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.


Navigation/Query Panel:
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 2730 to 2779 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1365 nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [swissprot;acc:q9ubu9] Subtracted 169.031 164.507 4.524
1366 activin a receptor, type ic; activin receptor-like kinase 7. [refseq;acc:nm_145259] Divided 223.884 228.795 1.02194
jm4 protein. [refseq;acc:nm_007213] Subtracted 199.643 204.163 4.52
1367 cytoskeleton related vitamin a responsive protein; glutamate transporter eeac1-associated protein; dermal papilla derived protein 11; putative mapk activating protein pm27. [refseq;acc:nm_006407] 199.771 204.287 4.516
neuronal calcium sensor 1 (ncs-1) (frequenin homolog) (frequenin-like protein) (frequenin-like ubiquitous protein). [swissprot;acc:p36610] Divided 223.887 228.799 1.02194
1368 epididymal secretory protein e1 precursor (niemann-pick disease type c2 protein) (epi-1) (he1) (epididymal secretory protein 14.6) (esp14.6). [swissprot;acc:q15668] Subtracted 205.204 200.71 4.494
polyamine oxidase isoform 1; polyamine oxidase; flavin-containing spermine oxidase; putative cyclin g1 interacting protein; flavin containing amine oxidase. [refseq;acc:nm_019025] Divided 228.644 223.736 1.02194
1369 cysteine-rich protein 1 (cysteine-rich intestinal protein) (crip) (cysteine-rich heart protein) (hcrhp). [swissprot;acc:p50238] Subtracted 221.152 216.659 4.493
cytochrome c-type heme lyase (ec 4.4.1.17) (cchl) (holocytochrome c- type synthase). [swissprot;acc:p53701] Divided 228.644 223.736 1.02194
1370 cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693] Subtracted 107.842 112.329 4.487
cytoplasmic protein nck1 (nck adaptor protein 1) (sh2/sh3 adaptor protein nck-alpha). [swissprot;acc:p16333] Divided 205.185 200.784 1.02192
1371 glutathione s-transferase theta 1 (ec 2.5.1.18) (gst class-theta) (glutathione transferase t1-1). [swissprot;acc:p30711] 228.646 223.744 1.02191
trs85 homolog. [swissprot;acc:q9y2l5] Subtracted 107.842 112.329 4.487
1372 a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] 129.913 134.399 4.486
suppressor of cytokine signaling 1 (socs-1) (jak-binding protein) (jab) (stat induced stat inhibitor 1) (ssi-1) (tec-interacting protein 3) (tip-3). [swissprot;acc:o15524] Divided 216.542 211.908 1.02187
1373 glia maturation factor gamma (gmf-gamma). [swissprot;acc:o60234]
raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] Subtracted 129.921 134.406 4.485
1374 asc-1 complex subunit p100. [refseq;acc:nm_032204] Divided 216.542 211.908 1.02187
wd-repeat protein wdc146. [swissprot;acc:q9c0j8] Subtracted 108.289 112.772 4.483
1375 cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]
fk506-binding protein 1a (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (12 kda fkbp) (fkbp-12) (immunophilin fkbp12). [swissprot;acc:p20071] Divided 216.542 211.908 1.02187
1376 eyes absent homolog 3. [swissprot;acc:q99504] 218.537 213.91 1.02163
uv excision repair protein rad23 homolog a (hhr23a). [swissprot;acc:p54725] Subtracted 220.987 225.468 4.481
1377 26s proteasome non-atpase regulatory subunit 4 (26s proteasome regulatory subunit s5a) (rpn10) (multiubiquitin chain binding protein) (antisecretory factor-1) (af) (asf). [swissprot;acc:p55036]
sal-like protein 2 (zinc finger protein sall2) (hsal2). [swissprot;acc:q9y467] Divided 218.471 213.876 1.02148
1378 inositol polyphosphate 5-phosphatase ocrl-1 (ec 3.1.3.36) (lowe's oculocerebrorenal syndrome protein). [swissprot;acc:q01968] Subtracted 220.987 225.468 4.481
sal-like protein 3 (zinc finger protein sall3) (hsall3). [swissprot;acc:q9bxa9] Divided 218.47 213.876 1.02148
1379 arginine-glutamic acid dipeptide (re) repeats; atrophin 1-like; arginine glutamic acid dipeptide re repeats. [refseq;acc:nm_012102] 213.875
uv excision repair protein rad23 homolog b (hhr23b) (xp-c repair complementing complex 58 kda protein) (p58). [swissprot;acc:p54727] Subtracted 220.987 225.468 4.481
1380 myosin vi. [swissprot;acc:q9um54]
ubiquitin carboxyl-terminal hydrolase 8 (ec 3.1.2.15) (ubiquitin thiolesterase 8) (ubiquitin-specific processing protease 8) (deubiquitinating enzyme 8). [swissprot;acc:p40818] Divided 218.47 213.876 1.02148
1381 maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168] Subtracted 228.513 232.983 4.47
rod1 regulator of differentiation 1; fission yeast differentiation regulator; regulator of differentiation (in s. pombi) 1; regulator of differentiation (in s. pombe) 1. [refseq;acc:nm_005156] Divided 218.47 213.876 1.02148
1382 polypyrimidine tract binding protein 2; neural polypyrimidine tract binding protein; ptb-like protein. [refseq;acc:nm_021190]
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] Subtracted 130.066 134.527 4.461
1383 adaptor-associated kinase 1. [refseq;acc:nm_014911] Divided 218.47 213.876 1.02148
cyclin g2. [swissprot;acc:q16589] Subtracted 130.066 134.527 4.461
1384 atrophin-1 (dentatorubral-pallidoluysian atrophy protein). [swissprot;acc:p54259] Divided 218.471 213.876 1.02148
cyclin g1 (cyclin g). [swissprot;acc:p51959] Subtracted 130.066 134.527 4.461
1385 dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [refseq;acc:nm_016355] Divided 218.47 213.875 1.02148
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] Subtracted 130.066 134.527 4.461
1386 rho-gtpase activating protein 10. [refseq;acc:nm_020824] Divided 218.47 213.876 1.02148
transportin-sr; importin 12. [refseq;acc:nm_012470] Subtracted 225.305 229.766 4.461
1387 my016 protein. [sptrembl;acc:q9h3k6] 224.755 229.2 4.445
sal-like protein 1 (zinc finger protein sall1) (spalt-like transcription factor 1) (hsal1). [swissprot;acc:q9nsc2] Divided 218.47 213.875 1.02148
1388 sal-like protein 4 (zinc finger protein sall4). [swissprot;acc:q9ujq4] 218.471 213.876
sodium/potassium-transporting atpase alpha-1 chain precursor (ec 3.6.3.9) (sodium pump 1) (na+/k+ atpase 1). [swissprot;acc:p05023] Subtracted 214.717 219.157 4.44
1389 2-oxoisovalerate dehydrogenase beta subunit, mitochondrial precursor (ec 1.2.4.4) (branched-chain alpha-keto acid dehydrogenase e1 component beta chain) (bckdh e1-beta). [swissprot;acc:p21953] Divided 218.47 213.875 1.02148
cathepsin l2 precursor (ec 3.4.22.43) (cathepsin v) (cathepsin u). [swissprot;acc:o60911] Subtracted 214.717 219.157 4.44
1390 cathepsin l precursor (ec 3.4.22.15) (major excreted protein) (mep). [swissprot;acc:p07711]

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/