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 10114 to 10163 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
2529 pinch protein (particularly interesting new cys-his protein) (lim and senescent cell antigen-like domains 1). [swissprot;acc:p48059] Rooted 62.4421 63.0512 1.00975
protein cgi-147. [swissprot;acc:q9y3e5] Measured 6436.43 6283 1.02442
rad9 homolog; cell cycle checkpoint control protein; rad9 homolog (s. pombe). [refseq;acc:nm_004584] Squared 30390.4 32033.8 1.05408
2530 28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933] Measured 3880.5 3788.42 1.02431
60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [swissprot;acc:p35268] Squared 38544.3 36568.4 1.05403
integrin-linked protein kinase 1 (ec 2.7.1.-) (ilk-1) (59 kda serine/threonine protein kinase) (p59ilk). [swissprot;acc:q13418] Rooted 62.4421 63.0512 1.00975
proteasome subunit beta type 8 precursor (ec 3.4.25.1) (proteasome component c13) (macropain subunit c13) (multicatalytic endopeptidase complex subunit c13). [swissprot;acc:p28062] Ranked 212.464 211.99 1.00224
2531 apurinic/apyrimidinic endonuclease 2; apurinic/apyrimidinic endonuclease-like 2; apex nuclease-like 2. [refseq;acc:nm_014481] 216.264 215.787 1.00221
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] Measured 6141.97 6291.08 1.02428
ras suppressor protein 1 (rsu-1) (rsp-1). [swissprot;acc:q15404] Rooted 62.4421 63.0512 1.00975
sin3 associated polypeptide p30; sin3-associated polypeptide, 30kd. [refseq;acc:nm_003864] Squared 38544.3 36568.4 1.05403
2532 54 kda nuclear rna- and dna-binding protein (p54(nrb)) (p54nrb) (55 kda nuclear protein) (nmt55) (non-pou domain-containing octamer- binding protein) (dna-binding p52/p100 complex, 52 kda subunit). [swissprot;acc:q15233] Ranked 190.405 190.812 1.00214
60s ribosomal protein l15. [swissprot;acc:p39030] Measured 4888.72 5006.1 1.02401
clathrin coat assembly protein ap50 (clathrin coat associated protein ap50) (plasma membrane adaptor ap-2 50 kda protein) (ha2 50 kda subunit) (clathrin assembly protein complex 2 medium chain) (ap-2 mu 2 chain). [swissprot;acc:p20172] Squared 38544.3 36568.4 1.05403
ras-gtpase-activating protein binding protein 2 (gap sh3-domain binding protein 2) (g3bp-2). [swissprot;acc:q9un86] Rooted 62.4421 63.0512 1.00975
2533 atp-binding cassette, sub-family c, member 10; multidrug resistance-associated protein 7. [refseq;acc:nm_033450] Squared 38544.3 36568.4 1.05403
dna-directed rna polymerase i 135 kda polypeptide (ec 2.7.7.6) (rna polymerase i subunit 2) (rpa135). [swissprot;acc:q9h9y6] Measured 3847.84 3759.28 1.02356
espin. [refseq;acc:nm_031475] Rooted 62.4421 63.0512 1.00975
paraspeckle protein 1. [refseq;acc:nm_018282] Ranked 190.417 190.824 1.00214
2534 cytochrome p450 2d6 (ec 1.14.14.1) (cypiid6) (p450-db1) (debrisoquine 4-hydroxylase). [swissprot;acc:p10635] Rooted 62.4421 63.0512 1.00975
glycerol-3-phosphate dehydrogenase, mitochondrial precursor (ec 1.1.99.5) (gpd-m) (gpdh-m). [swissprot;acc:p43304] Ranked 208 207.555 1.00214
lysosomal alpha-mannosidase precursor (ec 3.2.1.24) (mannosidase, alpha b) (lysosomal acid alpha-mannosidase) (laman) (mannosidase alpha class 2b member 1). [swissprot;acc:o00754] Squared 38544.3 36568.4 1.05403
thyroid receptor interacting protein 12 (trip12). [swissprot;acc:q14669] Measured 6452.33 6603.94 1.0235
2535 chromobox protein homolog 1 (heterochromatin protein 1 homolog beta) (hp1 beta) (modifier 1 protein) (m31) (heterochromatin protein p25). [swissprot;acc:p23197] Ranked 188.228 188.63 1.00214
dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial precursor (ec 2.3.1.61) (e2) (e2k). [swissprot;acc:p36957] Measured 6452.33 6603.94 1.0235
pleckstrin homology domain containing, family c (with ferm domain) member 1; mitogen inducible 2; kindlin 2. [refseq;acc:nm_006832] Rooted 62.4421 63.0512 1.00975
rna polymerase i transcription factor rrn3. [refseq;acc:nm_018427] Squared 38544.3 36568.4 1.05403
2536 geranylgeranyl pyrophosphate synthetase (ggpp synthetase) (ggppsase) (geranylgeranyl diphosphate synthase) [includes: dimethylallyltransferase (ec 2.5.1.1); geranyltranstransferase (ec 2.5.1.10); farnesyltranstransferase (ec 2.5.1.29)]. [swissprot;acc:o95749] Ranked 236.51 236.008 1.00213
lim and senescent cell antigen-like domains 2; ilk-binding protein. [refseq;acc:nm_017980] Rooted 62.4421 63.0512 1.00975
p300/cbp-associated factor (ec 2.3.1.-) (p/caf) (histone acetylase pcaf). [swissprot;acc:q92831] Squared 35120.4 37011.6 1.05385
sorting nexin 1. [swissprot;acc:q13596] Measured 5932.05 6071.35 1.02348
2537 d(4) dopamine receptor (d(2c) dopamine receptor). [swissprot;acc:p21917] Rooted 62.4421 63.0512 1.00975
general control of amino acid synthesis protein 5-like 2 (ec 2.3.1.-) (histone acetyltransferase gcn5) (hsgcn5). [swissprot;acc:q92830] Squared 35119.5 37010 1.05383
pyruvate dehydrogenase e1 component alpha subunit, testis-specific form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type ii). [swissprot;acc:p29803] Measured 6669.22 6824.41 1.02327
vacuolar protein sorting-associated protein 45 (h-vps45) (hlvps45). [swissprot;acc:q9nrw7] Ranked 215.964 216.421 1.00212
2538 estradiol 17 beta-dehydrogenase 4 (ec 1.1.1.62) (17-beta-hsd 4) (17-beta-hydroxysteroid dehydrogenase 4). [swissprot;acc:p51659] Measured 7121.07 7286.61 1.02325
iron-responsive element binding protein 1 (ire-bp 1) (iron regulatory protein 1) (irp1) (ferritin repressor protein) (aconitate hydratase) (ec 4.2.1.3) (citrate hydro-lyase) (aconitase). [swissprot;acc:p21399] Rooted 72.3793 73.0834 1.00973
nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [swissprot;acc:p25208] Squared 20778.7 21896.5 1.0538
splicing factor, proline-and glutamine-rich (polypyrimidine tract- binding protein-associated splicing factor) (ptb-associated splicing factor) (psf) (dna-binding p52/p100 complex, 100 kda subunit). [swissprot;acc:p23246] Ranked 190.765 191.163 1.00209
2539 gc-rich sequence dna-binding factor homolog. [swissprot;acc:q9y5b6] 217.144 216.699 1.00205
keratin associated protein 9-4; keratin associated protein 9.4. [refseq;acc:nm_033191] Rooted 62.4419 63.0455 1.00967
reticulon protein 3 (neuroendocrine-specific protein-like 2) (nsp-like protein ii) (nsplii). [swissprot;acc:o95197] Squared 26735.4 28134.5 1.05233
ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [swissprot;acc:p47985] Measured 3805.17 3718.86 1.02321
2540 complement component 1, q subcomponent binding protein, mitochondrial precursor (glycoprotein gc1qbp) (gc1q-r protein) (hyaluronan-binding protein 1) (p32) (p33). [swissprot;acc:q07021] Squared 29876.6 31434.6 1.05215
pyruvate dehydrogenase e1 component alpha subunit, somatic form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type i). [swissprot;acc:p08559] Measured 6672.69 6827.51 1.0232
rad50 homolog isoform 1. [refseq;acc:nm_005732] Rooted 70.2887 69.6155 1.00967
toll-like receptor 2 precursor (toll/interleukin 1 receptor-like protein 4). [swissprot;acc:o60603] Ranked 217.144 216.699 1.00205
2541 aspartyl-trna synthetase (ec 6.1.1.12) (aspartate--trna ligase) (asprs). [swissprot;acc:p14868] 194.505 194.902 1.00204
rna-binding protein 10 (rna binding motif protein 10) (dxs8237e). [swissprot;acc:p98175] Rooted 57.7168 58.2731 1.00964
sirtuin 1; sir2-like 1; sirtuin type 1; sir2alpha; sirtuin silent mating type information regulation 2 homolog 1 (s. cerevisiae). [refseq;acc:nm_012238] Squared 29876.6 31434.6 1.05215

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/