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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Value Type Gene Network Comparison Type description Rank Filtered Interaction Map network_comparison red green
Results: HTML CSV LaTeX Showing element 318 to 367 of 3228 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Interaction Map  : High confidence
description
Rank
network_comparison
red
green
arp2/3 complex 34 kda subunit (p34-arc) (actin-related protein 2/3 complex subunit 2). [swissprot;acc:o15144] 2697 1.00067 225.081 225.232
arp2/3 complex 41 kda subunit (p41-arc) (actin-related protein 2/3 complex subunit 1b). [swissprot;acc:o15143] 2629 1.00135 224.891 225.195
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 1.00527 200.158 201.213
aryl-hydrocarbon interacting protein-like 1. [swissprot;acc:q9nzn9] 1156 1.02646 224.307 230.242
asc-1 complex subunit p100. [refseq;acc:nm_032204] 1374 1.02187 216.542 211.908
asparagine synthetase [glutamine-hydrolyzing] (ec 6.3.5.4) (glutamine- dependent asparagine synthetase) (ts11 cell cycle control protein). [swissprot;acc:p08243] 1057 1.03079 219.01 212.468
asparaginyl-trna synthetase, cytoplasmic (ec 6.1.1.22) (asparagine-- trna ligase) (asnrs). [swissprot;acc:o43776] 2323 1.00476 192.773 193.691
aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468] 658 1.0577 229.072 216.576
aspartyl-trna synthetase (ec 6.1.1.12) (aspartate--trna ligase) (asprs). [swissprot;acc:p14868] 2541 1.00204 194.505 194.902
associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] 126 1.21277 94 114
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 1.03078 228.105 221.293
ataxin 2-binding protein. [swissprot;acc:q9nwb1] 1704 1.01362 218.514 215.577
ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] 1059 1.03078 228.105 221.293
ataxin-1 ubiquitin-like interacting protein. [refseq;acc:nm_020131] 2041 1.00854 196.808 195.141
atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] 149 1.19718 142 170
atp synthase alpha chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p25705] 1658 1.01443 217.925 214.826
atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539] 241 1.11785 227.357 254.15
atp synthase beta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p06576] 1655 1.01445 219.062 215.942
atp synthase coupling factor 6, mitochondrial precursor (ec 3.6.3.14) (f6). [swissprot;acc:p18859] 2893 1 0.00001 0.00001
atp synthase coupling factor b, mitochondrial precursor. [swissprot;acc:q99766] 2022 1.00893 208.601 210.464
atp synthase delta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p30049] 1687 1.01393 215.345 212.386
atp synthase f chain, mitochondrial (ec 3.6.3.14). [swissprot;acc:p56134] 2644 1.00119 194.097 194.328
atp synthase g chain, mitochondrial (ec 3.6.3.14) (atpase subunit g). [swissprot;acc:o75964] 2834 1 0.00001 0.00001
atp synthase gamma chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p36542] 1563 1.01648 218.277 214.739
atp synthase mitochondrial f1 complex assembly factor 2. [refseq;acc:nm_145691] 456 1.07779 210.225 226.578
atp synthase oligomycin sensitivity conferral protein, mitochondrial precursor (ec 3.6.3.14) (oscp). [swissprot;acc:p48047] 1564 1.01648 218.277 214.739
atp-binding cassette, sub-family c, member 10; multidrug resistance-associated protein 7. [refseq;acc:nm_033450] 2209 1.00645 199.129 200.413
atp-binding cassette, sub-family d, member 3 (70 kda peroxisomal membrane protein) (pmp70). [swissprot;acc:p28288] 2166 1.00673 215.925 214.481
atp-citrate synthase (ec 2.3.3.8) (atp-citrate (pro-s-)-lyase) (citrate cleavage enzyme). [swissprot;acc:p53396] 2689 1.00081 213.792 213.619
atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [swissprot;acc:o76031] 1871 1.01081 222.819 225.228
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 1.00033 221.001 220.927
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
atp-dependent dna helicase q5 (recq protein-like 5) (recq5). [swissprot;acc:o94762] 1703 1.01363 216.079 219.024
atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1] 529 1.06856 251.653 235.506
atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7] 328 1.09888 258.437 235.183
atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072] 428 1.0811 253.852 234.808
atp-dependent rna helicase rok1; atp-dependent rna helicase. [refseq;acc:nm_007010] 990 1.03367 243.297 235.373
atpase inhibitor, mitochondrial precursor. [swissprot;acc:q9uii2] 1365 1.02194 228.644 223.736
atpase, h+ transporting, lysosomal 38kda, v0 subunit d isoform 2. [refseq;acc:nm_152565] 1126 1.02742 218.487 212.656
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] 1120 1.02752 218.528 212.676
atrophin-1 (dentatorubral-pallidoluysian atrophy protein). [swissprot;acc:p54259] 1384 1.02148 218.471 213.876
atrophin-1 interacting protein 1; activin receptor interacting protein 1; likely ortholog of mouse activin receptor interacting protein 1; atrophin-1 interacting protein a; membrane associated guanylate kinase 2; activin receptor interacting p. [refseq;acc:nm_012301] 1035 1.03157 221.682 228.68
au rna-binding protein/enoyl-coenzyme a hydratase precursor; au rna-binding protein/enoyl-coenzyme a hydratase; 3-methylglutaconyl-coa hydratase; mga type i. [refseq;acc:nm_001698] 2913 1 0.00001 0.00001
autoantigen ngp-1. [swissprot;acc:q13823] 670 1.05694 250.302 236.817
autophagy protein 12-like (apg12-like). [swissprot;acc:o94817] 1729 1.01304 187.582 190.028
autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0] 1540 1.01721 240.077 236.015
axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645] 2003 1.00923 208.315 206.41
b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [refseq;acc:nm_181844] 1559 1.01655 196.191 192.996
b-cell lymphoma 3-encoded protein (bcl-3 protein). [swissprot;acc:p20749] 2655 1.0011 201.445 201.667

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/