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 1463 to 1512 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
732 septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] Divided 124.434 118.318 1.05169
translin. [swissprot;acc:q15631] Subtracted 224.385 235.131 10.746
733 acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] Divided 164 155.961 1.05154
translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598] Subtracted 224.385 235.131 10.746
734 polyglutamine binding protein 1; nuclear protein containing ww domain 38 kd. [refseq;acc:nm_005710]
presenilin-like protein 2 (ec 3.4.99.-) (sppl2a protein). [swissprot;acc:q8tct8] Divided 232.601 244.534 1.0513
735 gtp-binding nuclear protein ran (tc4) (ran gtpase) (androgen receptor- associated protein 24). [swissprot;acc:p17080]
hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [swissprot;acc:q9y5r4] Subtracted 229.045 218.343 10.702
736 presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7] Divided 232.601 244.534 1.0513
putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [swissprot;acc:q9y5n5] Subtracted 228.78 218.091 10.689
737 exocyst complex component sec15b. [swissprot;acc:q9y2d4] 221.968 211.326 10.642
septin 10 isoform 1. [refseq;acc:nm_144710] Divided 125.526 119.402 1.05129
738 exocyst complex component sec15a. [swissprot;acc:q8tag9] Subtracted 222.138 211.503 10.635
xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7] Divided 222.825 211.966 1.05123
739 3-phosphoinositide dependent protein kinase-1 (ec 2.7.1.37) (hpdk1). [swissprot;acc:o15530] Subtracted 272.878 283.472 10.594
phosphoribosylformylglycinamidine synthase (ec 6.3.5.3) (fgam synthase) (fgams) (formylglycinamide ribotide amidotransferase) (fgarat) (formylglycinamide ribotide synthetase). [swissprot;acc:o15067] Divided 223.58 235.027 1.0512
740 bifunctional purine biosynthesis protein purh [includes: phosphoribosylaminoimidazolecarboxamide formyltransferase (ec 2.1.2.3) (aicar transformylase); imp cyclohydrolase (ec 3.5.4.10) (inosinicase) (imp synthetase) (atic)]. [swissprot;acc:p31939]
u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695] Subtracted 223.463 212.875 10.588
741 multifunctional protein ade2 [includes: phosphoribosylaminoimidazole- succinocarboxamide synthase (ec 6.3.2.6) (saicar synthetase); phosphoribosylaminoimidazole carboxylase (ec 4.1.1.21) (air carboxylase) (airc)]. [swissprot;acc:p22234] Divided 223.58 235.027 1.0512
step ii splicing factor slu7. [refseq;acc:nm_006425] Subtracted 223.463 212.875 10.588
742 brain protein 44. [swissprot;acc:o95563] Divided 126.215 120.078 1.05111
histone deacetylase 2 (hd2). [swissprot;acc:q92769] Subtracted 226.003 215.541 10.462
743 multiple coagulation factor deficiency 2; neural stem cell derived neuronal survival protein; multiple coagulation factor deficiency protein 2. [refseq;acc:nm_139279] 225.996 215.535 10.461
septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] Divided 126.215 120.078 1.05111
744 dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8] Subtracted 225.996 215.535 10.461
septin 6. [swissprot;acc:q14141] Divided 126.604 120.463 1.05098
745 histone deacetylase 1 (hd1). [swissprot;acc:q13547] Subtracted 225.989 215.53 10.459
solute carrier family 35, member b1; udp-galactose transporter related. [refseq;acc:nm_005827] Divided 214.679 225.568 1.05072
746 eukaryotic translation initiation factor 3 subunit 2 (eif-3 beta) (eif3 p36) (eif3i) (tgf-beta receptor interacting protein 1) (trip-1). [swissprot;acc:q13347] 250.465 238.38 1.0507
protein tara (trio-associated repeat on actin) (hrihfb2122). [swissprot;acc:q9h2d6] Subtracted 213.804 224.226 10.422
747 rho interacting protein 3. [refseq;acc:nm_015134] 213.803 224.224 10.421
trinucleotide repeat containing 15. [refseq;acc:nm_015575] Divided 250.465 238.38 1.0507
748 fibrillarin (34 kda nucleolar scleroderma antigen). [swissprot;acc:p22087] 245.246 233.483 1.05038
u4/u6-associated rna splicing factor. [refseq;acc:nm_004698] Subtracted 222.082 211.707 10.375
749 dnaj homolog subfamily b member 4 (heat shock 40 kda protein 1 homolog) (heat shock protein 40 homolog) (hsp40 homolog). [swissprot;acc:q9udy4] 210.946 221.225 10.279
exocyst complex component sec15b. [swissprot;acc:q9y2d4] Divided 221.968 211.326 1.05036
750 cab2. [refseq;acc:nm_033419] Subtracted 210.946 221.225 10.279
exocyst complex component sec15a. [swissprot;acc:q8tag9] Divided 222.138 211.503 1.05028
751 dnaj homolog subfamily b member 5 (heat shock protein hsp40-3) (heat shock protein cognate 40) (hsc40) (hsp40-2). [swissprot;acc:o75953] Subtracted 210.946 221.225 10.279
u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695] Divided 223.463 212.875 1.04974
752 dnaj homolog subfamily b member 1 (heat shock 40 kda protein 1) (heat shock protein 40) (hsp40) (dnaj protein homolog 1) (hdj-1). [swissprot;acc:p25685] Subtracted 210.946 221.225 10.279
step ii splicing factor slu7. [refseq;acc:nm_006425] Divided 223.463 212.875 1.04974
753 eukaryotic peptide chain release factor subunit 1 (erf1) (eukaryotic release factor 1) (tb3-1) (c11 protein). [swissprot;acc:p46055] Subtracted 210.946 221.225 10.279
lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428] Divided 224.434 235.583 1.04968
754 microsomal signal peptidase 25 kda subunit (ec 3.4.-.-) (spase 25 kda subunit) (spc25). [swissprot;acc:q15005]
suppressor of actin mutations 2-like isoform b; dj1033b10.5. [refseq;acc:nm_022553] Subtracted 210.946 221.225 10.279
755 40s ribosomal protein sa (p40) (34/67 kda laminin receptor) (colon carcinoma laminin-binding protein) (nem/1chd4) (multidrug resistance- associated protein mgr1-ag). [swissprot;acc:p08865] 224.244 234.511 10.267
uridine 5'-monophosphate synthase (ump synthase) [includes: orotate phosphoribosyltransferase (ec 2.4.2.10) (oprtase); orotidine 5'- phosphate decarboxylase (ec 4.1.1.23) (ompdecase)]. [swissprot;acc:p11172] Divided 224.434 235.583 1.04968
756 40s ribosomal protein s21. [swissprot;acc:p35265] Subtracted 224.244 234.511 10.267
cleft lip and palate associated transmembrane protein 1. [refseq;acc:nm_001294] Divided 224.434 235.583 1.04968

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/