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 4358 to 4407 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
2179 heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107] Divided 210.961 209.563 1.00667
2180 heat shock cognate 71 kda protein. [swissprot;acc:p11142]
retinal pigment epithelium-specific protein 65kda; retinal pigment epithelium-specific protein (65kd); retinitis pigmentosa 20 (autosomal recessive). [refseq;acc:nm_000329] Subtracted 221.509 220.108 1.401
2181 calreticulin precursor (crp55) (calregulin) (hacbp) (erp60). [swissprot;acc:p27797] Divided 227.117 225.62 1.00664
indolethylamine n-methyltransferase (ec 2.1.1.49) (aromatic alkylamine n-methyltransferase) (indolamine n-methyltransferase) (arylamine n- methyltransferase) (amine n-methyltransferase). [swissprot;acc:o95050] Subtracted 221.509 220.108 1.401
2182 peroxisomal membrane protein 2 (22 kda peroxisomal membrane protein). [swissprot;acc:q9nr77] 210.961 209.563 1.398
twinkle; likely ortholog of mouse t7 gp4-like protein with intramitochondrial nucleoid localization. [refseq;acc:nm_021830] Divided 218.062 216.624 1.00664
2183 heat shock-related 70 kda protein 2 (heat shock 70 kda protein 2). [swissprot;acc:p54652] Subtracted 210.961 209.563 1.398
rabaptin, rab gtpase binding effector protein 1; rabaptin-5; neurocrescin. [refseq;acc:nm_004703] Divided 218.062 216.624 1.00664
2184 heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107] Subtracted 210.961 209.563 1.398
suppressor of var1, 3-like 1. [refseq;acc:nm_003171] Divided 211.713 210.318 1.00663
2185 bag-family molecular chaperone regulator-1 (bcl-2 binding athanogene- 1) (bag-1) (glucocorticoid receptor-associated protein rap46). [swissprot;acc:q99933]
heat shock cognate 71 kda protein. [swissprot;acc:p11142] Subtracted 210.961 209.563 1.398
2186 glycogen synthase kinase-3 alpha (ec 2.7.1.37) (gsk-3 alpha). [swissprot;acc:p49840] Divided 211.713 210.318 1.00663
seven in absentia homolog 1. [refseq;acc:nm_003031] Subtracted 223.608 225.005 1.397
2187 galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470] 206.401 207.796 1.395
glycogen synthase kinase-3 beta (ec 2.7.1.37) (gsk-3 beta). [swissprot;acc:p49841] Divided 211.713 210.318 1.00663
2188 protein disulfide isomerase precursor (pdi) (ec 5.3.4.1) (prolyl 4- hydroxylase beta subunit) (cellular thyroid hormone binding protein) (p55). [swissprot;acc:p07237] 209.54 208.162 1.00662
suppressor of var1, 3-like 1. [refseq;acc:nm_003171] Subtracted 211.713 210.318 1.395
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

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/