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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Rank Gene Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 3180 to 3229 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
Network Comparison Type
red
green
network_comparison
398 Ranked phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941] Subtracted 207.908 226.218 18.31
Squared imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549] Divided 18929.1 23222.8 1.22683
laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047] Subtracted 26157.6 20236.2 5921.4
Rooted docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704] 63.2134 69.352 6.1386
serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [swissprot;acc:q16537] Divided 116.707 106.044 1.10055
399 Measured neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] 5201.41 4479.76 1.16109
u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333] Subtracted 4633.92 5572.85 938.93
Ranked clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610] Divided 207.889 226.226 1.08821
dna repair protein rad52 homolog. [swissprot;acc:p43351] Subtracted 207.908 226.218 18.31
Squared microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378] Divided 18929.1 23222.8 1.22683
thymic stromal co-transporter. [refseq;acc:nm_033051] Subtracted 26157.6 20236.2 5921.4
Rooted cyclin g2. [swissprot;acc:q16589] Divided 116.707 106.044 1.10055
tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685] Subtracted 63.2134 69.352 6.1386
400 Measured adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306] Divided 5201.41 4479.76 1.16109
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] Subtracted 1834.73 895.893 938.837
Ranked clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675] 207.931 226.209 18.278
phosducin-like protein (phlp). [swissprot;acc:q13371] Divided 207.908 226.218 1.08807
Squared glycogen [starch] synthase, muscle (ec 2.4.1.11). [swissprot;acc:p13807] 39478.8 48419 1.22646
nadh-ubiquinone oxidoreductase b22 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b22) (ci-b22). [swissprot;acc:q9y6m9] Subtracted 33024.9 38867.8 5842.9
Rooted cyclin g1 (cyclin g). [swissprot;acc:p51959] Divided 116.707 106.044 1.10055
hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] Subtracted 79.931 86.0693 6.1383
401 Measured adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] Divided 5201.41 4479.76 1.16109
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] Subtracted 1835.3 896.972 938.328
Ranked mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390] 254.434 236.224 18.21
replication protein a 70 kda dna-binding subunit (rp-a) (rf-a) (replication factor-a protein 1) (single-stranded dna-binding protein). [swissprot;acc:p27694] Divided 207.908 226.218 1.08807
Squared axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645] 33044.3 40524.8 1.22638
phosphoglycerate kinase, testis specific (ec 2.7.2.3). [swissprot;acc:p07205] Subtracted 28188.7 33982.7 5794
Rooted serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, alpha isoform (pp2a, b subunit, b' alpha isoform) (pp2a, b subunit, b56 alpha isoform) (pp2a, b subunit, pr61 alpha isoform) (pp2a, b subunit, r5 alpha isoform). [swissprot;acc:q15172] Divided 116.707 106.044 1.10055
u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45] Subtracted 55.9231 62.0565 6.1334
402 Measured arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069] 6230.94 7168.2 937.26
leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] Divided 5201.41 4479.76 1.16109
Ranked highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101] Subtracted 231.802 249.983 18.181
replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [swissprot;acc:p15927] Divided 207.908 226.218 1.08807
Squared endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759] 39472 48393.1 1.22601
gamma enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (neural enolase) (nse) (enolase 2). [swissprot;acc:p09104] Subtracted 28190.4 33984.1 5793.7
Rooted eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [swissprot;acc:p56537] Divided 50.1918 55.2294 1.10037
ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315] Subtracted 59.5128 65.604 6.0912
403 Measured fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322] Divided 5201.41 4479.76 1.16109
ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385] Subtracted 6259.3 7190.91 931.61
Ranked microtubule-actin crosslinking factor 1, isoform 4. [swissprot;acc:q96pk2] 228.468 246.338 17.87
phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941] Divided 207.908 226.218 1.08807
Squared beta enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (skeletal muscle enolase) (mse) (enolase 3). [swissprot;acc:p13929] Subtracted 28190.4 33984.1 5793.7
glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840] Divided 39463.9 48362.1 1.22548
Rooted calcyphosine. [swissprot;acc:q13938] Subtracted 59.5128 65.604 6.0912
nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] Divided 59.6834 65.6741 1.10037
404 Measured importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [swissprot;acc:p55060] Subtracted 7802.31 8731.82 929.51
leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] Divided 5201.41 4479.76 1.16109
Ranked bullous pemphigoid antigen 1 isoforms 1/2/3/4/5/8 (230 kda bullous pemphigoid antigen) (bpa) (hemidesmosomal plaque protein) (dystonia musculorum protein) (fragment). [swissprot;acc:q03001] Subtracted 228.463 246.33 17.867
dna repair protein rad52 homolog. [swissprot;acc:p43351] Divided 207.908 226.218 1.08807
Squared adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [swissprot;acc:p30520] 26819.1 32855.4 1.22507

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/