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 Value Type Gene description Interaction Map Network Comparison Type Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 451 to 500 of 14920 in total
Interaction Map  : High confidence
Network Comparison Type  : Divided
Rank
Value Type
description
Filtered
green
red
network_comparison
57 Ranked guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] 1 336.233 266.856 1.25998
hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [swissprot;acc:q16543] 0 11134.8 8152.55 1.36581
Squared acyl-coa dehydrogenase, short/branched chain specific, mitochondrial precursor (ec 1.3.99.-) (sbcad) (2-methyl branched chain acyl-coa dehydrogenase) (2-mebcad) (2-methylbutyryl-coenzyme a dehydrogenase) (2-methylbutyryl-coa dehydrogenase). [swissprot;acc:p45954] 3.43037 0.849445 4.03837
melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] 1 129762 219048 1.68808
Rooted dead-box protein. [refseq;acc:nm_018665] 0 10.8929 16.237 1.4906
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] 1 28.9554 41.6879 1.43973
58 Measured 40s ribosomal protein s26. [swissprot;acc:p02383] 0 81.2233 150.741 1.85588
kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] 1 2664.55 1631.67 1.63302
Ranked dead-box protein. [refseq;acc:nm_018665] 0 14486 10628.3 1.36296
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] 1 336.191 266.863 1.25979
Squared melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] 129762 219048 1.68808
muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] 0 488.851 129.158 3.78491
Rooted potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] 1 28.9696 41.6969 1.43933
ribose-phosphate pyrophosphokinase iii (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase iii) (prs-iii). [swissprot;acc:p21108] 0 7.84538 11.6322 1.48268
59 Measured f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755] 279.24 150.673 1.85328
kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] 1 2664.55 1631.67 1.63302
Ranked glutamate dehydrogenase 2, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p49448] 0 11662.3 15863.6 1.36025
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] 1 336.19 266.863 1.25978
Squared dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743] 0 218.049 57.8417 3.76975
hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] 1 129762 219048 1.68808
Rooted metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832] 0 6.23127 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] 1 52.2064 37.2205 1.40262
60 Measured 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 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] 0 87.5499 47.4756 1.8441
Ranked glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926] 15924 11761 1.35397
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] 1 336.184 266.864 1.25976
Squared inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268] 0 59.1928 219.839 3.71395
melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] 1 129762 219048 1.68808
Rooted selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] 0 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] 1 49.8119 35.6294 1.39806
61 Measured glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712] 0 593.094 324.442 1.82804
glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] 1 2765.82 4489.19 1.6231
Ranked guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] 336.182 266.864 1.25975
testis-specific protein tpx-1 precursor (cysteine-rich secretory protein-2) (crisp-2). [swissprot;acc:p16562] 0 11346.5 15352 1.35302
Squared adp-ribosylation factor 3. [swissprot;acc:p16587] 123.56 33.5285 3.68522
necdin. [swissprot;acc:q99608] 1 129762 219048 1.68808
Rooted kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] 31.7159 43.4291 1.36932
transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [swissprot;acc:p15884] 0 4.58258 6.63325 1.44749
62 Measured dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743] 384.407 210.767 1.82385
glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] 1 2765.82 4489.19 1.6231
Ranked glycine receptor alpha-3 chain precursor. [swissprot;acc:o75311] 0 12695.6 9418.7 1.34791
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] 1 336.181 266.865 1.25974
Squared elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [swissprot;acc:p04720] 0 6.15501 21.2079 3.44563
melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] 1 129762 219048 1.68808
Rooted bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [swissprot;acc:p34820] 0 21.8314 15.0883 1.44691
potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] 1 31.7522 43.4519 1.36847
63 Measured myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] 2765.82 4489.19 1.6231
spir-2 protein (fragment). [sptrembl;acc:q8wwl2] 0 56.278 31.1429 1.80709
Ranked guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] 1 336.178 266.865 1.25973
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] 0 11453 8519.83 1.34428

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/