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.


Navigation/Query Panel:
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 3130 to 3179 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
783 phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941] Rooted 62.2361 58.3858 1.06595
translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598] Ranked 224.385 235.131 1.04789
vacuolar atp synthase subunit b, brain isoform (ec 3.6.3.14) (v-atpase b2 subunit) (vacuolar proton pump b isoform 2) (endomembrane proton pump 58 kda subunit) (ho57). [swissprot;acc:p21281] Measured 5874.78 6533.37 1.1121
784 dc11 protein. [refseq;acc:nm_020186] Squared 27407.7 31927.7 1.16492
dna repair protein rad52 homolog. [swissprot;acc:p43351] Rooted 62.2361 58.3858 1.06595
polyglutamine binding protein 1; nuclear protein containing ww domain 38 kd. [refseq;acc:nm_005710] Ranked 224.385 235.131 1.04789
vacuolar atp synthase subunit e (ec 3.6.3.14) (v-atpase e subunit) (vacuolar proton pump e subunit) (v-atpase 31 kda subunit) (p31). [swissprot;acc:p36543] Measured 5874.77 6533.36 1.1121
785 amyloid beta precursor protein-binding protein 1; amyloid protein-binding protein 1. [refseq;acc:nm_003905] Squared 27407.7 31927.7 1.16492
clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675] Rooted 62.2332 58.3925 1.06577
hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [swissprot;acc:q9y5r4] Measured 4997 5557.17 1.1121
neuroepithelial cell transforming gene 1; guanine nucleotide regulatory protein (oncogene); rho guanine nucleotide exchange factor (gef) 8. [refseq;acc:nm_005863] Ranked 244.447 233.508 1.04685
786 40s ribosomal protein s9. [swissprot;acc:p46781] Rooted 52.0101 48.813 1.0655
5-aminolevulinic acid synthase, erythroid-specific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-e). [swissprot;acc:p22557] Squared 27407.7 31927.7 1.16492
pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [swissprot;acc:p11498] Measured 9304.83 10347.3 1.11204
rho guanine nucleotide exchange factor 3; rhogef protein; 59.8 kda protein; exchange factor found in platelets and leukemic and neuronal tissues, xpln. [refseq;acc:nm_019555] Ranked 244.447 233.508 1.04685
787 down-regulated in metastasis. [refseq;acc:nm_014503]
uba/ubx 33.3 kda protein. [swissprot;acc:q04323] Rooted 64.5489 68.7769 1.0655
ubiquitin-activating enzyme e1c (uba3 homolog, yeast); ubiquitin-activating enzyme e1c (homologous to yeast uba3). [refseq;acc:nm_003968] Squared 27407.7 31927.7 1.16492
vacuolar proton translocating atpase 116 kda subunit a isoform 2 (v-atpase 116-kda isoform a2) (tj6). [swissprot;acc:q9y487] Measured 5890.49 6547.9 1.11161
788 ero1-like. [refseq;acc:nm_014584] Rooted 64.5489 68.7769 1.0655
hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] Ranked 138.705 132.538 1.04653
ubiquitin-activating enzyme e1 (a1s9 protein). [swissprot;acc:p22314] Squared 27407.7 31927.7 1.16492
vacuolar proton translocating atpase 116 kda subunit a isoform 3 (v- atpase 116-kda isoform a3) (osteoclastic proton pump 116 kda subunit) (oc-116 kda) (oc116) (t-cell immune regulator 1) (t cell immune response cdna7 protein) (tirc7). [swissprot;acc:q13488] Measured 5890.41 6547.81 1.11161
789 40s ribosomal protein sa (p40) (34/67 kda laminin receptor) (colon carcinoma laminin-binding protein) (nem/1chd4) (multidrug resistance- associated protein mgr1-ag). [swissprot;acc:p08865] Ranked 224.244 234.511 1.04578
atpase, h+ transporting, lysosomal v0 subunit a isoform 4; vacuolar proton pump 116 kda accessory subunit; vacuolar proton pump, subunit 2; h(+)-transporting two-sector atpase, noncatalytic accessory protein 1b; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1b; renal tubular acidosis; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 2 (38kd). [refseq;acc:nm_020632] Measured 5890.59 6547.99 1.1116
calcium-binding mitochondrial carrier protein aralar1 (solute carrier family 25, member 12). [swissprot;acc:o75746] Squared 27407.7 31927.7 1.16492
midasin (midas-containing protein). [swissprot;acc:q9nu22] Rooted 54.2779 57.8311 1.06546
790 40s ribosomal protein s21. [swissprot;acc:p35265] Ranked 224.244 234.511 1.04578
melanoma antigen recognized by t cells 2. [refseq;acc:nm_018194] Squared 27407.7 31927.7 1.16492
parafibromin. [refseq;acc:nm_024529] Rooted 53.2852 56.7723 1.06544
vacuolar proton translocating atpase 116 kda subunit a isoform 1 (clathrin-coated vesicle/synaptic vesicle proton pump 116 kda subunit) (vacuolar proton pump subunit 1) (vacuolar adenosine triphosphatase subunit ac116). [swissprot;acc:q93050] Measured 5890.88 6548.28 1.1116
791 5-aminolevulinic acid synthase, nonspecific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-h). [swissprot;acc:p13196] Squared 27407.7 31927.7 1.16492
cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [swissprot;acc:q15642] Rooted 62.5007 58.6648 1.06539
cytoplasmic antiproteinase 3 (cap3) (cap-3) (protease inhibitor 9) (serpin b9). [swissprot;acc:p50453] Ranked 224.244 234.511 1.04578
transducin beta-like 3; wd-repeat protein sazd. [refseq;acc:nm_006453] Measured 4025.3 4474.3 1.11154
792 axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645] 6772.75 7526.2 1.11125
calcium-binding mitochondrial carrier protein aralar2 (solute carrier family 25, member 13) (citrin). [swissprot;acc:q9ujs0] Squared 27407.7 31927.7 1.16492
maspin precursor (protease inhibitor 5). [swissprot;acc:p36952] Ranked 224.244 234.511 1.04578
proteasome subunit alpha type 5 (ec 3.4.25.1) (proteasome zeta chain) (macropain zeta chain) (multicatalytic endopeptidase complex zeta chain). [swissprot;acc:p28066] Rooted 63.8039 67.9633 1.06519
793 acyl carrier protein, mitochondrial precursor (acp) (nadh-ubiquinone oxidoreductase 9.6 kda subunit) (ci-sdap). [swissprot;acc:o14561] Squared 27407.7 31927.7 1.16492
beta-catenin (pro2286). [swissprot;acc:p35222] Rooted 60.2378 64.1631 1.06516
bomapin (protease inhibitor 10) (serpin b10). [swissprot;acc:p48595] Ranked 224.244 234.511 1.04578
putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [swissprot;acc:q9y5n5] Measured 5036.92 5596.36 1.11107
794 dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882] Rooted 57.9449 61.719 1.06513
dna damage binding protein 1 (damage-specific dna binding protein 1) (ddb p127 subunit) (ddba) (uv-damaged dna-binding protein 1) (uv-ddb 1) (xeroderma pigmentosum group e complementing protein) (xpce) (x- associated protein 1) (xap-1). [swissprot;acc:q16531] Squared 29554.6 34419.4 1.1646
dna topoisomerase ii, alpha isozyme (ec 5.99.1.3). [swissprot;acc:p11388] Measured 6441.17 7154.55 1.11075
plasminogen activator inhibitor-2 precursor (pai-2) (placental plasminogen activator inhibitor) (monocyte arg-serpin) (urokinase inhibitor). [swissprot;acc:p05120] Ranked 224.244 234.511 1.04578
795 dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880] Measured 6441.14 7154.13 1.11069
polymerase (rna) iii (dna directed) (62kd). [refseq;acc:nm_006468] Rooted 52.1577 48.9787 1.06491
propionyl-coa carboxylase beta chain, mitochondrial precursor (ec 6.4.1.3) (pccase beta subunit) (propanoyl-coa:carbon dioxide ligase beta subunit). [swissprot;acc:p05166] Squared 29554.6 34419.4 1.1646

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/