confidence 7987.95
923 4457.66 eukaryotic translation initiation factor 3 subunit 8 (eif3 p110) (eif3c). [swissprot;acc:q99613] 1.09861 High confidence 4057.54
8506.98 glycogenin-1 (ec 2.4.1.186). [swissprot;acc:p46976] 1.03915 Low confidence 8186.49
924 5939.42 opioid binding protein/cell adhesion molecule precursor (obcam) (opioid-binding cell adhesion molecule) (opcml). [swissprot;acc:q14982] 1.09857 High confidence 5406.5
9404.18 syndecan-3 (synd3). [swissprot;acc:o75056] 1.03912 Low confidence 9050.12
925 6193.07 [pyruvate dehydrogenase [lipoamide]] kinase isozyme 1, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 1). [swissprot;acc:q15118] 1.09856 High confidence 5637.43
8726.39 my016 protein. [sptrembl;acc:q9h3k6] 1.03909 Low confidence 8398.07
926 6193.08 [pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 2). [swissprot;acc:q15119] 1.09856 High confidence 5637.45
8366.23 tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685] 1.03905 Low confidence 8051.79
927 6194.22 dipeptidylpeptidase 10; dipeptidyl peptidase iv-related protein 3. [refseq;acc:nm_020868] 1.09853 High confidence 5638.64
8318.27 apurinic/apyrimidinic endonuclease 2; apurinic/apyrimidinic endonuclease-like 2; apex nuclease-like 2. [refseq;acc:nm_014481] 1.03902 Low confidence 8005.86
928 6194.04 cytochrome c oxidase assembly protein cox11, mitochondrial precursor. [swissprot;acc:q9y6n1] 1.09853 High confidence 5638.46
8610.75 junctional adhesion molecule 1 precursor (jam) (platelet adhesion molecule 1) (pam-1) (platelet f11 receptor). [swissprot;acc:q9y624] 1.03902 Low confidence 8287.37
929 6194.04 surfeit locus protein 1. [swissprot;acc:q15526] 1.09853 High confidence 5638.46
8385.43 citrate synthase, mitochondrial precursor (ec 2.3.3.1). [swissprot;acc:o75390] 1.03902 Low confidence 8070.54
930 6194.23 dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [swissprot;acc:p42658] 1.09853 High confidence 5638.65
8237.48 elongation factor ts, mitochondrial precursor (ef-ts) (ef-tsmt). [swissprot;acc:p43897] 1.039 Low confidence 7928.24
931 6194.17 seprase (ec 3.4.21.-) (fibroblast activation protein alpha) (integral membrane serine protease) (170-kda melanoma membrane-bound gelatinase). [swissprot;acc:q12884] 1.09853 High confidence 5638.59
7935.35 acidic leucine-rich nuclear phosphoprotein 32 family member c (tumorigenic protein pp32r1). [swissprot;acc:o43423] 1.03899 Low confidence 7637.56
932 6194.04 cox15 homolog isoform 2 precursor; cytochrome c oxidase subunit 15; cytochrome c oxidase assembly protein. [refseq;acc:nm_004376] 1.09853 High confidence 5638.46
7935.35 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] 1.03899 Low confidence 7637.56
933 6194.04 protoheme ix farnesyltransferase, mitochondrial precursor (ec 2.5.1.-) (heme o synthase). [swissprot;acc:q12887] 1.09853 High confidence 5638.46
7935.35 acidic leucine-rich nuclear phosphoprotein 32 family member d (tumorigenic protein pp32r2). [swissprot;acc:o95626] 1.03899 Low confidence 7637.56
934 6195.52 [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] 1.0985 High confidence 5640
7935.35 general vesicular transport factor p115 (transcytosis associated protein) (tap) (vesicle docking protein). [swissprot;acc:o60763] 1.03899 Low confidence 7637.56
935 5946.46 neurotrimin precursor (hnt). [swissprot;acc:q9p121] 1.09842 High confidence 5413.63
7935.35 acidic leucine-rich nuclear phosphoprotein 32 family member b (phapi2 protein) (silver-stainable protein ssp29) (acidic protein rich in leucines). [swissprot;acc:q92688] 1.03899 Low confidence 7637.56
936 6180.37 nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] 1.09811 High confidence 5628.21
7935.35 bromodomain containing 8; thyroid hormone receptor coactivating protein; skeletal muscle abundant protein. [refseq;acc:nm_006696] 1.03899 Low confidence 7637.56
937 6432.03 nucleobindin 1 precursor (calnuc). [swissprot;acc:q02818] 1.09776 High confidence 5859.25
8534.22 protein x 0001. [refseq;acc:nm_016302] 1.03895 Low confidence 8214.28
938 6432.03 dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692] 1.09776 High confidence 5859.25
8053.37 hiv tat specific factor 1; cofactor required for tat activation of hiv-1 transcription. [refseq;acc:nm_014500] 1.03891 Low confidence 7751.77
939 6432.03 nucleobindin 2 precursor (dna-binding protein nefa). [swissprot;acc:p80303] 1.09776 High confidence 5859.25
8783.33 mannose-6-phosphate isomerase (ec 5.3.1.8) (phosphomannose isomerase) (pmi) (phosphohexomutase). [swissprot;acc:p34949] 1.0389 Low confidence 8454.45
940 6113.35 adenosylhomocysteinase (ec 3.3.1.1) (s-adenosyl-l-homocysteine hydrolase) (adohcyase). [swissprot;acc:p23526] 1.09775 High confidence 5568.96
7863.85 nocturnin (ccr4 protein homolog). [swissprot;acc:q9uk39] 1.0389 Low confidence 7569.42
941 5455.34 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] 1.09761 High confidence 4970.21
8332.09 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] 1.0389 Low confidence 8020.09
942 7240.64 phosphoglycerate kinase, testis specific (ec 2.7.2.3). [swissprot;acc:p07205] 1.09747 High confidence 6597.56
8783.33 mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 1.0389 Low confidence 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/