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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description Gene Rank Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 301 to 350 of 3228 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
description
Rank
red
green
network_comparison
aquaporin 5. [swissprot;acc:p55064] 2692 188.192 188.048 1.00077
aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181] 2691 188.193
aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [swissprot;acc:p29972] 2694 188.223 188.081 1.00075
arf gtpase-activating protein git1 (g protein-coupled receptor kinase- interactor 1). [swissprot;acc:q9y2x7] 1184 216.729 222.334 1.02586
arf gtpase-activating protein git2 (g protein-coupled receptor kinase- interactor 2). [swissprot;acc:q14161] 1110 216.78 222.782 1.02769
arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069] 947 212.51 205.191 1.03567
arginase 1 (ec 3.5.3.1) (liver-type arginase). [swissprot;acc:p05089] 1885 204.44 206.615 1.01064
arginase ii, mitochondrial precursor (ec 3.5.3.1) (non-hepatic arginase) (kidney-type arginase). [swissprot;acc:p78540] 1886 204.512 206.682 1.01061
arginine-glutamic acid dipeptide (re) repeats; atrophin 1-like; arginine glutamic acid dipeptide re repeats. [refseq;acc:nm_012102] 1379 218.47 213.875 1.02148
arginine/serine-rich splicing factor 10 (transformer-2-beta) (htra2- beta) (transformer 2 protein homolog) (silica-induced protein 41) (ra301). [swissprot;acc:q15815] 1478 215.122 211.066 1.01922
argininosuccinate lyase (ec 4.3.2.1) (arginosuccinase) (asal). [swissprot;acc:p04424] 2108 216.36 217.93 1.00726
argininosuccinate synthase (ec 6.3.4.5) (citrulline--aspartate ligase). [swissprot;acc:p00966] 1546 217.769 221.474 1.01701
arginyl-trna synthetase-like; arginine-trna ligase. [refseq;acc:nm_020320] 2235 200.95 199.711 1.0062
ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [swissprot;acc:o95376] 2798 0.00001 0.00001 1
armet protein precursor (arginine-rich protein). [swissprot;acc:p55145] 1714 206.549 203.844 1.01327
arp2/3 complex 16 kda subunit (p16-arc) (actin-related protein 2/3 complex subunit 5). [swissprot;acc:o15511] 2602 224.875 225.192 1.00141
arp2/3 complex 21 kda subunit (p21-arc) (actin-related protein 2/3 complex subunit 3). [swissprot;acc:o15145] 2632 224.891 225.195 1.00135
arp2/3 complex 34 kda subunit (p34-arc) (actin-related protein 2/3 complex subunit 2). [swissprot;acc:o15144] 2697 225.081 225.232 1.00067
arp2/3 complex 41 kda subunit (p41-arc) (actin-related protein 2/3 complex subunit 1b). [swissprot;acc:o15143] 2629 224.891 225.195 1.00135
arsenical pump-driving atpase (ec 3.6.3.16) (arsenite-translocating atpase) (arsenical resistance atpase) (arsenite-transporting atpase) (arsa) (asna-i). [swissprot;acc:o43681] 2291 200.158 201.213 1.00527
aryl-hydrocarbon interacting protein-like 1. [swissprot;acc:q9nzn9] 1156 224.307 230.242 1.02646
asc-1 complex subunit p100. [refseq;acc:nm_032204] 1374 216.542 211.908 1.02187
asparagine synthetase [glutamine-hydrolyzing] (ec 6.3.5.4) (glutamine- dependent asparagine synthetase) (ts11 cell cycle control protein). [swissprot;acc:p08243] 1057 219.01 212.468 1.03079
asparaginyl-trna synthetase, cytoplasmic (ec 6.1.1.22) (asparagine-- trna ligase) (asnrs). [swissprot;acc:o43776] 2323 192.773 193.691 1.00476
aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468] 658 229.072 216.576 1.0577
aspartyl-trna synthetase (ec 6.1.1.12) (aspartate--trna ligase) (asprs). [swissprot;acc:p14868] 2541 194.505 194.902 1.00204
associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] 126 94 114 1.21277
associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] 128
ataxin 2 related protein isoform a; ataxin-2 domain protein. [refseq;acc:nm_007245] 1058 228.105 221.293 1.03078
ataxin 2-binding protein. [swissprot;acc:q9nwb1] 1704 218.514 215.577 1.01362
ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] 1059 228.105 221.293 1.03078
ataxin-1 ubiquitin-like interacting protein. [refseq;acc:nm_020131] 2041 196.808 195.141 1.00854
atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] 149 142 170 1.19718
atp synthase alpha chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p25705] 1658 217.925 214.826 1.01443
atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539] 241 227.357 254.15 1.11785
atp synthase beta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p06576] 1655 219.062 215.942 1.01445
atp synthase coupling factor 6, mitochondrial precursor (ec 3.6.3.14) (f6). [swissprot;acc:p18859] 2893 0.00001 0.00001 1
atp synthase coupling factor b, mitochondrial precursor. [swissprot;acc:q99766] 2022 208.601 210.464 1.00893
atp synthase delta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p30049] 1687 215.345 212.386 1.01393
atp synthase f chain, mitochondrial (ec 3.6.3.14). [swissprot;acc:p56134] 2644 194.097 194.328 1.00119
atp synthase g chain, mitochondrial (ec 3.6.3.14) (atpase subunit g). [swissprot;acc:o75964] 2834 0.00001 0.00001 1
atp synthase gamma chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p36542] 1563 218.277 214.739 1.01648
atp synthase mitochondrial f1 complex assembly factor 2. [refseq;acc:nm_145691] 456 210.225 226.578 1.07779
atp synthase oligomycin sensitivity conferral protein, mitochondrial precursor (ec 3.6.3.14) (oscp). [swissprot;acc:p48047] 1564 218.277 214.739 1.01648
atp-binding cassette, sub-family c, member 10; multidrug resistance-associated protein 7. [refseq;acc:nm_033450] 2209 199.129 200.413 1.00645
atp-binding cassette, sub-family d, member 3 (70 kda peroxisomal membrane protein) (pmp70). [swissprot;acc:p28288] 2166 215.925 214.481 1.00673
atp-citrate synthase (ec 2.3.3.8) (atp-citrate (pro-s-)-lyase) (citrate cleavage enzyme). [swissprot;acc:p53396] 2689 213.792 213.619 1.00081
atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [swissprot;acc:o76031] 1871 222.819 225.228 1.01081
atp-dependent dna helicase ii, 70 kda subunit (lupus ku autoantigen protein p70) (ku70) (70 kda subunit of ku antigen) (thyroid-lupus autoantigen) (tlaa) (ctc box binding factor 75 kda subunit) (ctcbf) (ctc75). [swissprot;acc:p12956] 2727 221.001 220.927 1.00033
atp-dependent dna helicase ii, 80 kda subunit (lupus ku autoantigen protein p86) (ku86) (ku80) (86 kda subunit of ku antigen) (thyroid- lupus autoantigen) (tlaa) (ctc box binding factor 85 kda subunit) (ctcbf) (ctc85) (nuclear factor iv) (dna-repair protein xrcc5). [swissprot;acc:p13010] 2728

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/