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 Network Comparison Type description Value Type red Interaction Map Filtered network_comparison green
Results: HTML CSV LaTeX Showing element 3180 to 3229 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Network Comparison Type
description
Value Type
red
network_comparison
green
398 Divided xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7] Measured 5084.26 1.16125 5904.1
Subtracted docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704] Rooted 63.2134 6.1386 69.352
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] Measured 1834.63 938.933 895.697
laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047] Squared 26157.6 5921.4 20236.2
phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941] Ranked 207.908 18.31 226.218
399 Divided clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610] 207.889 1.08821 226.226
cyclin g2. [swissprot;acc:q16589] Rooted 116.707 1.10055 106.044
microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378] Squared 18929.1 1.22683 23222.8
neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] Measured 5201.41 1.16109 4479.76
Subtracted dna repair protein rad52 homolog. [swissprot;acc:p43351] Ranked 207.908 18.31 226.218
thymic stromal co-transporter. [refseq;acc:nm_033051] Squared 26157.6 5921.4 20236.2
tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685] Rooted 63.2134 6.1386 69.352
u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333] Measured 4633.92 938.93 5572.85
400 Divided adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306] 5201.41 1.16109 4479.76
cyclin g1 (cyclin g). [swissprot;acc:p51959] Rooted 116.707 1.10055 106.044
glycogen [starch] synthase, muscle (ec 2.4.1.11). [swissprot;acc:p13807] Squared 39478.8 1.22646 48419
phosducin-like protein (phlp). [swissprot;acc:q13371] Ranked 207.908 1.08807 226.218
Subtracted clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675] 207.931 18.278 226.209
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] Measured 1834.73 938.837 895.893
hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] Rooted 79.931 6.1383 86.0693
nadh-ubiquinone oxidoreductase b22 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b22) (ci-b22). [swissprot;acc:q9y6m9] Squared 33024.9 5842.9 38867.8
401 Divided adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] Measured 5201.41 1.16109 4479.76
axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645] Squared 33044.3 1.22638 40524.8
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] Ranked 207.908 1.08807 226.218
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] Rooted 116.707 1.10055 106.044
Subtracted guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] Measured 1835.3 938.328 896.972
mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390] Ranked 254.434 18.21 236.224
phosphoglycerate kinase, testis specific (ec 2.7.2.3). [swissprot;acc:p07205] Squared 28188.7 5794 33982.7
u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45] Rooted 55.9231 6.1334 62.0565
402 Divided endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759] Squared 39472 1.22601 48393.1
eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [swissprot;acc:p56537] Rooted 50.1918 1.10037 55.2294
leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] Measured 5201.41 1.16109 4479.76
replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [swissprot;acc:p15927] Ranked 207.908 1.08807 226.218
Subtracted arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069] Measured 6230.94 937.26 7168.2
gamma enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (neural enolase) (nse) (enolase 2). [swissprot;acc:p09104] Squared 28190.4 5793.7 33984.1
highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101] Ranked 231.802 18.181 249.983
ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315] Rooted 59.5128 6.0912 65.604
403 Divided fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322] Measured 5201.41 1.16109 4479.76
glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840] Squared 39463.9 1.22548 48362.1
nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] Rooted 59.6834 1.10037 65.6741
phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941] Ranked 207.908 1.08807 226.218
Subtracted beta enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (skeletal muscle enolase) (mse) (enolase 3). [swissprot;acc:p13929] Squared 28190.4 5793.7 33984.1
calcyphosine. [swissprot;acc:q13938] Rooted 59.5128 6.0912 65.604
microtubule-actin crosslinking factor 1, isoform 4. [swissprot;acc:q96pk2] Ranked 228.468 17.87 246.338
ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385] Measured 6259.3 931.61 7190.91
404 Divided adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [swissprot;acc:p30520] Squared 26819.1 1.22507 32855.4
dna repair protein rad52 homolog. [swissprot;acc:p43351] Ranked 207.908 1.08807 226.218
leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] Measured 5201.41 1.16109 4479.76
nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] Rooted 59.6834 1.10037 65.6741
Subtracted alpha enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (non- neural enolase) (nne) (enolase 1) (phosphopyruvate hydratase). [swissprot;acc:p06733] Squared 28190.4 5793.7 33984.1

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/