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 2463 to 2512 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1232 nuclear factor, interleukin 3 regulated. [refseq;acc:nm_005384] Divided 5869.24 6367.8 1.08494
xap-5 protein (hxc-26 protein). [swissprot;acc:q14320] Subtracted 5894.47 6383.73 489.26
1233 midasin (midas-containing protein). [swissprot;acc:q9nu22] 4483.08 4971.62 488.54
tyrosinase precursor (ec 1.14.18.1) (monophenol monooxygenase) (tumor rejection antigen ab) (sk29-ab) (lb24-ab). [swissprot;acc:p14679] Divided 6004.54 6514.24 1.08489
1234 programmed cell death protein 5 (tfar19 protein) (tf-1 cell apoptosis related gene-19 protein). [swissprot;acc:o14737] Subtracted 4749.52 5237.77 488.25
similar to ecotropic viral integration site 5; neuroblastoma stage 4s gene. [refseq;acc:nm_145245] Divided 5807.83 6300.47 1.08482
1235 ecotropic viral integration site 5; neuroblastoma stage 4s gene. [refseq;acc:nm_005665]
p47 protein isoform a. [refseq;acc:nm_016143] Subtracted 6444.4 6932.39 487.99
1236 p10-binding protein. [refseq;acc:nm_024491] Divided 5594.18 6067.49 1.08461
presenilins associated rhomboid-like protein. [refseq;acc:nm_018622] Subtracted 6153.36 6640.77 487.41
1237 gamma-butyrobetaine,2-oxoglutarate dioxygenase (ec 1.14.11.1) (gamma-butyrobetaine hydroxylase) (gamma-bbh). [swissprot;acc:o75936]
tsc22-related inducible leucine zipper protein 2 (tsc-22-like protein thg-1). [swissprot;acc:q9y3q8] Divided 5873.56 6370.31 1.08457
1238 potential phospholipid-transporting atpase ih (ec 3.6.3.1) (atpase class i type 11a) (atpase is). [swissprot;acc:p98196] Subtracted 6153.36 6640.77 487.41
sphingolipid delta 4 desaturase; membrane fatty acid (lipid) desaturase; dihydroceramide desaturase. [refseq;acc:nm_003676] Divided 5873.56 6370.31 1.08457
1239 daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] 5654.53 6132.76
kccr13l. [refseq;acc:nm_139179] Subtracted 5538.8 6025.51 486.71
1240 dna repair protein rad51 homolog 1 (hrad51) (hsrad51). [swissprot;acc:q06609]
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

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/