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 [...,...].
Value Type Gene description Rank Interaction Map Network Comparison Type Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1032 to 1081 of 3228 in total
Value Type  : Ranked
Interaction Map  : High confidence
Network Comparison Type  : Divided
Filtered  : 1
description
Rank
red
green
network_comparison
fibrillin 2 precursor. [swissprot;acc:p35556] 2955 0.00001 0.00001 1
fibrillin 3. [refseq;acc:nm_032447] 2939
fibulin-1 precursor. [swissprot;acc:p23142] 2349 192.348 191.503 1.00441
fibulin-2 precursor. [swissprot;acc:p98095] 2245 191.618 190.448 1.00614
ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485] 40 322 253 1.27273
fidgetin-like 1. [refseq;acc:nm_022116] 2078 215.511 213.814 1.00794
filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] 191 226.582 198.444 1.14179
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] 1045 115.817 119.432 1.03121
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] 1375 216.542 211.908 1.02187
flap endonuclease-1 (ec 3.-.-.-) (maturation factor 1) (mf1). [swissprot;acc:p39748] 2831 0.00001 0.00001 1
flavoprotein oxidoreductase mical2. [refseq;acc:nm_014632] 541 222.156 208.201 1.06703
flotillin-1. [swissprot;acc:o75955] 1289 218.368 213.22 1.02414
folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932] 1224 225.906 231.524 1.02487
forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] 196 263.215 231.407 1.13745
forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488] 619 214.256 202.139 1.05994
forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] 197 263.215 231.407 1.13745
forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] 198 263.191 231.394 1.13741
formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] 178 226.887 194.72 1.1652
fos-related antigen 1 (fra-1). [swissprot;acc:p15407] 46 204.642 161.068 1.27053
fos-related antigen 2. [swissprot;acc:p15408] 44 204.641 161.046 1.2707
fragile x mental retardation 1 protein (protein fmr-1) (fmrp). [swissprot;acc:q06787] 1828 202.41 200.115 1.01147
fragile x mental retardation syndrome related protein 1. [swissprot;acc:p51114] 1825 202.386 200.086 1.0115
fragile x mental retardation syndrome related protein 2. [swissprot;acc:p51116] 1823
frg1 protein (fshd region gene 1 protein). [swissprot;acc:q14331] 2745 201.476 201.514 1.00019
fructose-1,6-bisphosphatase (ec 3.1.3.11) (d-fructose-1,6-bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:p09467] 2561 209.825 210.18 1.00169
fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] 2551 209.766 210.148 1.00182
fructose-bisphosphate aldolase a (ec 4.1.2.13) (muscle-type aldolase) (lung cancer antigen ny-lu-1). [swissprot;acc:p04075] 2907 0.00001 0.00001 1
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] 726 244.495 232.419 1.05196
fumarate hydratase, mitochondrial precursor (ec 4.2.1.2) (fumarase). [swissprot;acc:p07954] 731 208.874 219.708 1.05187
fuse binding protein 3 (fragment). [sptrembl;acc:q92946] 2668 217.176 216.944 1.00107
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] 1864 203.071 200.89 1.01086
fused toes homolog; likely ortholog of mouse fused toes. [refseq;acc:nm_022476] 2124 221.248 222.788 1.00696
fyve-finger-containing rab5 effector protein rabenosyn-5. [refseq;acc:nm_022340] 2998 0.00001 0.00001 1
fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263] 848 147.211 153.371 1.04184
g protein-coupled receptor 66. [refseq;acc:nm_006056] 2815 0.00001 0.00001 1
g-rich sequence factor-1 (grsf-1). [swissprot;acc:q12849] 1855 217.891 215.542 1.0109
g1 to s phase transition protein 1 homolog (gtp-binding protein gst1-hs). [swissprot;acc:p15170] 1631 218.789 215.533 1.01511
g2/mitotic-specific cyclin b1. [swissprot;acc:p14635] 1582 168.098 170.844 1.01634
g2/mitotic-specific cyclin b2. [swissprot;acc:o95067] 1580 168.018 170.769 1.01637
ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546] 883 227.596 219.017 1.03917
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] 48 65.4586 83.0461 1.26868
gaba-a receptor-associated protein. [sptrembl;acc:q9by60] 168 82.5916 98.0548 1.18722
galactose-1-phosphate uridylyltransferase (ec 2.7.7.12) (gal-1-p uridylyltransferase) (udp-glucose--hexose-1-phosphate uridylyltransferase). [swissprot;acc:p07902] 1337 215.162 210.412 1.02257
galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470] 2158 206.401 207.796 1.00676
galectin-9 (hom-hd-21) (ecalectin). [swissprot;acc:o00182] 2122 206.473 207.911 1.00696
gamma adducin (adducin-like protein 70). [swissprot;acc:q9uey8] 1934 224.264 222.055 1.00995

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/