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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Network Comparison Type Gene Value Type description green Rank network_comparison red Filtered Interaction Map
Results: HTML CSV LaTeX Showing element 1027 to 1076 of 3228 in total
Network Comparison Type  : Divided
Value Type  : Ranked
Filtered  : 1
Interaction Map  : High confidence
description
green
Rank
network_comparison
red
ferritin light chain (ferritin l subunit). [swissprot;acc:p02792] 209.118 709 1.05413 220.438
ferrochelatase, mitochondrial precursor (ec 4.99.1.1) (protoheme ferro-lyase) (heme synthetase). [swissprot;acc:p22830] 0.00001 3185 1 0.00001
fetal brain protein 239 (239fb). [swissprot;acc:q15777] 230.294 2339 1.00452 229.258
fibrillarin (34 kda nucleolar scleroderma antigen). [swissprot;acc:p22087] 233.483 748 1.05038 245.246
fibrillin 1 precursor. [swissprot;acc:p35555] 0.00001 2844 1 0.00001
fibrillin 2 precursor. [swissprot;acc:p35556] 2955
fibrillin 3. [refseq;acc:nm_032447] 2939
fibulin-1 precursor. [swissprot;acc:p23142] 191.503 2349 1.00441 192.348
fibulin-2 precursor. [swissprot;acc:p98095] 190.448 2245 1.00614 191.618
ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485] 253 40 1.27273 322
fidgetin-like 1. [refseq;acc:nm_022116] 213.814 2078 1.00794 215.511
filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] 198.444 191 1.14179 226.582
filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [refseq;acc:nm_001457] 186
fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] 119.432 1045 1.03121 115.817
fk506-binding protein 1a (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (12 kda fkbp) (fkbp-12) (immunophilin fkbp12). [swissprot;acc:p20071] 211.908 1375 1.02187 216.542
flap endonuclease-1 (ec 3.-.-.-) (maturation factor 1) (mf1). [swissprot;acc:p39748] 0.00001 2831 1 0.00001
flavoprotein oxidoreductase mical2. [refseq;acc:nm_014632] 208.201 541 1.06703 222.156
flotillin-1. [swissprot;acc:o75955] 213.22 1289 1.02414 218.368
folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932] 231.524 1224 1.02487 225.906
forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] 231.407 196 1.13745 263.215
forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488] 202.139 619 1.05994 214.256
forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] 231.407 197 1.13745 263.215
forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] 231.394 198 1.13741 263.191
formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] 194.72 178 1.1652 226.887
fos-related antigen 1 (fra-1). [swissprot;acc:p15407] 161.068 46 1.27053 204.642
fos-related antigen 2. [swissprot;acc:p15408] 161.046 44 1.2707 204.641
fragile x mental retardation 1 protein (protein fmr-1) (fmrp). [swissprot;acc:q06787] 200.115 1828 1.01147 202.41
fragile x mental retardation syndrome related protein 1. [swissprot;acc:p51114] 200.086 1825 1.0115 202.386
fragile x mental retardation syndrome related protein 2. [swissprot;acc:p51116] 1823
frg1 protein (fshd region gene 1 protein). [swissprot;acc:q14331] 201.514 2745 1.00019 201.476
fructose-1,6-bisphosphatase (ec 3.1.3.11) (d-fructose-1,6-bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:p09467] 210.18 2561 1.00169 209.825
fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] 210.148 2551 1.00182 209.766
fructose-bisphosphate aldolase a (ec 4.1.2.13) (muscle-type aldolase) (lung cancer antigen ny-lu-1). [swissprot;acc:p04075] 0.00001 2907 1 0.00001
fructose-bisphosphate aldolase b (ec 4.1.2.13) (liver-type aldolase). [swissprot;acc:p05062] 2973
fructose-bisphosphate aldolase c (ec 4.1.2.13) (brain-type aldolase). [swissprot;acc:p09972] 3087
ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [refseq;acc:nm_017647] 232.419 726 1.05196 244.495
fumarate hydratase, mitochondrial precursor (ec 4.2.1.2) (fumarase). [swissprot;acc:p07954] 219.708 731 1.05187 208.874
fuse binding protein 3 (fragment). [sptrembl;acc:q92946] 216.944 2668 1.00107 217.176
fuse-binding protein-interacting repressor isoform b; siah binding protein 1; pyrimidine tract binding splicing factor; ro ribonucleoprotein-binding protein 1; poly-u binding splicing factor puf60. [refseq;acc:nm_014281] 200.89 1864 1.01086 203.071
fused toes homolog; likely ortholog of mouse fused toes. [refseq;acc:nm_022476] 222.788 2124 1.00696 221.248
fyve-finger-containing rab5 effector protein rabenosyn-5. [refseq;acc:nm_022340] 0.00001 2998 1 0.00001
fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263] 153.371 848 1.04184 147.211
g protein-coupled receptor 66. [refseq;acc:nm_006056] 0.00001 2815 1 0.00001
g-rich sequence factor-1 (grsf-1). [swissprot;acc:q12849] 215.542 1855 1.0109 217.891
g1 to s phase transition protein 1 homolog (gtp-binding protein gst1-hs). [swissprot;acc:p15170] 215.533 1631 1.01511 218.789
g2/mitotic-specific cyclin b1. [swissprot;acc:p14635] 170.844 1582 1.01634 168.098
g2/mitotic-specific cyclin b2. [swissprot;acc:o95067] 170.769 1580 1.01637 168.018
ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546] 219.017 883 1.03917 227.596
ga binding protein beta-2 chain (gabp-beta-2 subunit) (transcription factor e4tf1-47) (gapbp-2) (nuclear respiratory factor-2 subunit gamma). [swissprot;acc:q06545] 884
gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] 83.0461 48 1.26868 65.4586

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/