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 6812 to 6861 of 29840 in total
Interaction Map  : High confidence
Rank
description
Value Type
Network Comparison Type
Filtered
red
green
network_comparison
426 ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260] Measured Divided 0 2071.59 2133.83 1.03004
similar to ribosomal protein, large, p0. [sptrembl;acc:q96fq9] Rooted Subtracted 22.7692 22.2374 0.5318
transcription initiation factor iie, beta subunit (tfiie-beta). [swissprot;acc:p29084] Measured 30 50 20
ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930] Squared Divided 1 20267.8 24644.8 1.21596
williams beuren syndrome critical region 20a isoform 2; nol1/nop2/sun gene family member; williams-beuren syndrome critical region protein 20 copy a; williams beuren syndrome chromosome region 20. [refseq;acc:nm_018044] Ranked Subtracted 0 16416.1 16721.6 305.5
427 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] Squared 0.872309 3.99932 3.12701
apoptosis inhibitor fksg2. [swissprot;acc:q9hau6] Ranked Divided 11276.1 11582.7 1.02719
bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132] Measured Subtracted 1337.29 1356.52 19.23
dna-directed rna polymerase ii 23 kda polypeptide (ec 2.7.7.6) (rpb25) (xap4) (rpb5) (rpabc1). [swissprot;acc:p19388] Ranked Divided 1 239.977 259.525 1.08146
estradiol 17 beta-dehydrogenase 1 (ec 1.1.1.62) (17-beta-hsd 1) (placental 17-beta-hydroxysteroid dehydrogenase) (20 alpha- hydroxysteroid dehydrogenase) (20-alpha-hsd) (e2dh). [swissprot;acc:p14061] Squared 0 14907.5 15522.7 1.04127
forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488] Measured Subtracted 1 6739.81 7644.62 904.81
homeobox protein hox-b9 (hox-2e) (hox-2.5). [swissprot;acc:p17482] Rooted 66.0817 71.6545 5.5728
myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] Divided 0 22.1458 22.7768 1.02849
neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] 1 54.4927 49.6125 1.09837
pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278] Squared 25380.3 30835.9 1.21495
potential carboxypeptidase-like protein x2 precursor. [swissprot;acc:q8n436] Subtracted 33104 38818.5 5714.5
putative inorganic polyphosphate/atp-nad kinase (ec 2.7.1.23) (poly(p)/atp nad kinase). [swissprot;acc:o95544] Measured Divided 0 1195.87 1161.29 1.02978
t-box transcription factor tbx6 (t-box protein 6). [swissprot;acc:o95947] Ranked Subtracted 1 212.547 229.411 16.864
transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] Rooted 0 15.7266 15.2103 0.5163
trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648] Measured Divided 1 11736.6 13531.9 1.15297
williams beuren syndrome chromosome region 20c isoform 1. [refseq;acc:nm_032158] Ranked Subtracted 0 16416.1 16721.6 305.5
428 adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306] Rooted Divided 1 54.4927 49.6125 1.09837
alpha-nac protein. [sptrembl;acc:q9h009] Subtracted 0 9.95878 9.44328 0.5155
atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072] Ranked Divided 1 253.852 234.808 1.0811
carboxypeptidase n catalytic chain precursor (ec 3.4.17.3) (arginine carboxypeptidase) (kininase 1) (serum carboxypeptidase n) (scpn) (anaphylatoxin inactivator) (plasma carboxypeptidase b). [swissprot;acc:p15169] Squared Subtracted 33104 38818.5 5714.5
cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240] Ranked Divided 0 11982.7 12301.2 1.02658
gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [swissprot;acc:q16445] Measured Subtracted 1 6739.82 7644.63 904.81
glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [swissprot;acc:o15488] Divided 0 14267.5 14688.8 1.02953
histone h4. [swissprot;acc:p02304] Ranked Subtracted 9611.37 9308.99 302.38
homeobox protein hox-a9 (hox-1g). [swissprot;acc:p31269] Rooted 1 66.0817 71.6543 5.5726
myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] Divided 0 22.1458 22.7768 1.02849
nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4] Measured 1 3721.19 4288.17 1.15237
phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [swissprot;acc:o00750] Subtracted 0 0 18 18
probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] Squared 2871.07 2873.96 2.89
swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497] Divided 1 29101.9 35347 1.21459
u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] Ranked Subtracted 227.748 210.888 16.86
ubiquitin protein ligase. [refseq;acc:nm_130466] Squared Divided 0 110.893 106.547 1.04079
429 60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914] Ranked 12318.7 12631.5 1.02539
adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] Rooted 1 54.4927 49.6125 1.09837
cpz gene product. [refseq;acc:nm_003652] Squared Subtracted 33104 38818.5 5714.5
dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0] Rooted 0 29.7773 29.2679 0.5094
homeobox protein hox-c9 (hox-3b). [swissprot;acc:p31274] 1 66.0818 71.6537 5.5719
interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123] Measured 6739.81 7644.62 904.81
myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] Rooted Divided 0 22.1458 22.7768 1.02849
polymerase (rna) iii (dna directed) (32kd). [refseq;acc:nm_006467] Ranked 1 239.709 259.038 1.08064
probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848] Subtracted 251.344 234.514 16.83
programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340] Squared Divided 29101.9 35347 1.21459
pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] Subtracted 0 0 2.81207 2.81207
rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372] Measured 18 0 18
splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] Ranked 11621.7 11913.4 291.7

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/