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 5062 to 5111 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1266 polymyositis/scleroderma autoantigen 2 (autoantigen pm/scl 2) (polymyositis/scleroderma autoantigen 100 kda) (pm/scl-100) (p100 polymyositis-scleroderma overlap syndrome associated autoantigen). [swissprot;acc:q01780] Squared 22590.9 25571.8 1.13195
rho-gtpase-activating protein 7 (rho-type gtpase-activating protein 7) (deleted in liver cancer 1 protein) (dlc-1) (hp protein) (star-related lipid transfer protein 12) (stard12) (start domain-containing protein 12). [swissprot;acc:q96qb1] Ranked 171.231 167.177 1.02425
sfrs protein kinase 2 isoform b. [refseq;acc:nm_182691] Measured 5894.47 6383.73 1.083
1267 cyclic-amp-dependent transcription factor atf-6 alpha (activating transcription factor 6 alpha) (atf6-alpha). [swissprot;acc:p18850]
deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (ec 3.6.1.23) (dutpase) (dutp pyrophosphatase). [swissprot;acc:p33316] Rooted 82.0343 78.529 1.04464
map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [swissprot;acc:p49137] Ranked 171.231 167.177 1.02425
rab3a interacting protein isoform alpha 1; rabin3; ssx2 interacting protein. [refseq;acc:nm_022456] Squared 31558.8 35722 1.13192
1268 hepatocyte nuclear factor 3-gamma (hnf-3g) (forkhead box protein a3) (fork head-related protein fkh h3). [swissprot;acc:p55318] Rooted 61.8154 64.5692 1.04455
neuronal acetylcholine receptor protein, alpha-6 chain precursor. [swissprot;acc:q15825] Ranked 171.231 167.177 1.02425
sfrs protein kinase 1; sr protein kinase 1. [refseq;acc:nm_003137] Measured 5894.47 6383.73 1.083
suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] Squared 14457.5 16362.6 1.13177
1269 nitrogen fixation cluster-like. [refseq;acc:nm_014301] Ranked 171.231 167.177 1.02425
peroxisomal membrane protein pex14 (peroxin-14) (peroxisomal membrane anchor protein pex14) (pts1 receptor docking protein). [swissprot;acc:o75381] Rooted 66.4107 69.3664 1.04451
transcription initiation factor iib (general transcription factor tfiib) (s300-ii). [swissprot;acc:q00403] Squared 18993.9 21492.5 1.13155
xap-5 protein (hxc-26 protein). [swissprot;acc:q14320] Measured 5894.47 6383.73 1.083
1270 casein kinase i, delta isoform (ec 2.7.1.-) (cki-delta) (ckid). [swissprot;acc:p48730] Rooted 58.0327 60.6143 1.04449
epidermal growth factor receptor pathway substrate 8-like protein 2; eps8-related protein 2; epidermal growth factor receptor pathway substrate 8-related protein 2. [refseq;acc:nm_022772] Measured 5685.08 6156.48 1.08292
star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [swissprot;acc:q9y3m8] Ranked 171.231 167.177 1.02425
thyroid receptor interacting protein 3 (trip-3) (fragment). [swissprot;acc:q15649] Squared 18993.9 21492.5 1.13155
1271 dna-(apurinic or apyrimidinic site) lyase (ec 4.2.99.18) (ap endonuclease 1) (apex nuclease) (apen) (ref-1 protein). [swissprot;acc:p27695] Rooted 64.9294 67.8184 1.04449
mitotic checkpoint serine/threonine-protein kinase bub1 beta (ec 2.7.1.-) (hbubr1) (mad3/bub1-related protein kinase) (mitotic checkpoint kinase mad3l). [swissprot;acc:o60566] Measured 5528.65 5985.58 1.08265
nhp2-like protein 1 (high mobility group-like nuclear protein 2 homolog 1) ([u4/u6.u5] tri-snrnp 15.5 kda protein) (otk27). [swissprot;acc:p55769] Squared 18993.9 21492.5 1.13155
star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [swissprot;acc:q92502] Ranked 171.231 167.177 1.02425
1272 neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822]
nuclear fragile x mental retardation protein interacting protein 1; nuclear fragile x mental retardation intercating protein 1; nuclear fragile x mental retardation protein-interacting protein 1. [refseq;acc:nm_012345] Squared 18993.9 21492.5 1.13155
pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] Measured 5528.65 5985.58 1.08265
serine hydroxymethyltransferase, cytosolic (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [swissprot;acc:p34896] Rooted 60.3351 63.0165 1.04444
1273 cyclin c. [swissprot;acc:p24863] Squared 30140.2 34102.8 1.13147
glutaminyl-trna synthetase (ec 6.1.1.18) (glutamine--trna ligase) (glnrs). [swissprot;acc:p47897] Rooted 60.5247 63.2144 1.04444
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

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/