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 4708 to 4757 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1177 phosphatidylinositol 3-kinase regulatory alpha subunit (pi3-kinase p85-alpha subunit) (ptdins-3-kinase p85-alpha) (pi3k). [swissprot;acc:p27986] Rooted 61.2655 64.1634 1.0473
1178 delta-sarcoglycan (sg-delta) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q92629] Ranked 218.186 212.672 1.02593
pepsin a precursor (ec 3.4.23.1). [swissprot;acc:p00790] Measured 4392.63 4776.19 1.08732
putative ankyrin-repeat containing protein. [refseq;acc:nm_025185] Squared 22813.2 25958.3 1.13786
ring finger protein 38. [refseq;acc:nm_022781] Rooted 61.2655 64.1634 1.0473
1179 cellular modulator of immune recognition. [refseq;acc:nm_145021] Ranked 218.186 212.672 1.02593
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] Squared 22813.2 25958.3 1.13786
phosphatidylinositol 3-kinase regulatory gamma subunit (pi3-kinase p85-gamma subunit) (ptdins-3-kinase p85-gamma) (p55pik). [swissprot;acc:q92569] Rooted 61.2655 64.1634 1.0473
solute carrier family 20 (phosphate transporter), member 2; glvr-2; pit-2; gibbon ape leukemia virus receptor 2; murine leukemia virus, amphotropic; receptor. [refseq;acc:nm_006749] Measured 4392.63 4776.19 1.08732
1180 farnesyl pyrophosphate synthetase (fpp synthetase) (fps) (farnesyl diphosphate synthetase) [includes: dimethylallyltransferase (ec 2.5.1.1); geranyltranstransferase (ec 2.5.1.10)]. [swissprot;acc:p14324]
protocadherin fat 2 precursor (hfat2) (multiple epidermal growth factor-like domains 1). [swissprot;acc:q9nyq8] Squared 22813.2 25958.3 1.13786
sterol regulatory element binding protein cleavage-activating protein (srebp cleavage-activating protein) (scap). [swissprot;acc:q12770] Rooted 61.2655 64.1634 1.0473
vacuolar atp synthase 21 kda proteolipid subunit (ec 3.6.3.14) (hatpl). [swissprot;acc:q99437] Ranked 218.186 212.672 1.02593
1181 atp synthase beta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p06576] Rooted 61.2655 64.1634 1.0473
cadherin-related tumor suppressor homolog precursor (fat protein homolog). [swissprot;acc:q14517] Squared 22813.2 25958.3 1.13786
gamma-sarcoglycan (gamma-sg) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q13326] Ranked 218.186 212.672 1.02593
protocadherin 15 precursor. [swissprot;acc:q96qu1] Measured 4392.63 4776.19 1.08732
1182 mln64 n-terminal domain homolog (stard3 n-terminal like protein). [swissprot;acc:o95772] Squared 22813.2 25958.3 1.13786
neurocalcin delta. [swissprot;acc:p29554] Ranked 225.104 230.931 1.02589
phosphatidylinositol 3-kinase regulatory beta subunit (pi3-kinase p85-beta subunit) (ptdins-3-kinase p85-beta). [swissprot;acc:o00459] Rooted 61.2655 64.1634 1.0473
solute carrier family 20 (phosphate transporter), member 1; glvr-1; pit-1; gibbon ape leukemia virus receptor 1. [refseq;acc:nm_005415] Measured 4392.63 4776.19 1.08732
1183 lipocalin-interacting membrane receptor. [refseq;acc:nm_018113]
neuron specific calcium-binding protein hippocalcin (p23k) (calcium- binding protein bdr-2). [swissprot;acc:p32076] Ranked 225.103 230.928 1.02588
prefoldin subunit 5 (c-myc binding protein mm-1) (myc modulator 1). [swissprot;acc:q99471] Squared 20094.7 22861.9 1.13771
ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304] Rooted 70.4902 73.8211 1.04725
1184 arf gtpase-activating protein git1 (g protein-coupled receptor kinase- interactor 1). [swissprot;acc:q9y2x7] Ranked 216.729 222.334 1.02586
cathepsin b precursor (ec 3.4.22.1) (cathepsin b1) (app secretase). [swissprot;acc:p07858] Rooted 64.7687 67.8232 1.04716
prefoldin subunit 6 (protein ke2). [swissprot;acc:o15212] Squared 20094.7 22861.9 1.13771
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

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/