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 Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 4736 to 4785 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1184 zinc finger protein gli1 (glioma-associated oncogene) (oncogene gli). [swissprot;acc:p08151] Measured 4392.63 4776.19 1.08732
1185 methyltransferase like 2. [refseq;acc:nm_018396] Rooted 100.169 95.6772 1.04695
nuclear factor, interleukin 3 regulated. [refseq;acc:nm_005384] Squared 25045.6 28494.3 1.1377
suppressor of fused. [refseq;acc:nm_016169] Measured 4392.63 4776.19 1.08732
visinin-like protein 3 (vilip-3) (calcium-binding protein bdr-1) (hlp2) (hippocalcin-like protein 1). [swissprot;acc:p37235] Ranked 225.094 230.913 1.02585
1186 adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559] 218.402 212.904 1.02582
cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763] Rooted 100.169 95.6772 1.04695
thymidylate synthase (ec 2.1.1.45) (ts) (tsase). [swissprot;acc:p04818] Squared 19807.6 22534.3 1.13766
zinc finger protein gli3. [swissprot;acc:p10071] Measured 4392.63 4776.19 1.08732
1187 dihydrofolate reductase (ec 1.5.1.3). [swissprot;acc:p00374] Squared 19807.6 22534.3 1.13766
fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263] Rooted 100.169 95.6772 1.04695
limb region 1 protein; limb region 1. [refseq;acc:nm_022458] Measured 4392.63 4776.19 1.08732
vacuolar atp synthase subunit d (ec 3.6.3.14) (v-atpase d subunit) (vacuolar proton pump d subunit) (v-atpase ac39 subunit) (v-atpase 40 kda accessory protein) (p39) (32 kda accessory protein). [swissprot;acc:p12953] Ranked 218.402 212.904 1.02582
1188 adp-ribosylation factor-like protein 4. [swissprot;acc:p40617]
gastricsin precursor (ec 3.4.23.3) (pepsinogen c). [swissprot;acc:p20142] Measured 4392.63 4776.19 1.08732
proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [swissprot;acc:q92824] Rooted 100.169 95.6772 1.04695
stromal cell-derived factor 2 precursor (sdf-2). [swissprot;acc:q99470] Squared 19807.6 22534.3 1.13766
1189 alpha-1-acid glycoprotein 2 precursor (agp 2) (orosomucoid 2) (omd 2). [swissprot;acc:p19652] Ranked 209.649 204.406 1.02565
biotin--protein ligase (ec 6.3.4.-) (biotin apo-protein ligase) [includes: biotin--[methylmalonyl-coa-carboxyltransferase] ligase (ec 6.3.4.9); biotin--[propionyl-coa-carboxylase [atp-hydrolyzing]] ligase (ec 6.3.4.10) (holocarboxylase synthetase) (hcs); biotin--[methylcrotonoyl-coa-carboxylase] ligase (ec 6.3.4.11); biotin--[acetyl-coa-carboxylase] ligase (ec 6.3.4.15)]. [swissprot;acc:p50747] Rooted 61.4258 64.3091 1.04694
stromal cell-derived factor 2-like protein 1 precursor (sdf2 like protein 1) (pwp1-interacting protein 8). [swissprot;acc:q9hcn8] Squared 19807.6 22534.3 1.13766
zinc finger protein gli2 (tax helper protein). [swissprot;acc:p10070] Measured 4392.63 4776.19 1.08732
1190 mitotic spindle assembly checkpoint protein mad2a (mad2-like 1) (hsmad2). [swissprot;acc:q13257] 6599.84 7174.29 1.08704
spectrin beta chain, brain 2 (spectrin, non-erythroid beta chain 2) (beta-iii spectrin). [swissprot;acc:o15020] Squared 21634.8 24608.1 1.13743
ubiquitin. [swissprot;acc:p02248] Ranked 209.6 204.372 1.02558
zinc finger protein zic 1 (zinc finger protein of the cerebellum 1). [swissprot;acc:q15915] Rooted 61.4873 64.3719 1.04691
1191 probable cation-transporting atpase 1 (ec 3.6.1.-). [swissprot;acc:q9nq11] Measured 6599.84 7174.29 1.08704
spectrin beta chain, brain 1 (spectrin, non-erythroid beta chain 1) (beta-ii spectrin) (fodrin beta chain). [swissprot;acc:q01082] Squared 21634.8 24608.1 1.13743
upstream binding protein 1 (lbp-1a). [refseq;acc:nm_014517] Ranked 220.742 215.237 1.02558
zinc finger protein zic 3 (zinc finger protein of the cerebellum 3). [swissprot;acc:o60481] Rooted 61.4869 64.3691 1.04688
1192 5'-methylthioadenosine phosphorylase (ec 2.4.2.28) (mta phosphorylase) (mtapase). [swissprot;acc:q13126] Squared 21639 24612.9 1.13743
tata box binding protein (transcription initiation factor tfiid) (tata-box factor) (tata sequence-binding protein) (tbp). [swissprot;acc:p20226] Measured 6599.84 7174.29 1.08704
transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653] Ranked 220.742 215.237 1.02558
zinc finger protein zic 2 (zinc finger protein of the cerebellum 2). [swissprot;acc:o95409] Rooted 61.4866 64.3673 1.04685
1193 44050 protein. [refseq;acc:nm_178832] 108.34 103.501 1.04675
lbp-9. [refseq;acc:nm_014553] Ranked 220.742 215.237 1.02558
putative eukaryotic translation initiation factor 3 subunit (eif-3) (fragment). [swissprot;acc:o75153] Measured 5464.9 5940.16 1.08697
putative ribosomal rna methyltransferase 1 (ec 2.1.1.-) (rrna (uridine-2'-o-)-methyltransferase) (jm23 protein). [swissprot;acc:q9uet6] Squared 21639 24612.9 1.13743
1194 nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [swissprot;acc:q12972] Rooted 108.34 103.501 1.04675
phosphoacetylglucosamine mutase (ec 5.4.2.3) (pagm) (acetylglucosamine phosphomutase) (n-acetylglucosamine-phosphate mutase) (phosphoglucomutase 3). [swissprot;acc:o95394] Squared 21634.8 24608.1 1.13743
splicing factor, arginine/serine-rich 3 (pre-mrna splicing factor srp20) (x16 protein). [swissprot;acc:p23152] Ranked 220.742 215.237 1.02558
t-complex protein 1, epsilon subunit (tcp-1-epsilon) (cct-epsilon). [swissprot;acc:p48643] Measured 8425.35 7751.57 1.08692
1195 40s ribosomal protein s30. [swissprot;acc:q05472] Squared 28134.5 31984.1 1.13683
camp response element-binding protein cre-bpa. [refseq;acc:nm_004904] Rooted 61.4842 64.3512 1.04663
similar to trna synthetase class ii. [refseq;acc:nm_152268] Measured 5439.56 5911.24 1.08671
skeletal muscle lim-protein 3 (slim 3) (lim-domain protein dral) (four and a half lim domains protein 2) (fhl-2). [swissprot;acc:q14192] Ranked 269.608 276.493 1.02554
1196 kappa b-ras 1. [refseq;acc:nm_020345] Measured 5721.19 6217.2 1.0867
kinesin protein. [refseq;acc:nm_032559] Ranked 224.858 219.264 1.02551
l-myc-1 proto-oncogene protein. [swissprot;acc:p12524] Squared 20812.4 23659.7 1.13681
myb proto-oncogene protein (c-myb). [swissprot;acc:p10242] Rooted 60.0873 62.8865 1.04659
1197 heat shock factor binding protein 1. [swissprot;acc:o75506] 62.6382 65.5533 1.04654

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/