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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2480 to 2529 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1240 retinoic acid induced 17; pias-like protein hzimp10. [refseq;acc:nm_020338] Divided 5654.54 6132.69 1.08456
1241 26s proteasome non-atpase regulatory subunit 2 (26s proteasome regulatory subunit s2) (26s proteasome subunit p97) (tumor necrosis factor type 1 receptor associated protein 2) (55.11 protein). [swissprot;acc:q13200] 6436.19 6980.13 1.08451
serologically defined colon cancer antigen 16. [refseq;acc:nm_006649] Subtracted 6268.94 6755.57 486.63
1242 delta-interacting protein a (hepatitis delta antigen interacting protein a). [swissprot;acc:q15834] 6274.62 6760.78 486.16
ubiquitin-conjugating enzyme e2 e1 (ec 6.3.2.19) (ubiquitin-protein ligase e1) (ubiquitin carrier protein e1) (ubch6). [swissprot;acc:p51965] Divided 11143.5 10276.3 1.08439
1243 phafin 2; ph and fyve domain-containing protein 2. [refseq;acc:nm_024613] Subtracted 5885 6371.14 486.14
ubiquitin-conjugating enzyme e2e 3; ubiquitin carrier protein; ubiquitin-protein ligase. [refseq;acc:nm_006357] Divided 11143.5 10276.3 1.08439
1244 3-oxo-5-alpha-steroid 4-dehydrogenase 1 (ec 1.3.99.5) (steroid 5-alpha-reductase 1) (sr type 1) (s5ar). [swissprot;acc:p18405] Subtracted 5885 6371.14 486.14
sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [refseq;acc:nm_016538] Divided 4835.55 5243.23 1.08431
1245 3-oxo-5-alpha-steroid 4-dehydrogenase 2 (ec 1.3.99.5) (steroid 5-alpha-reductase 2) (sr type 2) (5 alpha-sr2). [swissprot;acc:p31213] Subtracted 5885 6371.14 486.14
casein kinase ii beta chain (ck ii) (phosvitin) (g5a). [swissprot;acc:p13862] Divided 4835.55 5243.23 1.08431
1246 methionyl-trna formyltransferase, mitochondrial precursor (ec 2.1.2.9) (mtfmt). [swissprot;acc:q96dp5] Subtracted 5110.6 5596.73 486.13
p53-related protein kinase (ec 2.7.1.-) (nori-2). [swissprot;acc:q96s44] Divided 5346.11 5796.72 1.08429
1247 kinesin protein. [refseq;acc:nm_032559] Subtracted 5356.23 5842.15 485.92
protein-tyrosine phosphatase, non-receptor type 1 (ec 3.1.3.48) (protein-tyrosine phosphatase 1b) (ptp-1b). [swissprot;acc:p18031] Divided 6278.76 6807.51 1.08421
1248 ny-ren-62 antigen (fragment). [sptrembl;acc:q9y590] Subtracted 5358.18 5843.73 485.55
protein-tyrosine phosphatase, non-receptor type 2 (ec 3.1.3.48) (t- cell protein-tyrosine phosphatase) (tcptp). [swissprot;acc:p17706] Divided 6275.86 6803.95 1.08415
1249 kinesin-like protein kif2 (kinesin-2) (hk2). [swissprot;acc:o00139] Subtracted 5359.72 5844.97 485.25
trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] Divided 4413.55 4784.6 1.08407
1250 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] Subtracted 4970.21 5455.34 485.13
huntingtin interacting protein 1 (hip-i). [swissprot;acc:o00291] Divided 10733.4 9902.6 1.0839
1251 dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122] Subtracted 5678.02 6161.65 483.63
regulator of chromosome condensation (cell cycle regulatory protein). [swissprot;acc:p18754] Divided 8618.32 9340.98 1.08385
1252 metaxin 2. [swissprot;acc:o75431] Subtracted 7033.72 7516.77 483.05
zinc finger homeobox protein 1b (smad interacting protein 1) (smadip1) (hrihfb2411). [swissprot;acc:o60315] Divided 8618.32 9340.98 1.08385
1253 ribokinase (ec 2.7.1.15). [swissprot;acc:q9h477] Subtracted 6210.51 6693.49 482.98
transcription factor 8 (nil-2-a zinc finger protein) (negative regulator of il2). [swissprot;acc:p37275] Divided 8618.32 9340.98 1.08385
1254 delta-aminolevulinic acid dehydratase (ec 4.2.1.24) (porphobilinogen synthase) (aladh). [swissprot;acc:p13716] Subtracted 5489.18 5972.09 482.91
goodpasture antigen-binding protein (ec 2.7.1.37) (gpbp) (collagen type iv alpha 3 binding protein) (star-related lipid transfer protein 11) (stard11) (start domain-containing protein 11). [swissprot;acc:q9y5p4] Divided 10725.6 9896.32 1.0838
1255 dual specificity mitogen-activated protein kinase kinase 6 (ec 2.7.1.-) (map kinase kinase 6) (mapkk 6) (mapk/erk kinase 6) (sapkk3). [swissprot;acc:p52564] Subtracted 6105.23 6587.88 482.65
serine/threonine protein phosphatase 4 (ec 3.1.3.16) (pp4) (protein phosphatase x) (pp-x). [swissprot;acc:p33172] Divided 5438.66 5893.87 1.0837
1256 dual specificity mitogen-activated protein kinase kinase 3 (ec 2.7.1.-) (map kinase kinase 3) (mapkk 3) (mapk/erk kinase 3). [swissprot;acc:p46734] Subtracted 6104.11 6586.48 482.37
huntingtin interacting protein 1 related (hip1-related) (hip 12). [swissprot;acc:o75146] Divided 10719 9891.08 1.0837
1257 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] Subtracted 4254.62 4736.03 481.41
immunoglobulin-binding protein 1 (cd79a-binding protein 1) (b cell signal transduction molecule alpha 4) (alpha 4 protein). [swissprot;acc:p78318] Divided 5438.66 5893.87 1.0837
1258 glutamate carboxypeptidase-like protein 2 precursor. [swissprot;acc:q96kn2] 6251.32 6774.12 1.08363
serine/threonine-protein kinase nek1 (ec 2.7.1.37) (nima-related protein kinase 1) (ny-ren-55 antigen). [swissprot;acc:q96py6] Subtracted 5961.97 6443.07 481.1
1259 epidermal growth factor receptor pathway substrate 8-like protein 1 isoform c; epidermal growth factor receptor pathway substrate 8-related protein 1; eps8-related protein 1. [refseq;acc:nm_139204] Divided 5685.38 6157.7 1.08308
serine/threonine-protein kinase nek3 (ec 2.7.1.37) (nima-related protein kinase 3) (hspk 36). [swissprot;acc:p51956] Subtracted 5961.97 6443.07 481.1
1260 glyceraldehyde 3-phosphate dehydrogenase, liver (ec 1.2.1.12) (gapdh). [swissprot;acc:p04406]
rad54-like protein; rad54 homolog. [refseq;acc:nm_003579] Divided 5754.84 6232.83 1.08306
1261 43 kda receptor-associated protein of the synapse (rapsyn) (acetylcholine receptor-associated 43 kda protein) (43 kda postsynaptic protein). [swissprot;acc:q13702] Subtracted 6160.06 6640.78 480.72
epidermal growth factor receptor kinase substrate eps8. [swissprot;acc:q12929] Divided 5685.34 6157.53 1.08305
1262 prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [swissprot;acc:q15765] Subtracted 5207.39 5687.2 479.81
serine/threonine protein kinase 23 (ec 2.7.1.37) (muscle-specific serine kinase 1) (mssk-1). [swissprot;acc:q9upe1] Divided 5894.47 6383.73 1.083
1263 gtp binding protein 2. [refseq;acc:nm_019096]
prefoldin subunit 2 (hspc231). [swissprot;acc:q9uhv9] Subtracted 5207.39 5687.2 479.81
1264 cyclic-amp-dependent transcription factor atf-6 beta (activating transcription factor 6 beta) (atf6-beta) (camp responsive element binding protein-like 1) (camp response element binding protein-related protein) (creb-rp) (g13 protein). [swissprot;acc:q99941] Divided 5894.47 6383.73 1.083
uxt protein (ubiquitously expressed transcript protein) (hspc024). [swissprot;acc:q9ubk9] Subtracted 5207.39 5687.2 479.81
1265 6-phosphofructokinase, muscle type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme a) (pfk-a) (phosphofructokinase-m). [swissprot;acc:p08237] 4250.54 4729.67 479.13

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/