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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Gene Rank description Value Type Network Comparison Type Interaction Map green Filtered red network_comparison
Results: HTML CSV LaTeX Showing element 451 to 500 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Value Type
green
Filtered
red
network_comparison
57 dead-box protein. [refseq;acc:nm_018665] Rooted 10.8929 0 16.237 1.4906
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] Ranked 336.233 1 266.856 1.25998
hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [swissprot;acc:q16543] 11134.8 0 8152.55 1.36581
kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] Measured 2664.55 1 1631.67 1.63302
melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] Squared 129762 219048 1.68808
potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980] Rooted 28.9554 41.6879 1.43973
58 40s ribosomal protein s26. [swissprot;acc:p02383] Measured 81.2233 0 150.741 1.85588
dead-box protein. [refseq;acc:nm_018665] Ranked 14486 10628.3 1.36296
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] 336.191 1 266.863 1.25979
kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] Measured 2664.55 1631.67 1.63302
melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] Squared 129762 219048 1.68808
muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] 488.851 0 129.158 3.78491
potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] Rooted 28.9696 1 41.6969 1.43933
ribose-phosphate pyrophosphokinase iii (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase iii) (prs-iii). [swissprot;acc:p21108] 7.84538 0 11.6322 1.48268
59 dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743] Squared 218.049 57.8417 3.76975
f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755] Measured 279.24 150.673 1.85328
glutamate dehydrogenase 2, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p49448] Ranked 11662.3 15863.6 1.36025
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] 336.19 1 266.863 1.25978
hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Squared 129762 219048 1.68808
kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] Measured 2664.55 1631.67 1.63302
metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832] Rooted 6.23127 0 4.28588 1.45391
nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09] 52.2064 1 37.2205 1.40262
60 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] Measured 2765.82 4489.19 1.6231
adapter-related protein complex 1 sigma 1b subunit (sigma-adaptin 1b) (adaptor protein complex ap-1 sigma-1b subunit) (golgi adaptor ha1/ap1 adaptin sigma-1b subunit) (clathrin assembly protein complex 1 sigma- 1b small chain) (sigma 1b subunit of ap-1 clathrin) (dc22). [swissprot;acc:p56377] 87.5499 0 47.4756 1.8441
glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926] Ranked 15924 11761 1.35397
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] 336.184 1 266.864 1.25976
inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268] Squared 59.1928 0 219.839 3.71395
melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] 129762 1 219048 1.68808
selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] Rooted 12.2882 0 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 1 35.6294 1.39806
61 adp-ribosylation factor 3. [swissprot;acc:p16587] Squared 123.56 0 33.5285 3.68522
glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712] Measured 593.094 324.442 1.82804
glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] 2765.82 1 4489.19 1.6231
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] Ranked 336.182 266.864 1.25975
kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] Rooted 31.7159 43.4291 1.36932
necdin. [swissprot;acc:q99608] Squared 129762 219048 1.68808
testis-specific protein tpx-1 precursor (cysteine-rich secretory protein-2) (crisp-2). [swissprot;acc:p16562] Ranked 11346.5 0 15352 1.35302
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 bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [swissprot;acc:p34820] 21.8314 15.0883 1.44691
dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743] Measured 384.407 210.767 1.82385
elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [swissprot;acc:p04720] Squared 6.15501 21.2079 3.44563
glycine receptor alpha-3 chain precursor. [swissprot;acc:o75311] Ranked 12695.6 9418.7 1.34791
glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] Measured 2765.82 1 4489.19 1.6231
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] Ranked 336.181 266.865 1.25974
melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Squared 129762 219048 1.68808
potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] Rooted 31.7522 43.4519 1.36847
63 dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] 12.6095 0 18.1049 1.43581
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] Ranked 336.178 1 266.865 1.25973
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 31.7576 43.4554 1.36835
melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Squared 129762 219048 1.68808

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/