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 5108 to 5157 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1277 sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [swissprot;acc:q9nra0] Ranked 171.231 167.177 1.02425
1278 gcn5-like protein 1 (rt14 protein). [swissprot;acc:p78537] Rooted 71.8595 75.0311 1.04414
heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107] Measured 6437.99 6969.67 1.08258
ruvb-like 1 (ec 3.6.1.-) (49-kda tata box-binding protein-interacting protein) (49 kda tbp-interacting protein) (tip49a) (pontin 52) (nuclear matrix protein 238) (nmp 238) (54 kda erythrocyte cytosolic protein) (ecp-54) (tip60-associated protein 54-alpha) (tap54-alpha). [swissprot;acc:q9y265] Squared 28335.4 32042.6 1.13083
sestrin 3. [swissprot;acc:p58005] Ranked 218.368 213.219 1.02415
1279 cysteine-rich motor neuron 1; cysteine-rich repeat-containing protein s52 precursor. [refseq;acc:nm_016441] Rooted 63.8038 66.6135 1.04404
heat shock cognate 71 kda protein. [swissprot;acc:p11142] Measured 6437.99 6969.67 1.08258
interleukin-4 induced protein 1 precursor (fig-1 protein). [swissprot;acc:q96rq9] Squared 26765.8 30265 1.13073
sestrin 2 (hi95). [swissprot;acc:p58004] Ranked 218.368 213.219 1.02415
1280 cytochrome p450 4a11 precursor (ec 1.14.15.3) (cypiva11) (fatty acid omega-hydroxylase) (p-450 hk omega) (lauric acid omega-hydroxylase) (cyp4aii) (p450-hl-omega). [swissprot;acc:q02928] 213.22 1.02414
dehydrodolichyl diphosphate synthase. [refseq;acc:nm_024887] Measured 6350.81 6874.88 1.08252
endonuclease g, mitochondrial precursor (ec 3.1.30.-) (endo g). [swissprot;acc:q14249] Rooted 61.2224 58.6404 1.04403
midasin (midas-containing protein). [swissprot;acc:q9nu22] Squared 17961 20308.8 1.13072
1281 cytochrome p450 4f3 (ec 1.14.13.30) (cypivf3) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:q08477] Ranked 218.368 213.22 1.02414
nadh-ubiquinone oxidoreductase pdsw subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-pdsw) (ci-pdsw). [swissprot;acc:o96000] Squared 32053.5 36239.4 1.13059
orphan nuclear receptor hmr (early response protein nak1) (tr3 orphan receptor). [swissprot;acc:p22736] Measured 6230.49 6744.5 1.0825
programmed cell death protein 8, mitochondrial precursor (ec 1.-.-.-) (apoptosis-inducing factor). [swissprot;acc:o95831] Rooted 61.2224 58.6404 1.04403
1282 cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187] Ranked 218.368 213.22 1.02414
nuclear hormone receptor nor-1 (neuron-derived orphan receptor 1) (mitogen induced nuclear orphan receptor). [swissprot;acc:q92570] Measured 6230.38 6744.35 1.08249
t-box transcription factor tbx6 (t-box protein 6). [swissprot;acc:o95947] Rooted 61.2224 58.6404 1.04403
uba/ubx 33.3 kda protein. [swissprot;acc:q04323] Squared 34152.7 38610.6 1.13053
1283 adenosylhomocysteinase (ec 3.3.1.1) (s-adenosyl-l-homocysteine hydrolase) (adohcyase). [swissprot;acc:p23526] Rooted 62.0594 64.7888 1.04398
ero1-like. [refseq;acc:nm_014584] Squared 34152.7 38610.6 1.13053
likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033] Ranked 218.368 213.22 1.02414
orphan nuclear receptor nurr1 (immediate-early response protein not) (transcriptionally inducible nuclear receptor). [swissprot;acc:p43354] Measured 6229.16 6742.79 1.08246
1284 cda11 protein. [refseq;acc:nm_032026] Squared 24855.8 28097.9 1.13044
cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2] Ranked 218.368 213.22 1.02414
trimethyllysine dioxygenase, mitochondrial precursor (ec 1.14.11.8) (epsilon-trimethyllysine 2-oxoglutarate dioxygenase) (tml-alpha- ketoglutarate dioxygenase) (tml hydroxylase) (tml dioxygenase) (tmld). [swissprot;acc:q9nvh6] Rooted 64.9605 67.8088 1.04385
xenotropic and polytropic retrovirus receptor. [refseq;acc:nm_004736] Measured 6413.32 6941.48 1.08235
1285 cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329] Ranked 218.368 213.22 1.02414
cytosolic nonspecific dipeptidase (glutamate carboxypeptidase-like protein 1). [swissprot;acc:q96kp4] Measured 6207.57 6718.7 1.08234
dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779] Squared 14701.3 16618.9 1.13044
gtp-binding protein era homolog (hera) (fragment). [swissprot;acc:o75616] Rooted 64.9605 67.8088 1.04385
1286 cytochrome p450 4a11 precursor (ec 1.14.15.3) (cypiva11) (fatty acid omega-hydroxylase) (p-450 hk omega) (lauric acid omega-hydroxylase) (cyp4aii) (p450-hl-omega). [swissprot;acc:q02928] Measured 5655.85 6120.64 1.08218
cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6] Ranked 218.368 213.22 1.02414
grpe protein homolog 2, mitochondrial precursor (mt-grpe#2). [swissprot;acc:q8taa5] Rooted 53.457 55.8006 1.04384
rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749] Squared 15001.4 16951.5 1.12999
1287 cytochrome p450 4f3 (ec 1.14.13.30) (cypivf3) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:q08477] Measured 5655.85 6120.64 1.08218
dj18d14.4 (cytochrome p450, subfamily iva, polypeptide 11). [sptrembl;acc:q9ntl5] Ranked 218.368 213.22 1.02414
grpe protein homolog 1, mitochondrial precursor (mt-grpe#1) (hmge). [swissprot;acc:q9hav7] Rooted 53.457 55.8006 1.04384
rac-gamma serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-gamma) (protein kinase akt-3) (protein kinase b, gamma) (pkb gamma) (stk-2). [swissprot;acc:q9y243] Squared 15001.4 16951.5 1.12999
1288 cytochrome p450 4b1 (ec 1.14.14.1) (cypivb1) (p450-hp). [swissprot;acc:p13584] Ranked 218.368 213.22 1.02414
cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187] Measured 5655.85 6120.64 1.08218
rac-beta serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-beta) (protein kinase akt-2) (protein kinase b, beta) (pkb beta). [swissprot;acc:p31751] Squared 15001.4 16951.5 1.12999
swi/snf-related matrix-associated actin-dependent regulator of chromatin d2; rsc6p; mammalian chromatin remodeling complex brg1-associated factor 60b; swp73-like protein; chromatin remodeling complex baf60b subunit; swi/snf complex 60 kda subunit b. [refseq;acc:nm_003077] Rooted 53.457 55.8006 1.04384
1289 flotillin-1. [swissprot;acc:o75955] Ranked 218.368 213.22 1.02414
likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033] Measured 5655.85 6120.64 1.08218
pescadillo homolog 1. [swissprot;acc:o00541] Squared 14342.2 16206.3 1.12997
swi/snf-related matrix-associated actin-dependent regulator of chromatin d3; rsc6p; mammalian chromatin remodeling complex brg1-associated factor 60c; swp73-like protein; chromatin remodeling complex baf60c subunit; swi/snf complex 60 kda subunit c. [refseq;acc:nm_003078] Rooted 53.457 55.8006 1.04384
1290 cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2] Measured 5655.85 6120.64 1.08218

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/