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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 4858 to 4907 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
2429 sphingosine-1-phosphate lyase 1; sphingosine-1-phosphate lyase. [refseq;acc:nm_003901] Low confidence 198.047 194.468 1.0184
2430 epsin 1; eh domain-binding mitotic phosphoprotein. [refseq;acc:nm_013333] High confidence 217.873 218.644 1.00354
transmembrane 9 superfamily protein member 3 precursor (sm-11044 binding protein) (ep70-p-iso). [swissprot;acc:q9hd45] Low confidence 201.516 197.878 1.01839
2431 dna-directed rna polymerases iii 39 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c39 subunit). [swissprot;acc:q9h1d9] 201.946 198.301 1.01838
proteasome subunit alpha type 2 (ec 3.4.25.1) (proteasome component c3) (macropain subunit c3) (multicatalytic endopeptidase complex subunit c3). [swissprot;acc:p25787] High confidence 213.048 212.3 1.00352
2432 26s proteasome non-atpase regulatory subunit 6 (26s proteasome regulatory subunit s10) (p42a) (proteasome regulatory particle subunit p44s10). [swissprot;acc:q15008] 215.807 216.556 1.00347
hexaprenyldihydroxybenzoate methyltransferase, mitochondrial precursor (ec 2.1.1.114) (dihydroxyhexaprenylbenzoate methyltransferase) (3,4- dihydroxy-5-hexaprenylbenzoate methyltransferase) (dhhb methyltransferase) (dhhb-mt) (dhhb-mtase). [swissprot;acc:q9nzj6] Low confidence 198.399 194.819 1.01838
2433 elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [swissprot;acc:p04720] High confidence 217.366 218.117 1.00346
putative sialoglycoprotease type 2. [refseq;acc:nm_022353] Low confidence 200.495 196.876 1.01838
2434 cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941] 200.752 197.128
methylenetetrahydrofolate reductase (ec 1.5.1.20). [swissprot;acc:p42898] High confidence 213.021 212.286 1.00346
2435 serine/threonine protein kinase 23 (ec 2.7.1.37) (muscle-specific serine kinase 1) (mssk-1). [swissprot;acc:q9upe1] Low confidence 202.421 198.77 1.01837
zinc-finger protein zpr1 (zinc finger protein 259). [swissprot;acc:o75312] High confidence 217.366 218.117 1.00346
2436 elongation factor 1-alpha 2 (ef-1-alpha-2) (elongation factor 1 a-2) (eef1a-2) (statin s1). [swissprot;acc:q05639]
inositol hexaphosphate kinase 1. [refseq;acc:nm_153273] Low confidence 199.117 195.526 1.01837
2437 guanylate kinase (ec 2.7.4.8) (gmp kinase). [swissprot;acc:q16774] High confidence 219.361 220.116 1.00344
programmed cell death protein 5 (tfar19 protein) (tf-1 cell apoptosis related gene-19 protein). [swissprot;acc:o14737] Low confidence 202.072 198.428 1.01836
2438 proteasome subunit alpha type 4 (ec 3.4.25.1) (proteasome component c9) (macropain subunit c9) (multicatalytic endopeptidase complex subunit c9) (proteasome subunit l). [swissprot;acc:p25789] High confidence 214.049 213.323 1.0034
sex comb on midleg homolog 1. [refseq;acc:nm_012236] Low confidence 203.896 200.219 1.01836
2439 14-3-3 protein beta/alpha (protein kinase c inhibitor protein-1) (kcip-1) (protein 1054). [swissprot;acc:p31946] High confidence 220.681 221.425 1.00337
j kappa-recombination signal binding protein (rbp-j kappa). [swissprot;acc:q06330] Low confidence 198.685 195.104 1.01835
2440 26s proteasome non-atpase regulatory subunit 3 (26s proteasome regulatory subunit s3) (proteasome subunit p58). [swissprot;acc:o43242] High confidence 217.645 218.376 1.00336
synaptosomal-associated protein 25 (snap-25) (super protein) (sup). [swissprot;acc:p13795] Low confidence 198.68 195.1 1.01835
2441 dgcr8 protein (digeorge syndrome critical region 8). [swissprot;acc:q8wyq5] 198.685 195.104
electron transfer flavoprotein alpha-subunit, mitochondrial precursor (alpha-etf). [swissprot;acc:p13804] High confidence 180.137 180.732 1.0033
2442 ribonuclease iii (ec 3.1.26.3) (rnase iii) (p241). [swissprot;acc:q9nrr4] Low confidence 198.685 195.104 1.01835
transcription initiation factor tfiid 70 kda subunit (tafii-70) (tafii-80) (tafii80). [swissprot;acc:p49848] High confidence 204.419 203.748 1.00329
2443 nadh-ubiquinone oxidoreductase b18 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b18) (ci-b18) (cell adhesion protein sqm1). [swissprot;acc:p17568] Low confidence 198.685 195.104 1.01835
ubiquitin-like protein sumo-1 conjugating enzyme (ec 6.3.2.19) (sumo- 1-protein ligase) (ubiquitin carrier protein) (ubiquitin-conjugating enzyme ubce2a) (p18). [swissprot;acc:p50550] High confidence 217.073 216.364 1.00328
2444 zinc finger protein 288 (dendritic-derived btb/poz zinc finger protein). [swissprot;acc:q9hc78] 206.086 206.753 1.00324
zinc finger protein 40 (human immunodeficiency virus type i enhancer- binding protein 1) (hiv-ep1) (major histocompatibility complex binding protein 1) (mbp-1) (positive regulatory domain ii binding factor 1) (prdii-bf1). [swissprot;acc:p15822] Low confidence 198.685 195.104 1.01835
2445 kruppel-related zinc finger protein hckrox. [refseq;acc:nm_015872] High confidence 206.088 206.756 1.00324
synaptosomal-associated protein 23 (snap-23) (vesicle-membrane fusion protein snap-23). [swissprot;acc:o00161] Low confidence 198.68 195.1 1.01835
2446 epoxide hydrolase 1 (ec 3.3.2.3) (microsomal epoxide hydrolase) (epoxide hydratase). [swissprot;acc:p07099] High confidence 182.272 181.683 1.00324
g protein-coupled receptor 142. [refseq;acc:nm_181790] Low confidence 200.512 196.901 1.01834
2447 peroxisomal targeting signal 2 receptor (pts2 receptor) (peroxin-7). [swissprot;acc:o00628] High confidence 206.084 206.752 1.00324
ras gtpase-activating-like protein iqgap2. [swissprot;acc:q13576] Low confidence 199.294 195.705 1.01834
2448 glycine dehydrogenase [decarboxylating], mitochondrial precursor (ec 1.4.4.2) (glycine decarboxylase) (glycine cleavage system p- protein). [swissprot;acc:p23378] High confidence 212.446 211.766 1.00321
translation initiation factor eif-2b epsilon subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q13144] Low confidence 200.578 196.965 1.01834
2449 histone-lysine n-methyltransferase, h3 lysine-9 specific 4 (ec 2.1.1.43) (histone h3-k9 methyltransferase 4) (h3-k9-hmtase 4) (set domain bifurcated 1) (erg-associated protein with set domain) (eset). [swissprot;acc:q15047] 203.547 199.882
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] High confidence 204.717 205.371 1.00319
2450 proteasome subunit beta type 6 precursor (ec 3.4.25.1) (proteasome delta chain) (macropain delta chain) (multicatalytic endopeptidase complex delta chain) (proteasome subunit y). [swissprot;acc:p28072] 213.85 213.177 1.00316
quaking isoform 6. [sptrembl;acc:q9p0x9] Low confidence 203.547 199.882 1.01834
2451 60s ribosomal protein l35a. [swissprot;acc:p18077] 200.987 197.369 1.01833
secretory carrier-associated membrane protein 2. [swissprot;acc:o15127] High confidence 204.688 205.333 1.00315
2452 ras gtpase-activating-like protein iqgap1 (p195). [swissprot;acc:p46940] Low confidence 199.295 195.707 1.01833
secretory carrier-associated membrane protein 3. [swissprot;acc:o14828] High confidence 204.688 205.333 1.00315
2453 protein hspc134 (protein cda04). [swissprot;acc:q9by43] Low confidence 197.86 201.487 1.01833
secretory carrier-associated membrane protein 1. [swissprot;acc:o15126] High confidence 204.688 205.332 1.00315
2454 ruvb-like 1 (ec 3.6.1.-) (49-kda tata box-binding protein-interacting protein) (49 kda tbp-interacting protein) (tip49a) (pontin 52) (nuclear matrix protein 238) (nmp 238) (54 kda erythrocyte cytosolic protein) (ecp-54) (tip60-associated protein 54-alpha) (tap54-alpha). [swissprot;acc:q9y265] Low confidence 198.737 195.161 1.01832

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/