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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Rank Gene description Value Type Interaction Map Network Comparison Type Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 551 to 600 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
description
Interaction Map
Network Comparison Type
red
green
network_comparison
138 serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] High confidence Divided 194.372 234.204 1.20493
transgelin 2 (sm22-alpha homolog). [swissprot;acc:p37802] Low confidence 218.36 205.4 1.0631
139 amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410] High confidence 271.752 225.68 1.20415
chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] Subtracted 287.41 256.835 30.575
dnaj homolog subfamily c member 8 (splicing protein spf31) (hspc315). [swissprot;acc:o75937] Low confidence 219.838 207.417 12.421
testican-1 precursor (spock protein). [swissprot;acc:q08629] Divided 220.254 234.111 1.06291
140 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] High confidence Subtracted 228.306 198.011 30.295
c3hc4-type zinc finger protein; likely ortholog of mouse dioxin inducible factor 3. [refseq;acc:nm_024835] Low confidence 219.838 207.417 12.421
ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] High confidence Divided 59 49 1.20408
testican-2 precursor. [swissprot;acc:q92563] Low confidence 220.222 234.047 1.06278
141 cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] High confidence Subtracted 239.991 269.238 29.247
endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase (ec 3.2.1.113) (er alpha-1,2-mannosidase) (mannosidase alpha class 1b member 1) (man9glcnac2-specific processing alpha-mannosidase). [swissprot;acc:q9ukm7] Low confidence 211.056 198.732 12.324
ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] High confidence Divided 59 49 1.20408
rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [swissprot;acc:q14155] Low confidence 219.344 206.52 1.0621
142 endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase (ec 3.2.1.113) (er alpha-1,2-mannosidase) (mannosidase alpha class 1b member 1) (man9glcnac2-specific processing alpha-mannosidase). [swissprot;acc:q9ukm7] 211.056 198.732 1.06201
presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Subtracted 12.324
ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] High confidence Divided 59 49 1.20408
thrombospondin 3 precursor. [swissprot;acc:p49746] Subtracted 239.99 269.234 29.244
143 anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] Divided 59 49 1.20408
f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315] Low confidence Subtracted 211.056 198.732 12.324
presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Divided 1.06201
splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] High confidence Subtracted 240.133 211.382 28.751
144 cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291] 239.35 267.915 28.565
f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315] Low confidence Divided 211.056 198.732 1.06201
kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] High confidence 265.686 319.651 1.20312
presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Low confidence Subtracted 211.056 198.732 12.324
145 likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] High confidence 239.336 267.881 28.545
potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] Divided 265.639 319.546 1.20293
presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Low confidence 211.056 198.732 1.06201
sentrin-specific protease 8 (ec 3.4.22.-) (sentrin/sumo-specific protease senp8) (cysteine protease fksg8). [swissprot;acc:q96ld8] Subtracted 210.579 198.33 12.249
146 kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193] High confidence Divided 265.632 319.531 1.20291
nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181] Low confidence 226.892 213.661 1.06193
smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527] High confidence Subtracted 239.336 267.879 28.543
ubiquitin-like protein nedd8. [swissprot;acc:q15843] Low confidence 210.579 198.33 12.249
147 calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] 222.508 210.345 12.163
lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461] High confidence 239.32 267.842 28.522
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Divided 50.7983 42.3003 1.2009
rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052] Low confidence 219.273 206.507 1.06182
148 calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [swissprot;acc:p17655] Subtracted 222.502 210.342 12.16
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] High confidence 226.582 198.444 28.138
sad1/unc-84 protein-like 1. [swissprot;acc:o94901] Divided 296.677 247.559 1.19841
sentrin-specific protease 8 (ec 3.4.22.-) (sentrin/sumo-specific protease senp8) (cysteine protease fksg8). [swissprot;acc:q96ld8] Low confidence 210.579 198.33 1.06176
149 atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] High confidence 142 170 1.19718
high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339] Low confidence Subtracted 202.996 190.854 12.142
rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] High confidence 226.582 198.444 28.138
ubiquitin-like protein nedd8. [swissprot;acc:q15843] Low confidence Divided 210.579 198.33 1.06176
150 cathepsin l2 precursor (ec 3.4.22.43) (cathepsin v) (cathepsin u). [swissprot;acc:o60911] Subtracted 211.818 199.734 12.084
myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] High confidence Divided 55 46 1.19565
protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] Subtracted 226.582 198.444 28.138
serine/threonine-protein kinase plk (ec 2.7.1.-) (plk-1) (serine- threonine protein kinase 13) (stpk13). [swissprot;acc:p53350] Low confidence Divided 206.516 194.554 1.06148

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/