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 25676 to 25725 of 29840 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
2708 j domain protein c21orf55. [swissprot;acc:q9nx36] Measured Divided 8979.78 9012.42 1.00363
porphobilinogen deaminase (ec 4.3.1.8) (hydroxymethylbilane synthase) (hmbs) (pre-uroporphyrinogen synthase) (pbg-d). [swissprot;acc:p08397] Ranked 227.796 227.66 1.0006
succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521] Subtracted 188.435 188.31 0.125
tfiih basal transcription factor complex helicase subunit (ec 3.6.1.-) (dna-repair protein complementing xp-d cells) (xeroderma pigmentosum group d complementing protein) (cxpd) (dna excision repair protein ercc-2). [swissprot;acc:p18074] Rooted Divided 72.1471 72.3052 1.00219
zinc finger protein 444; endothelial zinc finger protein 2. [refseq;acc:nm_018337] Subtracted 44.6114 44.4835 0.1279
2709 atrophin-1 interacting protein 1; activin receptor interacting protein 1; likely ortholog of mouse activin receptor interacting protein 1; atrophin-1 interacting protein a; membrane associated guanylate kinase 2; activin receptor interacting p. [refseq;acc:nm_012301] Divided 59.5057 59.62 1.00192
Subtracted 0.1143
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] Squared 2557.92 2299.4 258.52
importin 7; ran-binding protein 7. [refseq;acc:nm_006391] Ranked Divided 220.521 220.395 1.00057
palmitoyl-protein thioesterase 1 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 1). [swissprot;acc:p50897] Measured Subtracted 5603.24 5583.64 19.6
similar to trna synthetase class ii. [refseq;acc:nm_152268] Ranked 220.224 220.348 0.124
testis-specific protein tex28. [swissprot;acc:o15482] Measured Divided 5603.24 5583.64 1.00351
ubiquitin-conjugating enzyme e2 g2 (ec 6.3.2.19) (ubiquitin-protein ligase g2) (ubiquitin carrier protein g2). [swissprot;acc:p56554] Squared 27920.7 28336.5 1.01489
2710 38 kda fk-506 binding protein homolog (fkbpr38) (fk506-binding protein 8). [swissprot;acc:q14318]
beta-soluble nsf attachment protein (snap-beta) (n-ethylmaleimide- sensitive factor attachment protein, beta). [swissprot;acc:q9h115] Measured Subtracted 5603.24 5583.64 19.6
dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0] Rooted Divided 55.7482 55.846 1.00175
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] Squared Subtracted 2558.19 2299.7 258.49
importin 8; ran-binding protein 8. [refseq;acc:nm_006390] Ranked Divided 220.521 220.395 1.00057
protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [swissprot;acc:p23467] Subtracted 188.435 188.311 0.124
similar to nuclear protein e3-3 orf1. [sptrembl;acc:q9bu61] Measured Divided 5603.24 5583.64 1.00351
sorting nexin 1. [swissprot;acc:q13596] Rooted Subtracted 64.0665 63.9543 0.1122
2711 brefeldin a-inhibited guanine nucleotide-exchange protein 2 (brefeldin a-inhibited gep 2). [swissprot;acc:q9y6d5] Ranked Divided 220.521 220.395 1.00057
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] Squared Subtracted 2559.56 2301.28 258.28
n-acetyllactosaminide beta-1,3-n-acetylglucosaminyltransferase (ec 2.4.1.149) (poly-n-acetyllactosamine extension enzyme) (i-beta- 1,3-n-acetylglucosaminyltransferase) (ignt) (udp-glcnac:betagal beta- 1,3-n-acetylglucosaminyltransferase 6). [swissprot;acc:o43505] Measured Divided 5332.98 5351.72 1.00351
pyruvate dehydrogenase e1 component alpha subunit, somatic form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type i). [swissprot;acc:p08559] Rooted Subtracted 67.6485 67.7581 0.1096
rna, u transporter 1; snurportin-1. [refseq;acc:nm_005701] Squared Divided 40468.1 39911.9 1.01394
sorting nexin 1. [swissprot;acc:q13596] Rooted 64.0665 63.9543 1.00175
syntaxin 16 (syn16). [swissprot;acc:o14662] Measured Subtracted 5603.24 5583.64 19.6
thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7] Ranked 188.435 188.311 0.124
2712 27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [swissprot;acc:o14653] Measured 5603.24 5583.64 19.6
a kindred of iglon. [refseq;acc:nm_173808] Divided 1.00351
fragile x mental retardation 1 protein (protein fmr-1) (fmrp). [swissprot;acc:q06787] Squared 36808.5 36316 1.01356
gk001 protein. [refseq;acc:nm_020198] Ranked Subtracted 188.435 188.311 0.124
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] Squared 2560.11 2301.92 258.19
hsgcn1 (fragment). [sptrembl;acc:q99736] Ranked Divided 220.521 220.395 1.00057
pyruvate dehydrogenase e1 component alpha subunit, somatic form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type i). [swissprot;acc:p08559] Rooted 67.6485 67.7581 1.00162
pyruvate dehydrogenase e1 component alpha subunit, testis-specific form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type ii). [swissprot;acc:p29803] Subtracted 67.6363 67.7446 0.1083
2713 ankyrin-repeat family a protein 2 (rfxank-like 2). [swissprot;acc:q9h9e1] Measured Divided 5603.24 5583.64 1.00351
brefeldin a-inhibited guanine nucleotide-exchange protein 1 (brefeldin a-inhibited gep 1) (p200 arf-gep1) (p200 arf guanine nucleotide exchange factor). [swissprot;acc:q9y6d6] Ranked 220.521 220.395 1.00057
calsyntenin-2 precursor. [swissprot;acc:q9h4d0] Subtracted 188.457 188.334 0.123
dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0] Rooted 55.7482 55.846 0.0978
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] Squared 2560.39 2302.24 258.15
nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] Divided 36802.9 36313.4 1.01348
pyruvate dehydrogenase e1 component alpha subunit, testis-specific form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type ii). [swissprot;acc:p29803] Rooted 67.6363 67.7446 1.0016
syntaxin 1a (neuron-specific antigen hpc-1). [swissprot;acc:q16623] Measured Subtracted 5603.24 5583.64 19.6
2714 alpha-soluble nsf attachment protein (snap-alpha) (n-ethylmaleimide- sensitive factor attachment protein, alpha). [swissprot;acc:p54920]
calsyntenin-3 precursor. [swissprot;acc:q9bqt9] Ranked 188.459 188.336 0.123
dna polymerase epsilon p17 subunit (dna polymerase epsilon subunit 3) (chromatin accessibility complex 17) (huchrac17) (chrac-17). [swissprot;acc:q9nrf9] Rooted Divided 48.4125 48.4851 1.0015
fragile x mental retardation syndrome related protein 2. [swissprot;acc:p51116] Squared 36800.7 36312.3 1.01345
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] Subtracted 2561.25 2303.22 258.03

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/