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 5408 to 5457 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1352 repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] Ranked 211.513 206.941 1.02209
1353 cyclin c. [swissprot;acc:p24863] Measured 6200.93 6690.57 1.07896
heparin sulfate n-deacetylase/n-sulfotransferase (ec 2.8.2.-) (n- hsst) (n-heparin sulfate sulfotransferase) (glucosaminyl n- deacetylase/n-sulfotransferase). [swissprot;acc:p52849] Ranked 228.409 223.475 1.02208
orphan nuclear receptor hmr (early response protein nak1) (tr3 orphan receptor). [swissprot;acc:p22736] Rooted 65.1528 67.8168 1.04089
pdz/coiled-coil domain binding partner for the rho-family gtpase tc10; fused in glioblastoma; golgi associated pdz and coiled-coil motif containing protein; cftr-associated ligand. [refseq;acc:nm_020399] Squared 26925.7 30311.3 1.12574
1354 actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571] Measured 6036.22 6512.64 1.07893
n-deacetylase/n-sulfotransferase (heparan glucosaminyl) 3. [refseq;acc:nm_004784] Ranked 228.409 223.475 1.02208
nucleoporin-like protein rip (hiv-1 rev-binding protein) (rev interacting protein) (rev/rex activation domain-binding protein). [swissprot;acc:p52594] Rooted 60.4911 58.1154 1.04088
rad54-like protein; rad54 homolog. [refseq;acc:nm_003579] Squared 25950.5 29212.5 1.1257
1355 glycine dehydrogenase [decarboxylating], mitochondrial precursor (ec 1.4.4.2) (glycine decarboxylase) (glycine cleavage system p- protein). [swissprot;acc:p23378] 25294.8 28473 1.12565
intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811] Rooted 60.4911 58.1154 1.04088
n-deacetylase/n-sulfotransferase 4. [refseq;acc:nm_022569] Ranked 228.409 223.475 1.02208
ornithine carbamoyltransferase, mitochondrial precursor (ec 2.1.3.3) (otcase) (ornithine transcarbamylase). [swissprot;acc:p00480] Measured 5783.9 6240.19 1.07889
1356 calcipressin 1 (down syndrome critical region protein 1) (myocyte- enriched calcineurin interacting protein 1) (mcip1) (adapt78). [swissprot;acc:p53805] 5657.71 6103.57 1.07881
heparan sulfate n-deacetylase/n-sulfotransferase (ec 2.8.2.8) (n-hsst) (hsnst) ([heparan sulfate]-glucosamine n-sulfotransferase) (n-heparan sulfate sulfotransferase) (glucosaminyl n-deacetylase/n- sulfotransferase). [swissprot;acc:p52848] Ranked 228.409 223.475 1.02208
hydroxyindole o-methyltransferase (ec 2.1.1.4) (hiomt) (acetylserotonin o-methyltransferase) (asmt). [swissprot;acc:p46597] Squared 23066.6 25964.6 1.12564
pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152] Rooted 60.4911 58.1154 1.04088
1357 dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2] Measured 5657.71 6103.54 1.0788
importin 7; ran-binding protein 7. [refseq;acc:nm_006391] Squared 24948.9 28072.6 1.1252
nuclear hormone receptor nor-1 (neuron-derived orphan receptor 1) (mitogen induced nuclear orphan receptor). [swissprot;acc:q92570] Rooted 65.1521 67.8158 1.04088
protein cdc27hs (cell division cycle protein 27 homolog) (h-nuc). [swissprot;acc:p30260] Ranked 228.409 223.475 1.02208
1358 importin 8; ran-binding protein 8. [refseq;acc:nm_006390] Squared 24948.9 28072.6 1.1252
intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3] Rooted 60.4911 58.1154 1.04088
upstream stimulatory factor 1 (major late transcription factor 1). [swissprot;acc:p22415] Ranked 214.987 210.359 1.022
zinc finger protein zic 4 (zinc finger protein of the cerebellum 4) (fragment). [swissprot;acc:q8n9l1] Measured 5657.71 6103.54 1.0788
1359 brefeldin a-inhibited guanine nucleotide-exchange protein 2 (brefeldin a-inhibited gep 2). [swissprot;acc:q9y6d5] Squared 24948.9 28072.6 1.1252
dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7] Measured 5657.71 6103.54 1.0788
glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712] Ranked 228.642 223.726 1.02197
hiv-1 rev binding protein-like; rev/rex activation domain binding protein-related. [refseq;acc:nm_006076] Rooted 60.4911 58.1154 1.04088
1360 calcipressin 2 (thyroid hormone-responsive protein zaki-4) (down syndrome candidate region 1-like 1) (myocyte-enriched calcineurin interacting protein 2) (mcip2). [swissprot;acc:q14206] Measured 5657.72 6103.52 1.07879
cgthba protein (-14 gene protein). [swissprot;acc:q12980] Rooted 60.4911 58.1154 1.04088
hsgcn1 (fragment). [sptrembl;acc:q99736] Squared 24948.9 28072.6 1.1252
tgf-beta receptor type i precursor (ec 2.7.1.37) (tgfr-1) (tgf-beta type i receptor) (serine/threonine-protein kinase receptor r4) (skr4) (activin receptor-like kinase 5) (alk-5). [swissprot;acc:p36897] Ranked 223.89 228.805 1.02195
1361 brefeldin a-inhibited guanine nucleotide-exchange protein 1 (brefeldin a-inhibited gep 1) (p200 arf-gep1) (p200 arf guanine nucleotide exchange factor). [swissprot;acc:q9y6d6] Squared 24948.9 28072.6 1.1252
calcipressin 3 (down syndrome candidate region 1-like protein 2) (myocyte-enriched calcineurin interacting protein 3) (mcip3). [swissprot;acc:q9uka8] Measured 5657.72 6103.52 1.07879
hiv tat specific factor 1; cofactor required for tat activation of hiv-1 transcription. [refseq;acc:nm_014500] Rooted 60.4911 58.1154 1.04088
upstream stimulatory factor 2 (upstream transcription factor 2) (fos-interacting protein) (fip) (major late transcription factor 2). [swissprot;acc:q15853] Ranked 214.971 210.354 1.02195
1362 5-methyltetrahydrofolate--homocysteine methyltransferase (ec 2.1.1.13) (methionine synthase, vitamin-b12 dependent) (ms). [swissprot;acc:q99707] Rooted 61.5231 64.0358 1.04084
peroxisomal n1-acetyl-spermine/spermidine oxidase. [refseq;acc:nm_152911] Ranked 228.644 223.736 1.02194
sequestosome 1; ubiquitin-binding protein p62; phosphotyrosine independent ligand for the lck sh2 domain p62. [refseq;acc:nm_003900] Measured 6322.75 6820.5 1.07872
zinc finger protein t86. [swissprot;acc:o00488] Squared 16283.6 18321.8 1.12517
1363 camp response element-binding protein cre-bpa. [refseq;acc:nm_004904] Ranked 218.591 213.899 1.02194
hydroxyacid oxidase 1 (ec 1.1.3.15) (haox1) (glycolate oxidase) (gox). [swissprot;acc:q9ujm8] Squared 17915.5 20153.8 1.12494
nonspecific lipid-transfer protein, mitochondrial precursor (nsl-tp) (sterol carrier protein 2) (scp-2) (sterol carrier protein x) (scp-x) (scpx). [swissprot;acc:p22307] Measured 6322.75 6820.5 1.07872
orphan nuclear receptor nurr1 (immediate-early response protein not) (transcriptionally inducible nuclear receptor). [swissprot;acc:p43354] Rooted 65.1444 67.8042 1.04083
1364 diphosphomevalonate decarboxylase (ec 4.1.1.33) (mevalonate pyrophosphate decarboxylase) (mevalonate (diphospho)decarboxylase). [swissprot;acc:p53602] Squared 17001.7 19119 1.12453
protein c20orf4 (protein cgi-23) (pro0225). [swissprot;acc:q9y312] Measured 5815.14 6272.66 1.07868
putative sialoglycoprotease type 2. [refseq;acc:nm_022353] Rooted 60.4563 62.9199 1.04075
serine/threonine-protein kinase receptor r2 precursor (ec 2.7.1.37) (skr2) (activin receptor-like kinase 4) (alk-4) (actr-ib). [swissprot;acc:p36896] Ranked 223.885 228.797 1.02194
1365 atpase inhibitor, mitochondrial precursor. [swissprot;acc:q9uii2] 228.644 223.736

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/