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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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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 3736 to 3785 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
1868 protein kinase nyd-sp25. [refseq;acc:nm_033516] High confidence 207.642 209.895 1.01085
1869 lanc lantibiotic synthetase component c-like 2; testis-specific adriamycin sensitivity protein; lanc (bacterial lantibiotic synthetase component c)-like 2; g protein-coupled receptor 69b. [refseq;acc:nm_018697] 220.107 217.75 1.01082
ubiquitin-conjugating enzyme e2-17 kda 2 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 2). [swissprot;acc:p51669] Low confidence 203.016 199.062 1.01986
1870 lanthionine synthetase c-like protein 1; g protein-coupled receptor 69a; lanc (bacterial lantibiotic synthetase component c)-like 1; lanc (bacterial lantibiotic synthetase component). [refseq;acc:nm_006055] High confidence 220.107 217.75 1.01082
neurofibromin (neurofibromatosis-related protein nf-1) [contains: neurofibromin truncated]. [swissprot;acc:p21359] Low confidence 199.289 195.409 1.01986
1871 atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [swissprot;acc:o76031] High confidence 222.819 225.228 1.01081
serine hydroxymethyltransferase, cytosolic (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [swissprot;acc:p34896] Low confidence 201.627 197.703 1.01985
1872 dna polymerase delta p38 subunit. [refseq;acc:nm_015584] High confidence 222.819 225.228 1.01081
signal recognition particle 68 kda protein (srp68). [swissprot;acc:q9uhb9] Low confidence 202.408 198.469 1.01985
1873 10-formyltetrahydrofolate dehydrogenase (ec 1.5.1.6) (10-fthfdh). [swissprot;acc:o75891] 203.414 199.455
scratch; scratch 1. [refseq;acc:nm_031309] High confidence 210.55 208.305 1.01078
1874 bifunctional aminoacyl-trna synthetase [includes: glutamyl-trna synthetase (ec 6.1.1.17) (glutamate--trna ligase); prolyl-trna synthetase (ec 6.1.1.15) (proline--trna ligase)]. [swissprot;acc:p07814] Low confidence 200.85 196.94 1.01985
williams-beuren syndrome critical region protein 20 copy b. [refseq;acc:nm_145645] High confidence 223.862 226.271 1.01076
1875 dek protein. [swissprot;acc:p35659] Low confidence 203.415 199.456 1.01985
williams beuren syndrome critical region 20a isoform 2; nol1/nop2/sun gene family member; williams-beuren syndrome critical region protein 20 copy a; williams beuren syndrome chromosome region 20. [refseq;acc:nm_018044] High confidence 223.862 226.271 1.01076
1876 myosin vi. [swissprot;acc:q9um54] Low confidence 203.415 199.456 1.01985
williams beuren syndrome chromosome region 20c isoform 1. [refseq;acc:nm_032158] High confidence 223.862 226.271 1.01076
1877 branched-chain amino acid aminotransferase, mitochondrial precursor (ec 2.6.1.42) (bcat(m)) (placental protein 18) (pp18). [swissprot;acc:o15382] Low confidence 199.88 195.99 1.01985
nucleobindin 1 precursor (calnuc). [swissprot;acc:q02818] High confidence 212.186 214.467 1.01075
1878 dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692]
tetratricopeptide repeat protein 7 (tpr repeat protein 7) (fragment). [swissprot;acc:q9ult0] Low confidence 202.408 198.469 1.01985
1879 nucleobindin 2 precursor (dna-binding protein nefa). [swissprot;acc:p80303] High confidence 212.186 214.467 1.01075
transaldolase (ec 2.2.1.2). [swissprot;acc:p37837] Low confidence 200.883 196.975 1.01984
1880 atp synthase f chain, mitochondrial (ec 3.6.3.14). [swissprot;acc:p56134] 202.925 198.978
cytidine deaminase (ec 3.5.4.5) (cytidine aminohydrolase). [swissprot;acc:p32320] High confidence 220.852 223.225 1.01074
1881 dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03] 210.592 208.355
dual specificity protein phosphatase 1 (ec 3.1.3.48) (ec 3.1.3.16) (map kinase phosphatase-1) (mkp-1) (protein-tyrosine phosphatase cl100) (dual specificity protein phosphatase hvh1). [swissprot;acc:p28562] Low confidence 199.96 196.072 1.01983
1882 60s ribosomal protein l28. [swissprot;acc:p46779] High confidence 215.896 213.61 1.0107
dual specificity protein phosphatase 16 (ec 3.1.3.48) (ec 3.1.3.16) (mitogen-activated protein kinase phosphatase 7) (map kinase phosphatase 7) (mkp-7). [swissprot;acc:q9by84] Low confidence 199.962 196.074 1.01983
1883 6-phosphofructokinase, type c (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme c) (pfk-c) (6-phosphofructokinase, platelet type). [swissprot;acc:q01813] High confidence 240.317 242.881 1.01067
myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] Low confidence 197.596 193.753 1.01983
1884 putative gtp-binding protein ptd004 (pro2455). [swissprot;acc:q9ntk5] High confidence 215.081 217.373 1.01066
uv excision repair protein rad23 homolog a (hhr23a). [swissprot;acc:p54725] Low confidence 203.385 199.432 1.01982
1885 arginase 1 (ec 3.5.3.1) (liver-type arginase). [swissprot;acc:p05089] High confidence 204.44 206.615 1.01064
dna-repair protein complementing xp-f cell (xeroderma pigmentosum group f complementing protein) (dna excision repair protein ercc-4). [swissprot;acc:q92889] Low confidence 200.886 196.982 1.01982
1886 arginase ii, mitochondrial precursor (ec 3.5.3.1) (non-hepatic arginase) (kidney-type arginase). [swissprot;acc:p78540] High confidence 204.512 206.682 1.01061
dual specificity protein phosphatase 2 (ec 3.1.3.48) (ec 3.1.3.16) (dual specificity protein phosphatase pac-1). [swissprot;acc:q05923] Low confidence 199.961 196.074 1.01982
1887 dual specificity protein phosphatase 6 (ec 3.1.3.48) (ec 3.1.3.16) (mitogen-activated protein kinase phosphatase 3) (map kinase phosphatase 3) (mkp-3) (dual specificity protein phosphatase pyst1). [swissprot;acc:q16828] 199.964 196.077
sterile alpha and tir motif containing 1; sterile alpha and heat/armadillo motif protein, ortholog of drosophila. [refseq;acc:nm_015077] High confidence 220.896 218.577 1.01061
1888 immature colon carcinoma transcript 1 (digestion substraction 1) (ds- 1). [swissprot;acc:q14197] 218.414 216.131 1.01056
vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504] Low confidence 201.895 197.971 1.01982
1889 dual specificity protein phosphatase 4 (ec 3.1.3.48) (ec 3.1.3.16) (mitogen-activated protein kinase phosphatase-2) (map kinase phosphatase-2) (mkp-2) (dual specificity protein phosphatase hvh2). [swissprot;acc:q13115] 199.96 196.073
rab3a interacting protein (rabin3)-like 1. [refseq;acc:nm_013401] High confidence 211.27 209.067 1.01054
1890 inositol-1(or 4)-monophosphatase 2 (ec 3.1.3.25) (impase 2) (imp 2) (inositol monophosphatase 2) (myo-inositol monophosphatase a2). [swissprot;acc:o14732] Low confidence 198.008 194.162 1.01981
rab3a interacting protein isoform alpha 1; rabin3; ssx2 interacting protein. [refseq;acc:nm_022456] High confidence 211.314 209.111 1.01054
1891 dna replication licensing factor mcm3 (dna polymerase alpha holoenzyme-associated protein p1) (rlf beta subunit) (p102 protein) (p1-mcm3). [swissprot;acc:p25205] 233.828 231.395 1.01051
wd-repeat protein 3. [swissprot;acc:q9unx4] Low confidence 204.329 200.36 1.01981
1892 dual specificity protein phosphatase 18 (ec 3.1.3.48) (low molecular weight dual specificity phosphatase 20). [swissprot;acc:q8nej0] 202.485 198.553 1.0198
kelch-like ech-associated protein 1 (cytosolic inhibitor of nrf2). [swissprot;acc:q14145] High confidence 233.828 231.395 1.01051
1893 gdp-mannose pyrophosphorylase b isoform 1; mannose-1-phosphate guanylyltransferase; amphoterin induced gene 3. [refseq;acc:nm_013334] 222.842 225.17 1.01045

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/