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 [...,...].
Rank Gene description Network Comparison Type Value Type Interaction Map red Filtered network_comparison green
Results: HTML CSV LaTeX Showing element 551 to 600 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
description
Network Comparison Type
Interaction Map
red
network_comparison
green
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] Divided High confidence 194.372 1.20493 234.204
transgelin 2 (sm22-alpha homolog). [swissprot;acc:p37802] Low confidence 218.36 1.0631 205.4
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 1.20415 225.68
chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] Subtracted 287.41 30.575 256.835
dnaj homolog subfamily c member 8 (splicing protein spf31) (hspc315). [swissprot;acc:o75937] Low confidence 219.838 12.421 207.417
testican-1 precursor (spock protein). [swissprot;acc:q08629] Divided 220.254 1.06291 234.111
140 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] Subtracted High confidence 228.306 30.295 198.011
c3hc4-type zinc finger protein; likely ortholog of mouse dioxin inducible factor 3. [refseq;acc:nm_024835] Low confidence 219.838 12.421 207.417
ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] Divided High confidence 59 1.20408 49
testican-2 precursor. [swissprot;acc:q92563] Low confidence 220.222 1.06278 234.047
141 cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] Subtracted High confidence 239.991 29.247 269.238
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 12.324 198.732
ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] Divided High confidence 59 1.20408 49
rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [swissprot;acc:q14155] Low confidence 219.344 1.0621 206.52
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 1.06201 198.732
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] Divided High confidence 59 1.20408 49
thrombospondin 3 precursor. [swissprot;acc:p49746] Subtracted 239.99 29.244 269.234
143 anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] Divided 59 1.20408 49
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] Subtracted Low confidence 211.056 12.324 198.732
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] Subtracted High confidence 240.133 28.751 211.382
144 cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291] 239.35 28.565 267.915
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] Divided Low confidence 211.056 1.06201 198.732
kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] High confidence 265.686 1.20312 319.651
presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Subtracted Low confidence 211.056 12.324 198.732
145 likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] High confidence 239.336 28.545 267.881
potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] Divided 265.639 1.20293 319.546
presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Low confidence 211.056 1.06201 198.732
sentrin-specific protease 8 (ec 3.4.22.-) (sentrin/sumo-specific protease senp8) (cysteine protease fksg8). [swissprot;acc:q96ld8] Subtracted 210.579 12.249 198.33
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] Divided High confidence 265.632 1.20291 319.531
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 1.06193 213.661
smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527] Subtracted High confidence 239.336 28.543 267.879
ubiquitin-like protein nedd8. [swissprot;acc:q15843] Low confidence 210.579 12.249 198.33
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 12.163 210.345
lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461] High confidence 239.32 28.522 267.842
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Divided 50.7983 1.2009 42.3003
rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052] Low confidence 219.273 1.06182 206.507
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 12.16 210.342
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 28.138 198.444
sad1/unc-84 protein-like 1. [swissprot;acc:o94901] Divided 296.677 1.19841 247.559
sentrin-specific protease 8 (ec 3.4.22.-) (sentrin/sumo-specific protease senp8) (cysteine protease fksg8). [swissprot;acc:q96ld8] Low confidence 210.579 1.06176 198.33
149 atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] High confidence 142 1.19718 170
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] Subtracted Low confidence 202.996 12.142 190.854
rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] High confidence 226.582 28.138 198.444
ubiquitin-like protein nedd8. [swissprot;acc:q15843] Divided Low confidence 210.579 1.06176 198.33
150 cathepsin l2 precursor (ec 3.4.22.43) (cathepsin v) (cathepsin u). [swissprot;acc:o60911] Subtracted 211.818 12.084 199.734
myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] Divided High confidence 55 1.19565 46
protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] Subtracted 226.582 28.138 198.444
serine/threonine-protein kinase plk (ec 2.7.1.-) (plk-1) (serine- threonine protein kinase 13) (stpk13). [swissprot;acc:p53350] Divided Low confidence 206.516 1.06148 194.554

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/