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.


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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 5091 to 5140 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1273 mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635] Ranked 171.231 167.177 1.02425
phafin 2; ph and fyve domain-containing protein 2. [refseq;acc:nm_024613] Measured 5885 6371.14 1.08261
1274 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]
mitogen-activated protein kinase 14 (ec 2.7.1.37) (mitogen-activated protein kinase p38alpha) (map kinase p38alpha) (cytokine suppressive anti-inflammatory drug binding protein) (csaid binding protein) (csbp) (max-interacting protein 2) (map kinase mxi2) (sapk2a). [swissprot;acc:q16539] Ranked 171.231 167.177 1.02425
phenylalanyl-trna synthetase beta chain (ec 6.1.1.20) (phenylalanine-- trna ligase beta chain) (phers) (hspc173). [swissprot;acc:q9nsd9] Squared 22287.6 25217.3 1.13145
spermidine synthase (ec 2.5.1.16) (putrescine aminopropyltransferase) (spdsy). [swissprot;acc:p19623] Rooted 60.5247 63.2144 1.04444
1275 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] Measured 5885 6371.14 1.08261
glycyl-trna synthetase (ec 6.1.1.14) (glycine--trna ligase) (glyrs). [swissprot;acc:p41250] Rooted 60.5247 63.2144 1.04444
neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681] Ranked 171.231 167.177 1.02425
synaptotagmin xii (sytxii). [swissprot;acc:q8iv01] Squared 22271.6 25198.4 1.13141
1276 glutamyl trna synthetase. [sptrembl;acc:o14563] Rooted 60.5247 63.2144 1.04444
mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390] Squared 13569.3 15352.1 1.13138
neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297] Ranked 171.231 167.177 1.02425
peroxisomal membrane protein 2 (22 kda peroxisomal membrane protein). [swissprot;acc:q9nr77] Measured 6437.99 6969.67 1.08258
1277 dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122] Rooted 61.682 64.4174 1.04435
heat shock-related 70 kda protein 2 (heat shock 70 kda protein 2). [swissprot;acc:p54652] Measured 6437.99 6969.67 1.08258
junctional adhesion molecule 1 precursor (jam) (platelet adhesion molecule 1) (pam-1) (platelet f11 receptor). [swissprot;acc:q9y624] Squared 24508.9 27722.8 1.13113
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

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/