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 description Value Type Gene Network Comparison Type Interaction Map green red network_comparison Filtered
Results: HTML CSV LaTeX Showing element 951 to 1000 of 38536 in total
Network Comparison Type  : Divided
Rank
description
Value Type
Interaction Map
green
red
network_comparison
Filtered
60 fos39347_1. [sptrembl;acc:o75863] Squared Low confidence 5.11062 21.3143 4.17059 0
glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926] Ranked High confidence 15924 11761 1.35397
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] 336.184 266.864 1.25976 1
homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Measured Low confidence 17572.7 15464.1 1.13635
inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268] Squared High confidence 59.1928 219.839 3.71395 0
melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] 129762 219048 1.68808 1
nadph oxidase homolog 1 (nox-1) (noh-1) (nadh/nadph mitogenic oxidase subunit p65-mox) (mitogenic oxidase 1) (mox1). [swissprot;acc:q9y5s8] Measured Low confidence 315.567 147.143 2.14463 0
selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] Rooted High confidence 12.2882 8.48528 1.44818
son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583] 49.8119 35.6294 1.39806 1
zona pellucida sperm-binding protein 3 precursor (zona pellucida glycoprotein zp3) (zona pellucida protein c) (sperm receptor) (zp3a/zp3b). [swissprot;acc:p21754] Low confidence 10.4861 15.3893 1.46759 0
61 adp-ribosylation factor 3. [swissprot;acc:p16587] Squared High confidence 123.56 33.5285 3.68522
b24o18.3 (pom121 membrane glycoprotein (rat homolog)-like 2). [sptrembl;acc:q96kw2] Rooted Low confidence 10.5233 15.4026 1.46367
cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] Squared 71796.4 92920.4 1.29422 1
glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712] Measured High confidence 593.094 324.442 1.82804 0
glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] 2765.82 4489.19 1.6231 1
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] Ranked 336.182 266.864 1.25975
homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] Measured Low confidence 17572.7 15464.1 1.13635
kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] Rooted High confidence 31.7159 43.4291 1.36932
laminin beta-1 chain precursor (laminin b1 chain). [swissprot;acc:p07942] Squared Low confidence 5.58446 23.0581 4.12898 0
necdin. [swissprot;acc:q99608] High confidence 129762 219048 1.68808 1
protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Ranked Low confidence 182.974 202.792 1.10831
protein kinase, lysine deficient 3. [refseq;acc:nm_020922] 10324.5 13320.5 1.29018 0
selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] Measured 151 72 2.09722
set and mynd domain containing 2; hskm-b protein; zinc finger, mynd domain containing 14. [refseq;acc:nm_020197] Rooted 66.0541 59.2532 1.11478 1
testis-specific protein tpx-1 precursor (cysteine-rich secretory protein-2) (crisp-2). [swissprot;acc:p16562] Ranked High confidence 11346.5 15352 1.35302 0
transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [swissprot;acc:p15884] Rooted 4.58258 6.63325 1.44749
62 anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801] Measured Low confidence 4356 2082 2.09222
ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] Ranked 6438 5029 1.28017
bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [swissprot;acc:p34820] Rooted High confidence 21.8314 15.0883 1.44691
cytohesin 4. [swissprot;acc:q9uia0] Squared Low confidence 71400.2 92262.9 1.29219 1
dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743] Measured High confidence 384.407 210.767 1.82385 0
dj254p11.1 (novel protein similar to rna polymerase ii elongation factor siii, subunit p15). [sptrembl;acc:q9h575] Squared Low confidence 5.15101 21.2387 4.12321
elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [swissprot;acc:p04720] High confidence 6.15501 21.2079 3.44563
fos-related antigen 1 (fra-1). [swissprot;acc:p15407] Ranked Low confidence 183.017 202.79 1.10804 1
glycine receptor alpha-3 chain precursor. [swissprot;acc:o75311] High confidence 12695.6 9418.7 1.34791 0
glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] Measured 2765.82 4489.19 1.6231 1
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] Ranked 336.181 266.865 1.25974
homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] Measured Low confidence 17572.7 15464.1 1.13635
melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Squared High confidence 129762 219048 1.68808
metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832] Rooted Low confidence 6.23127 4.28588 1.45391 0
potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] High confidence 31.7522 43.4519 1.36847 1
set and mynd domain containing protein 1. [sptrembl;acc:q8nb12] Low confidence 66.0541 59.2532 1.11478
63 60s ribosomal protein l37a. [swissprot;acc:p12751] Ranked 15783.5 12374.3 1.27551 0
core1 udp-galactose:n-acetylgalactosamine-alpha-r beta 1,3-galac. [refseq;acc:nm_020156] Squared 57498.7 73677.6 1.28138 1
dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Rooted High confidence 12.6095 18.1049 1.43581 0
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] Ranked 336.178 266.865 1.25973 1
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Measured Low confidence 17572.7 15464.1 1.13635
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] Rooted High confidence 31.7576 43.4554 1.36835
laminin beta-1 chain precursor (laminin b1 chain). [swissprot;acc:p07942] Measured Low confidence 75.6508 154.208 2.03842 0
melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Squared High confidence 129762 219048 1.68808 1

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/