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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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 5436 to 5485 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1359 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
dpy-30-like protein. [swissprot;acc:q9c005] Rooted 60.8705 63.3375 1.04053
gamma adducin (adducin-like protein 70). [swissprot;acc:q9uey8] Measured 5799.14 6255.04 1.07862
trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] Squared 17539.2 19723.3 1.12453
1366 activin a receptor, type ic; activin receptor-like kinase 7. [refseq;acc:nm_145259] Ranked 223.884 228.795 1.02194
megf11 protein. [refseq;acc:nm_032445] Measured 5793.55 6248.79 1.07858
rab coupling protein; rab-interacting recycling protein; rab effector protein; rab11-family interacting protein 1. [refseq;acc:nm_025151] Rooted 60.8705 63.3375 1.04053
trimethyllysine dioxygenase, mitochondrial precursor (ec 1.14.11.8) (epsilon-trimethyllysine 2-oxoglutarate dioxygenase) (tml-alpha- ketoglutarate dioxygenase) (tml hydroxylase) (tml dioxygenase) (tmld). [swissprot;acc:q9nvh6] Squared 30488.9 34284.9 1.1245
1367 gamma-snap-associated factor 1; rab11-interacting protein. [refseq;acc:nm_015470] Rooted 60.8705 63.3375 1.04053
gtp-binding protein era homolog (hera) (fragment). [swissprot;acc:o75616] Squared 30488.9 34284.9 1.1245
megf10 protein. [refseq;acc:nm_032446] Measured 5793.47 6248.71 1.07858
neuronal calcium sensor 1 (ncs-1) (frequenin homolog) (frequenin-like protein) (frequenin-like ubiquitous protein). [swissprot;acc:p36610] Ranked 223.887 228.799 1.02194
1368 beta adducin (erythrocyte adducin beta subunit). [swissprot;acc:p35612] Measured 5793.29 6248.51 1.07858
fibrillarin (34 kda nucleolar scleroderma antigen). [swissprot;acc:p22087] Squared 15565.5 17500.6 1.12432
neighbor of cox4. [swissprot;acc:o43402] Rooted 60.8705 63.3375 1.04053
polyamine oxidase isoform 1; polyamine oxidase; flavin-containing spermine oxidase; putative cyclin g1 interacting protein; flavin containing amine oxidase. [refseq;acc:nm_019025] Ranked 228.644 223.736 1.02194
1369 alpha adducin (erythrocyte adducin alpha subunit). [swissprot;acc:p35611] Measured 5786.71 6241.16 1.07853
cytochrome c-type heme lyase (ec 4.4.1.17) (cchl) (holocytochrome c- type synthase). [swissprot;acc:p53701] Ranked 228.644 223.736 1.02194
protein c14orf122 (cgi-112). [swissprot;acc:q9y3b6] Rooted 60.8705 63.3375 1.04053
tryptophan 2,3-dioxygenase (ec 1.13.11.11) (tryptophan pyrrolase) (tryptophanase) (tryptophan oxygenase) (tryptamin 2,3-dioxygenase) (trpo). [swissprot;acc:p48775] Squared 22572.9 25377.6 1.12425
1370 cytoplasmic protein nck1 (nck adaptor protein 1) (sh2/sh3 adaptor protein nck-alpha). [swissprot;acc:p16333] Ranked 205.185 200.784 1.02192
potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110] Rooted 60.8705 63.3375 1.04053
serine hydroxymethyltransferase, cytosolic (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [swissprot;acc:p34896] Squared 22959.6 25806.2 1.12398
t-complex associated-testis-expressed 1-like (protein 91/23). [swissprot;acc:p51808] Measured 10231.8 9487.34 1.07847
1371 dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0] Squared 18598.9 20901.3 1.12379
double-strand break repair protein mre11a (mre11 homolog 1). [swissprot;acc:p49959] Measured 10231.8 9487.34 1.07847
glutathione s-transferase theta 1 (ec 2.5.1.18) (gst class-theta) (glutathione transferase t1-1). [swissprot;acc:p30711] Ranked 228.646 223.744 1.02191
secreted modular calcium-binding protein 1. [refseq;acc:nm_022137] Rooted 62.3839 64.9113 1.04051
1372 dynactin complex 50 kda subunit (50 kda dynein-associated polypeptide) (dynamitin) (dctn-50) (dynactin 2). [swissprot;acc:q13561] Squared 23319.2 26205 1.12375

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/