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 12814 to 12863 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
2702 protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [swissprot;acc:p23467] Ranked 188.435 188.311 1.00066
ral-a exchange factor ralgps2. [refseq;acc:nm_152663] Squared 31182.7 31851.7 1.02145
zinc finger protein 444; endothelial zinc finger protein 2. [refseq;acc:nm_018337] Rooted 44.6114 44.4835 1.00288
2703 creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [swissprot;acc:p12532] Measured 8972.87 9007.71 1.00388
integral membrane protein cii-3b. [sptrembl;acc:o75609] Rooted 65.6868 65.5154 1.00262
stip1 homology and u-box containing protein 1; serologically defined colon cancer antigen 7; carboxy terminus of hsp70p-interacting protein; heat shock protein a binding protein 2 (c-terminal). [refseq;acc:nm_005861] Squared 31182.7 31851.7 1.02145
thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7] Ranked 188.435 188.311 1.00066
2704 creatine kinase, m chain (ec 2.7.3.2) (m-ck). [swissprot;acc:p06732] Measured 8980.12 9013.33 1.0037
gk001 protein. [refseq;acc:nm_020198] Ranked 188.435 188.311 1.00066
proteasome subunit beta type 1 (ec 3.4.25.1) (proteasome component c5) (macropain subunit c5) (multicatalytic endopeptidase complex subunit c5) (proteasome gamma chain). [swissprot;acc:p20618] Squared 34346.5 34937.9 1.01722
succinate dehydrogenase cytochrome b560 subunit, mitochondrial precursor (integral membrane protein cii-3) (qps1) (qps-1) (succinate dehydrogenase complex subunit c) (succinate-ubiquinone oxidoreductase cytochrome b large subunit) (cybl). [swissprot;acc:q99643] Rooted 65.6874 65.5164 1.00261
2705 arf gtpase-activating protein git2 (g protein-coupled receptor kinase- interactor 2). [swissprot;acc:q14161] 62.4411 62.5908 1.0024
calsyntenin-2 precursor. [swissprot;acc:q9h4d0] Ranked 188.457 188.334 1.00065
protein cgi-27 (c21orf19-like protein). [swissprot;acc:q9y316] Measured 4137.61 4152.72 1.00365
sqv-7-like protein (fragment). [sptrembl;acc:o95454] Squared 22233.9 21876.3 1.01635
2706 calsyntenin-3 precursor. [swissprot;acc:q9bqt9] Ranked 188.459 188.336 1.00065
nucleoporin like 1. [refseq;acc:nm_014089] Squared 30868.3 31361.7 1.01598
peptidyl prolyl isomerase h; cyclophilin h. [refseq;acc:nm_006347] Measured 8979.61 9012.31 1.00364
succinate dehydrogenase [ubiquinone] iron-sulfur protein, mitochondrial precursor (ec 1.3.5.1) (ip) (iron-sulfur subunit of complex ii). [swissprot;acc:p21912] Rooted 65.5744 65.4175 1.0024
2707 prp18 pre-mrna processing factor 18 homolog. [refseq;acc:nm_003675] Measured 8979.61 9012.31 1.00364
red cell acid phosphatase 1, isozyme f (ec 3.1.3.2) (acp1) (low molecular weight phosphotyrosine protein phosphatase) (ec 3.1.3.48) (adipocyte acid phosphatase, isozyme alpha). [swissprot;acc:p24666] Ranked 215.096 215.232 1.00063
rho guanine nucleotide exchange factor 4 isoform a; apc-stimulated guanine nucleotide exchange factor. [refseq;acc:nm_015320] Squared 30868.3 31361.7 1.01598
ubiquitin-conjugating enzyme e2-17 kda 2 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 2). [swissprot;acc:p51669] Rooted 74.0281 74.1998 1.00232
2708 cdc42 guanine exchange factor 9; hpem-2 collybistin. [refseq;acc:nm_015185] Squared 30868.3 31361.7 1.01598
j domain protein c21orf55. [swissprot;acc:q9nx36] Measured 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
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 72.1471 72.3052 1.00219
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] 59.5057 59.62 1.00192
importin 7; ran-binding protein 7. [refseq;acc:nm_006391] Ranked 220.521 220.395 1.00057
testis-specific protein tex28. [swissprot;acc:o15482] Measured 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]
dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0] Rooted 55.7482 55.846 1.00175
importin 8; ran-binding protein 8. [refseq;acc:nm_006390] Ranked 220.521 220.395 1.00057
similar to nuclear protein e3-3 orf1. [sptrembl;acc:q9bu61] Measured 5603.24 5583.64 1.00351
2711 brefeldin a-inhibited guanine nucleotide-exchange protein 2 (brefeldin a-inhibited gep 2). [swissprot;acc:q9y6d5] Ranked 220.521 220.395 1.00057
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 5332.98 5351.72 1.00351
rna, u transporter 1; snurportin-1. [refseq;acc:nm_005701] Squared 40468.1 39911.9 1.01394
sorting nexin 1. [swissprot;acc:q13596] Rooted 64.0665 63.9543 1.00175
2712 a kindred of iglon. [refseq;acc:nm_173808] Measured 5603.24 5583.64 1.00351
fragile x mental retardation 1 protein (protein fmr-1) (fmrp). [swissprot;acc:q06787] Squared 36808.5 36316 1.01356
hsgcn1 (fragment). [sptrembl;acc:q99736] Ranked 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
2713 ankyrin-repeat family a protein 2 (rfxank-like 2). [swissprot;acc:q9h9e1] Measured 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
nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] Squared 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
2714 dna polymerase epsilon p17 subunit (dna polymerase epsilon subunit 3) (chromatin accessibility complex 17) (huchrac17) (chrac-17). [swissprot;acc:q9nrf9] 48.4125 48.4851 1.0015
fragile x mental retardation syndrome related protein 2. [swissprot;acc:p51116] Squared 36800.7 36312.3 1.01345
inflammation-related g protein-coupled receptor ex33. [refseq;acc:nm_020370] Measured 5603.24 5583.64 1.00351

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/