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 6812 to 6861 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
852 hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] Ranked Divided 193.114 185.412 1.04154
peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570] Rooted 58.5869 62.2732 1.06292
ras-gtpase-activating protein binding protein 1 (gap sh3-domain binding protein 1) (g3bp-1). [swissprot;acc:q13283] Squared 31100.1 36086.4 1.16033
solute carrier family 13, member 2 (renal sodium/dicarboxylate cotransporter) (na(+)/dicarboxylate cotransporter 1) (nadc-1). [swissprot;acc:q13183] Measured Subtracted 6439.66 7032.22 592.56
sterol regulatory element binding protein cleavage-activating protein (srebp cleavage-activating protein) (scap). [swissprot;acc:q12770] Squared 24242.8 28127.6 3884.8
853 apoptosis antagonizing transcription factor. [refseq;acc:nm_012138] Measured Divided 4078.45 4502.32 1.10393
atp synthase beta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p06576] Squared Subtracted 24242.8 28127.6 3884.8
ga binding protein beta-2 chain (gabp-beta-2 subunit) (transcription factor e4tf1-47) (gapbp-2) (nuclear respiratory factor-2 subunit gamma). [swissprot;acc:q06545] Ranked 227.596 219.017 8.579
nadh-ubiquinone oxidoreductase b22 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b22) (ci-b22). [swissprot;acc:q9y6m9] Rooted 66.4035 70.2633 3.8598
ras-gtpase-activating protein binding protein 2 (gap sh3-domain binding protein 2) (g3bp-2). [swissprot;acc:q9un86] Squared Divided 31100.1 36086.4 1.16033
secretory carrier-associated membrane protein 1. [swissprot;acc:o15126] Measured Subtracted 6439.35 7031.8 592.45
target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077] Rooted Divided 64.0287 68.0566 1.06291
wd-repeat protein wdc146. [swissprot;acc:q9c0j8] Ranked 108.289 112.772 1.0414
854 cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]
importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [swissprot;acc:o00505] Rooted 64.0316 68.0597 1.06291
keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966] Squared 31100.2 36086.5 1.16033
nadh-ubiquinone oxidoreductase 23 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-23kd) (ci-23kd) (tyky subunit). [swissprot;acc:o00217] Ranked Subtracted 227.596 219.017 8.579
phosphatidylinositol 3-kinase regulatory beta subunit (pi3-kinase p85-beta subunit) (ptdins-3-kinase p85-beta). [swissprot;acc:o00459] Squared 24242.8 28127.6 3884.8
secretory carrier-associated membrane protein 2. [swissprot;acc:o15127] Measured 6439.3 7031.73 592.43
syntaxin 10 (syn10). [swissprot;acc:o60499] Rooted 57.2102 53.3508 3.8594
uba/ubx 33.3 kda protein. [swissprot;acc:q04323] Measured Divided 6562.98 7242.37 1.10352
855 clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610] Rooted Subtracted 62.2385 58.38 3.8585
elongation of very long chain fatty acids protein 1 (cgi-88). [swissprot;acc:q9bw60] Ranked 227.596 219.018 8.578
ero1-like. [refseq;acc:nm_014584] Measured Divided 6562.98 7242.37 1.10352
espin. [refseq;acc:nm_031475] Squared 31100.1 36086.4 1.16033
glycerol-3-phosphate dehydrogenase, mitochondrial precursor (ec 1.1.99.5) (gpd-m) (gpdh-m). [swissprot;acc:p43304] Subtracted 25108.4 28986.7 3878.3
importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629] Rooted Divided 64.0262 68.0537 1.0629
secretory carrier-associated membrane protein 3. [swissprot;acc:o14828] Measured Subtracted 6439.3 7031.73 592.43
tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452] Ranked Divided 178.514 171.42 1.04138
856 bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132] Measured Subtracted 5734.15 6326.41 592.26
cytochrome p450 2d6 (ec 1.14.14.1) (cypiid6) (p450-db1) (debrisoquine 4-hydroxylase). [swissprot;acc:p10635] Squared Divided 31100.1 36086.4 1.16033
grb2-related adaptor protein. [swissprot;acc:q13588] Subtracted 29854.9 33731 3876.1
heparin sulfate n-deacetylase/n-sulfotransferase (ec 2.8.2.-) (n- hsst) (n-heparin sulfate sulfotransferase) (glucosaminyl n- deacetylase/n-sulfotransferase). [swissprot;acc:p52849] Measured Divided 5210.58 5749.33 1.1034
mannose-p-dolichol utilization defect 1 protein (suppressor of lec15 and lec35 glycosylation mutation homolog) (sl15). [swissprot;acc:o75352] Rooted 58.5944 62.2766 1.06284
myc proto-oncogene protein (c-myc). [swissprot;acc:p01106] Ranked Subtracted 227.585 219.037 8.548
syntaxin 6. [swissprot;acc:o43752] Rooted 57.2202 53.3639 3.8563
xenotropic and polytropic retrovirus receptor. [refseq;acc:nm_004736] Ranked Divided 215.028 206.623 1.04068
857 breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872] Squared Subtracted 23148.8 27021.5 3872.7
midasin (midas-containing protein). [swissprot;acc:q9nu22] Ranked 237.218 228.698 8.52
mitochondrial translational release factor 1-like. [refseq;acc:nm_019041] Rooted Divided 58.6002 62.2793 1.06278
n-deacetylase/n-sulfotransferase (heparan glucosaminyl) 3. [refseq;acc:nm_004784] Measured 5210.58 5749.33 1.1034
phosducin-like protein (phlp). [swissprot;acc:q13371] Rooted Subtracted 62.2361 58.3858 3.8503
phosphatidate cytidylyltransferase 2 (ec 2.7.7.41) (cdp-diglyceride synthetase 2) (cdp-diglyceride pyrophosphorylase 2) (cdp- diacylglycerol synthase 2) (cds 2) (ctp:phosphatidate cytidylyltransferase 2) (cdp-dag synthase 2) (cdp-dg synthetase 2). [swissprot;acc:o95674] Measured 6437.49 7029.22 591.73
pleckstrin homology domain containing, family c (with ferm domain) member 1; mitogen inducible 2; kindlin 2. [refseq;acc:nm_006832] Squared Divided 31100.1 36086.4 1.16033
putatative 28 kda protein. [refseq;acc:nm_020143] Ranked 227.241 236.467 1.0406
858 calcium-transporting atpase type 2c, member 1 (ec 3.6.3.8) (atpase 2c1) (atp-dependent ca(2+) pump pmr1) (hussy-28). [swissprot;acc:p98194] Rooted 65.1843 69.2736 1.06273
cdc5-like; cdc5 (cell division cycle 5, s. pombe, homolog)-like; cell division cycle 5, s. pombe, homolog-like; cdc5-related protein. [refseq;acc:nm_001253] Squared Subtracted 23148.8 27021.5 3872.7
dna-(apurinic or apyrimidinic site) lyase (ec 4.2.99.18) (ap endonuclease 1) (apex nuclease) (apen) (ref-1 protein). [swissprot;acc:p27695] Measured 6393.81 6984.94 591.13
lim and senescent cell antigen-like domains 2; ilk-binding protein. [refseq;acc:nm_017980] Squared Divided 31100.1 36086.4 1.16033
n-deacetylase/n-sulfotransferase 4. [refseq;acc:nm_022569] Measured 5210.58 5749.33 1.1034

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/