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 4377 to 4426 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
2189 3-hydroxyanthranilate 3,4-dioxygenase (ec 1.13.11.6) (3-hao) (3-hydroxyanthranilic acid dioxygenase) (3-hydroxyanthranilate oxygenase). [swissprot;acc:p46952] Divided 209.54 208.162 1.00662
bag-family molecular chaperone regulator-1 (bcl-2 binding athanogene- 1) (bag-1) (glucocorticoid receptor-associated protein rap46). [swissprot;acc:q99933] Subtracted 211.713 210.318 1.395
2190 glycogen synthase kinase-3 alpha (ec 2.7.1.37) (gsk-3 alpha). [swissprot;acc:p49840]
zinc finger protein-like 1; zinc-finger protein in men1 region. [refseq;acc:nm_006782] Divided 209.54 208.162 1.00662
2191 glycogen synthase kinase-3 beta (ec 2.7.1.37) (gsk-3 beta). [swissprot;acc:p49841] Subtracted 211.713 210.318 1.395
hus1 checkpoint protein; hus1 (s. pombe) checkpoint homolog; hus1+-like protein. [refseq;acc:nm_004507] Divided 209.54 208.162 1.00662
2192 hyaluronan binding protein 4; intracellular antigen detected by monoclonal antibody ki-1; intracellular hyaluronan-binding protein; chromodomain helicase dna binding protein 3 interacting protein. [refseq;acc:nm_014282]
p47 protein isoform a. [refseq;acc:nm_016143] Subtracted 213.642 212.254 1.388
2193 cofilin, non-muscle isoform (18 kda phosphoprotein) (p18). [swissprot;acc:p23528] 217.955 219.336 1.381
prolyl 4-hydroxylase alpha-1 subunit precursor (ec 1.14.11.2) (4-ph alpha-1) (procollagen-proline,2-oxoglutarate-4-dioxygenase alpha-1 subunit). [swissprot;acc:p13674] Divided 209.54 208.162 1.00662
2194 cofilin, muscle isoform (cofilin 2). [swissprot;acc:q9y281] Subtracted 217.955 219.336 1.381
homeobox prospero-like protein prox1 (prox 1). [swissprot;acc:q92786] Divided 209.54 208.162 1.00662
2195 rad1 homolog isoform 1; exonuclease homolog rad1; cell cycle checkpoint protein rad1 a/b; rad1-like protein; cell cycle checkpoint protein hrad1; dna repair exonuclease (rec1); dna repair protein rad1; rad1-like dna damage checkpoint protein. [refseq;acc:nm_002853]
transitional endoplasmic reticulum atpase (ter atpase) (15s mg(2+)- atpase p97 subunit) (valosin containing protein) (vcp) [contains: valosin]. [swissprot;acc:p55072] Subtracted 215.571 214.19 1.381
2196 destrin (actin-depolymerizing factor) (adf). [swissprot;acc:p18282] 217.955 219.336
prolyl 4-hydroxylase alpha-2 subunit precursor (ec 1.14.11.2) (4-ph alpha-2) (procollagen-proline,2-oxoglutarate-4-dioxygenase alpha-2 subunit). [swissprot;acc:o15460] Divided 209.54 208.162 1.00662
2197 ubiquinone biosynthesis monooxgenase coq6 (ec 1.14.13.-) (cgi-10). [swissprot;acc:q9y2z9] 193.787 195.064 1.00659
ubiquitin fusion degradation protein 1 homolog (ub fusion protein 1). [swissprot;acc:q92890] Subtracted 217.955 219.336 1.381
2198 kynurenine 3-monooxygenase (kynurenine 3-hydroxylase). [refseq;acc:nm_003679] Divided 193.787 195.064 1.00659
protein disulfide isomerase precursor (pdi) (ec 5.3.4.1) (prolyl 4- hydroxylase beta subunit) (cellular thyroid hormone binding protein) (p55). [swissprot;acc:p07237] Subtracted 209.54 208.162 1.378
2199 protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981] 222.959 224.337
squalene monooxygenase (ec 1.14.99.7) (squalene epoxidase) (se). [swissprot;acc:q14534] Divided 193.787 195.064 1.00659
2200 bromodomain-containing protein 3 (ring3-like protein). [swissprot;acc:q15059] Subtracted 222.965 224.343 1.378
insulin gene enhancer protein isl-2 (islet-2). [swissprot;acc:q96a47] Divided 196.748 195.466 1.00656
2201 3-hydroxyanthranilate 3,4-dioxygenase (ec 1.13.11.6) (3-hao) (3-hydroxyanthranilic acid dioxygenase) (3-hydroxyanthranilate oxygenase). [swissprot;acc:p46952] Subtracted 209.54 208.162 1.378
p47 protein isoform a. [refseq;acc:nm_016143] Divided 213.642 212.254 1.00654
2202 tumor susceptibility gene 101 protein. [swissprot;acc:q99816] 195.97 194.7 1.00652
zinc finger protein-like 1; zinc-finger protein in men1 region. [refseq;acc:nm_006782] Subtracted 209.54 208.162 1.378
2203 bromodomain-containing protein 4 (hunk1 protein). [swissprot;acc:o60885] 222.959 224.337
symplekin. [swissprot;acc:q92797] Divided 162.741 163.8 1.00651
2204 ruvb-like 2 (ec 3.6.1.-) (48-kda tata box-binding protein-interacting protein) (48-kda tbp-interacting protein) (tip49b) (repressing pontin 52) (reptin 52) (51 kda erythrocyte cytosolic protein) (ecp-51) (tip60-associated protein 54-beta) (tap54-beta) (cgi-46). [swissprot;acc:q9y230] 219.377 220.8 1.00649
testis-specific bromodomain protein. [refseq;acc:nm_001726] Subtracted 222.958 224.336 1.378
2205 60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [swissprot;acc:p35268] Divided 199.129 200.413 1.00645
hus1 checkpoint protein; hus1 (s. pombe) checkpoint homolog; hus1+-like protein. [refseq;acc:nm_004507] Subtracted 209.54 208.162 1.378
2206 hyaluronan binding protein 4; intracellular antigen detected by monoclonal antibody ki-1; intracellular hyaluronan-binding protein; chromodomain helicase dna binding protein 3 interacting protein. [refseq;acc:nm_014282]
transitional endoplasmic reticulum atpase (ter atpase) (15s mg(2+)- atpase p97 subunit) (valosin containing protein) (vcp) [contains: valosin]. [swissprot;acc:p55072] Divided 215.571 214.19 1.00645
2207 nag14 protein. [refseq;acc:nm_022143] Subtracted 222.959 224.337 1.378
sin3 associated polypeptide p30; sin3-associated polypeptide, 30kd. [refseq;acc:nm_003864] Divided 199.129 200.413 1.00645
2208 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]
prolyl 4-hydroxylase alpha-1 subunit precursor (ec 1.14.11.2) (4-ph alpha-1) (procollagen-proline,2-oxoglutarate-4-dioxygenase alpha-1 subunit). [swissprot;acc:p13674] Subtracted 209.54 208.162 1.378
2209 atp-binding cassette, sub-family c, member 10; multidrug resistance-associated protein 7. [refseq;acc:nm_033450] Divided 199.129 200.413 1.00645
homeobox prospero-like protein prox1 (prox 1). [swissprot;acc:q92786] Subtracted 209.54 208.162 1.378
2210 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] Divided 199.129 200.413 1.00645
rad1 homolog isoform 1; exonuclease homolog rad1; cell cycle checkpoint protein rad1 a/b; rad1-like protein; cell cycle checkpoint protein hrad1; dna repair exonuclease (rec1); dna repair protein rad1; rad1-like dna damage checkpoint protein. [refseq;acc:nm_002853] Subtracted 209.54 208.162 1.378
2211 bromodomain-containing protein 2 (ring3 protein) (o27.1.1). [swissprot;acc:p25440] 222.96 224.338
rna polymerase i transcription factor rrn3. [refseq;acc:nm_018427] Divided 199.129 200.413 1.00645
2212 28s ribosomal protein s16, mitochondrial precursor (mrp-s16) (cgi- 132). [swissprot;acc:q9y3d3] 224.411 225.854 1.00643
prolyl 4-hydroxylase alpha-2 subunit precursor (ec 1.14.11.2) (4-ph alpha-2) (procollagen-proline,2-oxoglutarate-4-dioxygenase alpha-2 subunit). [swissprot;acc:o15460] Subtracted 209.54 208.162 1.378
2213 dimeric dihydrodiol dehydrogenase; 3-deoxyglucosone reductase. [refseq;acc:nm_014475] Divided 210.127 211.475 1.00642
mitochondrial ribosomal protein l18. [refseq;acc:nm_014161] Subtracted 223.58 224.943 1.363

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/