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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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 2480 to 2529 of 8289 in total
Value Type  : Measured
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
1240 retinoic acid induced 17; pias-like protein hzimp10. [refseq;acc:nm_020338] High confidence 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
rab gdp dissociation inhibitor alpha (rab gdi alpha) (gdi-1) (xap-4) (oligophrenin 2). [swissprot;acc:p31150] Low confidence 7892.49 8175.52 1.03586
1242 rab coupling protein; rab-interacting recycling protein; rab effector protein; rab11-family interacting protein 1. [refseq;acc:nm_025151] 7937.31 8221.8 1.03584
ubiquitin-conjugating enzyme e2 e1 (ec 6.3.2.19) (ubiquitin-protein ligase e1) (ubiquitin carrier protein e1) (ubch6). [swissprot;acc:p51965] High confidence 11143.5 10276.3 1.08439
1243 arf gtpase-activating protein git1 (g protein-coupled receptor kinase- interactor 1). [swissprot;acc:q9y2x7] Low confidence 7722.82 7999.54 1.03583
ubiquitin-conjugating enzyme e2e 3; ubiquitin carrier protein; ubiquitin-protein ligase. [refseq;acc:nm_006357] High confidence 11143.5 10276.3 1.08439
1244 rna-binding protein s1, serine-rich domain; sr protein. [refseq;acc:nm_006711] Low confidence 7716.12 7992.54 1.03582
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] High confidence 4835.55 5243.23 1.08431
1245 arf gtpase-activating protein git2 (g protein-coupled receptor kinase- interactor 2). [swissprot;acc:q14161] Low confidence 7710.26 7986.43 1.03582
casein kinase ii beta chain (ck ii) (phosvitin) (g5a). [swissprot;acc:p13862] High confidence 4835.55 5243.23 1.08431
1246 p53-related protein kinase (ec 2.7.1.-) (nori-2). [swissprot;acc:q96s44] 5346.11 5796.72 1.08429
rab gdp dissociation inhibitor beta (rab gdi beta) (gdi-2). [swissprot;acc:p50395] Low confidence 7891.9 8174.55 1.03582
1247 5-oxoprolinase (ec 3.5.2.9) (5-oxo-l-prolinase) (pyroglutamase) (5-opase) (fragment). [swissprot;acc:o14841] 8601.93 8909.86 1.0358
protein-tyrosine phosphatase, non-receptor type 1 (ec 3.1.3.48) (protein-tyrosine phosphatase 1b) (ptp-1b). [swissprot;acc:p18031] High confidence 6278.76 6807.51 1.08421
1248 protein-tyrosine phosphatase, non-receptor type 2 (ec 3.1.3.48) (t- cell protein-tyrosine phosphatase) (tcptp). [swissprot;acc:p17706] 6275.86 6803.95 1.08415
sco1 protein homolog, mitochondrial precursor. [swissprot;acc:o75880] Low confidence 7971.79 8257.18 1.0358
1249 orphan nuclear receptor hmr (early response protein nak1) (tr3 orphan receptor). [swissprot;acc:p22736] 7859.58 8140.96
trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] High confidence 4413.55 4784.6 1.08407
1250 huntingtin interacting protein 1 (hip-i). [swissprot;acc:o00291] 10733.4 9902.6 1.0839
nuclear hormone receptor nor-1 (neuron-derived orphan receptor 1) (mitogen induced nuclear orphan receptor). [swissprot;acc:q92570] Low confidence 7859.55 8140.85 1.03579
1251 cytochrome c-type heme lyase (ec 4.4.1.17) (cchl) (holocytochrome c- type synthase). [swissprot;acc:p53701] 8225.07 8519.37 1.03578
regulator of chromosome condensation (cell cycle regulatory protein). [swissprot;acc:p18754] High confidence 8618.32 9340.98 1.08385
1252 vacuolar atp synthase subunit h (ec 3.6.3.14) (v-atpase h subunit) (vacuolar proton pump h subunit) (v-atpase 50/57 kda subunits) (vacuolar proton pump subunit sfd) (cgi-11). [swissprot;acc:q9ui12] Low confidence 8162.24 8454.02 1.03575
zinc finger homeobox protein 1b (smad interacting protein 1) (smadip1) (hrihfb2411). [swissprot;acc:o60315] High confidence 8618.32 9340.98 1.08385
1253 gamma-snap-associated factor 1; rab11-interacting protein. [refseq;acc:nm_015470] Low confidence 7939.04 8222.82 1.03574
transcription factor 8 (nil-2-a zinc finger protein) (negative regulator of il2). [swissprot;acc:p37275] High confidence 8618.32 9340.98 1.08385
1254 eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730] Low confidence 8006.71 8292.73 1.03572
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] High confidence 10725.6 9896.32 1.0838
1255 eukaryotic translation initiation factor 4e binding protein 2; eukaryotic translation initiation factor-4e binding protein-1. [refseq;acc:nm_004096] Low confidence 8006.71 8292.73 1.03572
serine/threonine protein phosphatase 4 (ec 3.1.3.16) (pp4) (protein phosphatase x) (pp-x). [swissprot;acc:p33172] High confidence 5438.66 5893.87 1.0837
1256 eukaryotic translation initiation factor 4e binding protein 3; eukaryotic initiation factor 4e-binding protein 3. [refseq;acc:nm_003732] Low confidence 8006.71 8292.73 1.03572
huntingtin interacting protein 1 related (hip1-related) (hip 12). [swissprot;acc:o75146] High confidence 10719 9891.08 1.0837
1257 hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [swissprot;acc:q9y5r4] Low confidence 7983.04 8268.18 1.03572
immunoglobulin-binding protein 1 (cd79a-binding protein 1) (b cell signal transduction molecule alpha 4) (alpha 4 protein). [swissprot;acc:p78318] High confidence 5438.66 5893.87 1.0837
1258 bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933] Low confidence 8006.71 8292.73 1.03572
glutamate carboxypeptidase-like protein 2 precursor. [swissprot;acc:q96kn2] High confidence 6251.32 6774.12 1.08363
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] 5685.38 6157.7 1.08308
sco2 protein homolog, mitochondrial precursor. [swissprot;acc:o43819] Low confidence 7975.38 8260.16 1.03571
1260 rad54-like protein; rad54 homolog. [refseq;acc:nm_003579] High confidence 5754.84 6232.83 1.08306
solute carrier family 35, member b1; udp-galactose transporter related. [refseq;acc:nm_005827] Low confidence 8270.72 8565.95 1.0357
1261 epidermal growth factor receptor kinase substrate eps8. [swissprot;acc:q12929] High confidence 5685.34 6157.53 1.08305
orphan nuclear receptor nurr1 (immediate-early response protein not) (transcriptionally inducible nuclear receptor). [swissprot;acc:p43354] Low confidence 7859.26 8139.7 1.03568
1262 nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [swissprot;acc:q13232] 8171.23 8462.7 1.03567
serine/threonine protein kinase 23 (ec 2.7.1.37) (muscle-specific serine kinase 1) (mssk-1). [swissprot;acc:q9upe1] High confidence 5894.47 6383.73 1.083
1263 eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] Low confidence 7704.6 7979.43 1.03567
gtp binding protein 2. [refseq;acc:nm_019096] High confidence 5894.47 6383.73 1.083
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]
inositol oxygenase (ec 1.13.99.1) (myo-inositol oxygenase) (aldehyde reductase-like 6) (renal-specific oxidoreductase) (kidney-specific protein 32). [swissprot;acc:q9ugb7] Low confidence 7448.76 7714.49 1.03567
1265 dna segment on chromosome 6(unique) 2654 expressed sequence; dna segment on chromosome x (unique) 2654 expressed sequence. [refseq;acc:nm_012135] High confidence 5894.47 6383.73 1.083

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/