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 Rank Gene description Interaction Map Network Comparison Type Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 551 to 600 of 29840 in total
Value Type  : Measured
Interaction Map  : High confidence
Rank
description
Network Comparison Type
Filtered
red
green
network_comparison
138 tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [swissprot;acc:q13625] Subtracted 1 15182.5 13277.9 1904.6
ubiquitin-conjugating enzyme e2-17 kda 3 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 3). [swissprot;acc:p47986] Divided 0 204.382 154.804 1.32026
139 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] 736.737 561.038 1.31317
cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493] Subtracted 1 12780.7 10876.4 1904.3
peroxisomal 3,2-trans-enoyl-coa isomerase (ec 5.3.3.8) (dodecenoyl-coa delta-isomerase) (d3,d2-enoyl-coa isomerase) (dbi-related protein 1) (drs-1) (hepatocellular carcinoma-associated antigen 88). [swissprot;acc:o75521] 0 3161.12 2924.8 236.32
potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] Divided 1 2759.61 2099.49 1.31442
140 homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] Subtracted 2597.5 698.5 1899
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 2760.28 2100.27 1.31425
tigger transposable element derived 6. [refseq;acc:nm_030953] Subtracted 0 202.374 438.605 236.231
vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [swissprot;acc:o95670] Divided 934.726 1222.89 1.30829
141 ccr4-not transcription complex, subunit 7 (ccr4-associated factor 1) (caf1) (btg1 binding factor 1). [swissprot;acc:q9uiv1] 1161.88 891.114 1.30385
hbs1-like. [refseq;acc:nm_006620] Subtracted 1 2597.5 698.5 1899
small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] Divided 4405.4 5782.08 1.3125
tigger transposable element derived 7; jerky (mouse) homolog-like. [refseq;acc:nm_033208] Subtracted 0 202.163 438.035 235.872
142 metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] Divided 1 9276.47 7090.37 1.30832
presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7] 0 874 1139 1.3032
tigger transposable element derived 1; jerky (mouse) homolog-like. [refseq;acc:nm_145702] Subtracted 202.156 438.016 235.86
transcription factor jun-d. [swissprot;acc:p17535] 1 5638.2 7523.39 1885.19
143 40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880] 0 1499.4 1735.23 235.83
beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] Divided 1 9275.1 7089.65 1.30826
cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240] Subtracted 15427.2 13572.8 1854.4
putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] Divided 0 187 144 1.29861
144 integrin beta-3 precursor (platelet membrane glycoprotein iiia) (gpiiia) (cd61 antigen). [swissprot;acc:p05106] Subtracted 1612.86 1843.92 231.06
nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] 1 4133.47 5945.32 1811.85
sad1/unc-84 protein-like 1. [swissprot;acc:o94901] Divided 3349.9 4362.61 1.30231
uridine kinase-like 1. [swissprot;acc:q9nwz5] 0 633.433 821.711 1.29723
145 likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033] 287.903 372.961 1.29544
nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] Subtracted 1 4136.36 5943.56 1807.2
rna-binding protein nova-1 (neuro-oncological ventral antigen 1) (onconeural ventral antigen-1) (paraneoplastic ri antigen) (ventral neuron-specific protein 1). [swissprot;acc:p51513] 0 2162.33 1932 230.33
ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] Divided 1 16771.5 12889.1 1.30122
146 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] 11068 8508.5 1.30082
cop9 signalosome complex subunit 1 (g protein pathway suppressor 1) (gps1 protein) (mfh protein). [swissprot;acc:q13098] Subtracted 0 17356 17126 230
cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2] Divided 291.639 377.574 1.29466
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] Subtracted 1 2671 871 1800
147 cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6] Divided 0 292.152 378.206 1.29455
nanos (fragment). [sptrembl;acc:q8wy41] Subtracted 377 151 226
protein x 0004. [refseq;acc:nm_016301] 1 2671 871 1800
putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] Divided 11068 8508.5 1.30082
148 associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463]
cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187] 0 293.178 379.474 1.29435
pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322] Subtracted 1249.24 1023.76 225.48
symplekin. [swissprot;acc:q92797] 1 15213.4 13418.1 1795.3
149 cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329] Divided 0 293.178 379.474 1.29435
neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] 1 11068 8508.5 1.30082
polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393] Subtracted 0 323.79 544.991 221.201
trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648] 1 11736.6 13531.9 1795.3
150 metaxin 1. [swissprot;acc:q13505] Divided 0 933.395 723.368 1.29035
pnas-18. [sptrembl;acc:q9bzu3] Subtracted 2256.05 2035.28 220.77
protein hspc134 (protein cda04). [swissprot;acc:q9by43] Divided 1 11068 8508.5 1.30082
small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Subtracted 4172.91 5954.48 1781.57

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/