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.


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 2525 to 2574 of 8289 in total
Value Type  : Measured
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
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
vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504] Low confidence 7983.11 8267.56 1.03563
1266 f-actin capping protein alpha-3 subunit (capz alpha-3) (germ cell- specific protein 3). [swissprot;acc:q96kx2] 8035.14 8321.34 1.03562
sfrs protein kinase 2 isoform b. [refseq;acc:nm_182691] High confidence 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]
elongation protein 3 homolog; likely ortholog of mouse elongation protein 3 homolog (s. cerevisiae). [refseq;acc:nm_018091] Low confidence 7980.57 8264.85 1.03562
1268 protease inhibitor 15 preproprotein; 25 kda trypsin inhibitor. [refseq;acc:nm_015886] 7869.55 8149.35 1.03555
sfrs protein kinase 1; sr protein kinase 1. [refseq;acc:nm_003137] High confidence 5894.47 6383.73 1.083
1269 r3h domain (binds single-stranded nucleic acids) containing-like. [refseq;acc:nm_178491] Low confidence 7869.55 8149.35 1.03555
xap-5 protein (hxc-26 protein). [swissprot;acc:q14320] High confidence 5894.47 6383.73 1.083
1270 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] 5685.08 6156.48 1.08292
general transcription factor iiic, polypeptide 3, 102kda; general transcription factor iiic, polypeptide 3 (102kd); transcription factor iiic, 102 kd. [refseq;acc:nm_012086] Low confidence 7251.82 7509.54 1.03554
1271 mitochondrial carnitine/acylcarnitine carrier protein (carnitine/acylcarnitine translocase) (cac). [swissprot;acc:o43772] 8043.23 8329.04 1.03553
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] High confidence 5528.65 5985.58 1.08265
1272 nucleosome assembly protein 1-like 2 (brain-specific protein, x- linked). [swissprot;acc:q9ulw6] Low confidence 8100.63 8388.35 1.03552
pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] High confidence 5528.65 5985.58 1.08265
1273 breast cancer type 1 susceptibility protein. [swissprot;acc:p38398] Low confidence 8184.5 8475.14 1.03551
phafin 2; ph and fyve domain-containing protein 2. [refseq;acc:nm_024613] High confidence 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]
myg1 protein. [swissprot;acc:q9hb07] Low confidence 8091.56 8378.83 1.0355
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] High confidence 5885 6371.14 1.08261
nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [swissprot;acc:q99733] Low confidence 8101.04 8388.51 1.03549
1276 peroxisomal membrane protein 2 (22 kda peroxisomal membrane protein). [swissprot;acc:q9nr77] High confidence 6437.99 6969.67 1.08258
ras-related protein rap-2b. [swissprot;acc:p17964] Low confidence 7922.09 8203.19 1.03548
1277 heat shock-related 70 kda protein 2 (heat shock 70 kda protein 2). [swissprot;acc:p54652] High confidence 6437.99 6969.67 1.08258
sphingosine-1-phosphate lyase 1; sphingosine-1-phosphate lyase. [refseq;acc:nm_003901] Low confidence 8404.42 8702.63 1.03548
1278 heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107] High confidence 6437.99 6969.67 1.08258
sphingolipid delta 4 desaturase; membrane fatty acid (lipid) desaturase; dihydroceramide desaturase. [refseq;acc:nm_003676] Low confidence 7917.56 8198.48 1.03548
1279 heat shock cognate 71 kda protein. [swissprot;acc:p11142] High confidence 6437.99 6969.67 1.08258
putative alpha-mannosidase kiaa0212 (ec 3.2.1.-). [swissprot;acc:q92611] Low confidence 8154.99 8444.29 1.03548
1280 dehydrodolichyl diphosphate synthase. [refseq;acc:nm_024887] High confidence 6350.81 6874.88 1.08252
hexaprenyldihydroxybenzoate methyltransferase, mitochondrial precursor (ec 2.1.1.114) (dihydroxyhexaprenylbenzoate methyltransferase) (3,4- dihydroxy-5-hexaprenylbenzoate methyltransferase) (dhhb methyltransferase) (dhhb-mt) (dhhb-mtase). [swissprot;acc:q9nzj6] Low confidence 8306.5 8601.18 1.03548
1281 orphan nuclear receptor hmr (early response protein nak1) (tr3 orphan receptor). [swissprot;acc:p22736] High confidence 6230.49 6744.5 1.0825
ras-related protein rap-2a. [swissprot;acc:p10114] Low confidence 7922.09 8203.19 1.03548
1282 nuclear hormone receptor nor-1 (neuron-derived orphan receptor 1) (mitogen induced nuclear orphan receptor). [swissprot;acc:q92570] High confidence 6230.38 6744.35 1.08249
rap2c, member of ras oncogene family. [refseq;acc:nm_021183] Low confidence 7922.09 8203.19 1.03548
1283 orphan nuclear receptor nurr1 (immediate-early response protein not) (transcriptionally inducible nuclear receptor). [swissprot;acc:p43354] High confidence 6229.16 6742.79 1.08246
polymerase (dna directed) sigma; topoisomerase-related function protein 4-1; polymerase (dna-directed) sigma. [refseq;acc:nm_006999] Low confidence 7937.99 8219.61 1.03548
1284 dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial precursor (ec 2.3.1.61) (e2) (e2k). [swissprot;acc:p36957] 8123.15 8411.27 1.03547
xenotropic and polytropic retrovirus receptor. [refseq;acc:nm_004736] High confidence 6413.32 6941.48 1.08235
1285 cytosolic nonspecific dipeptidase (glutamate carboxypeptidase-like protein 1). [swissprot;acc:q96kp4] 6207.57 6718.7 1.08234
potential phospholipid-transporting atpase ia (ec 3.6.3.1) (chromaffin granule atpase ii) (atpase class i type 8a member 1). [swissprot;acc:q9y2q0] Low confidence 8090.84 8377.72 1.03546
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] High confidence 5655.85 6120.64 1.08218
protein cgi-147. [swissprot;acc:q9y3e5] Low confidence 7984.82 8267.92 1.03545
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] High confidence 5655.85 6120.64 1.08218
nucleosome assembly protein 1-like 1 (nap-1 related protein). [swissprot;acc:p55209] Low confidence 8101.59 8388.73 1.03544

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/