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 5908 to 5957 of 8289 in total
Value Type  : Measured
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
2954 nadh-ubiquinone oxidoreductase 39 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-39kd) (ci-39kd). [swissprot;acc:q16795] High confidence 0.00001 0.00001 1
2955 fibrillin 2 precursor. [swissprot;acc:p35556]
protein c20orf24 (rab5-interacting protein) (rip5) (pnas-11). [swissprot;acc:q9buv8] Low confidence 7992.87 8218.76 1.02826
2956 mitochondrial ferritin; ferritin heavy chain-like; ferritin h subunit. [refseq;acc:nm_177478] 7835.04 8056.35 1.02825
protein transport protein sec24b (sec24-related protein b). [swissprot;acc:o95487] High confidence 0.00001 0.00001 1
2957 aldehyde dehydrogenase family 7 member a1 (ec 1.2.1.3) (antiquitin 1). [swissprot;acc:p49419] Low confidence 7963.39 8188.28 1.02824
glutamyl aminopeptidase (ec 3.4.11.7) (eap) (aminopeptidase a) (apa) (differentiation antigen gp160). [swissprot;acc:q07075] High confidence 0.00001 0.00001 1
2958 60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815] Low confidence 7805.71 8026.07 1.02823
ccr4-not transcription complex, subunit 6-like. [refseq;acc:nm_144571] High confidence 0.00001 0.00001 1
2959 60s ribosomal protein l37a. [swissprot;acc:p12751]
homeodomain interacting protein kinase 3; homeodomain-interacting protein kinase 3. [refseq;acc:nm_005734] Low confidence 8101.36 8329.94 1.02822
2960 aldehyde oxidase (ec 1.2.3.1). [swissprot;acc:q06278] High confidence 0.00001 0.00001 1
homeodomain-interacting protein kinase 2 (ec 2.7.1.-). [swissprot;acc:q9h2x6] Low confidence 8101.28 8329.86 1.02822
2961 homeodomain-interacting protein kinase 1; homeodomain interacting protein kinase 1-like protein; nuclear body associated kinase 2b. [refseq;acc:nm_152696] 8101.27 8329.84 1.02821
ras-related protein rab-1a (ypt1-related protein). [swissprot;acc:p11476] High confidence 0.00001 0.00001 1
2962 atp-dependent rna helicase rok1; atp-dependent rna helicase. [refseq;acc:nm_007010] Low confidence 7773.28 7992.6 1.02821
dynein 2 light intermediate chain. [refseq;acc:nm_016008] High confidence 0.00001 0.00001 1
2963 ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8] Low confidence 7835.11 8056.17 1.02821
geranylgeranyl transferase type ii beta subunit (ec 2.5.1.-) (rab geranylgeranyltransferase beta subunit) (rab geranyl- geranyltransferase beta subunit) (rab gg transferase beta) (rab ggtase beta). [swissprot;acc:p53611] High confidence 0.00001 0.00001 1
2964 p300/cbp-associated factor (ec 2.3.1.-) (p/caf) (histone acetylase pcaf). [swissprot;acc:q92831] Low confidence 8040.5 8267.31 1.02821
semaphorin 6d isoform 3 precursor. [refseq;acc:nm_153617] High confidence 0.00001 0.00001 1
2965 poly(rc)-binding protein 3 (alpha-cp3). [swissprot;acc:p57721] Low confidence 7827.31 8048.03 1.0282
solute carrier family 21 member 15 (organic anion transporter polypeptide-related protein 4) (oatp-rp4) (oatprp4). [swissprot;acc:q9h2y9] High confidence 0.00001 0.00001 1
2966 myotubularin related protein 6 (ec 3.1.3.-). [swissprot;acc:q9y217] Low confidence 8036.46 8263.09 1.0282
protease inhibitor 15 preproprotein; 25 kda trypsin inhibitor. [refseq;acc:nm_015886] High confidence 0.00001 0.00001 1
2967 myotubularin related protein 8. [refseq;acc:nm_017677] Low confidence 8036.46 8263.09 1.0282
taube nuss. [refseq;acc:nm_138572] High confidence 0.00001 0.00001 1
2968 ba528a10.3.2 (novel protein similar to kiaa0161, isoform 2) (fragment). [sptrembl;acc:q9bx39]
poly(rc)-binding protein 4 (alpha-cp4). [swissprot;acc:p57723] Low confidence 7827.17 8047.86 1.0282
2969 transcription factor ap-2 alpha (ap2-alpha) (activating enhancer- binding protein 2 alpha) (ap-2 transcription factor) (activator protein-2) (ap-2). [swissprot;acc:p05549] High confidence 0.00001 0.00001 1
upstream regulatory element binding protein 1; hect domain protein lasu1; bj-hcc-24 tumor antigen. [refseq;acc:nm_031407] Low confidence 8036.46 8263.09 1.0282
2970 myotubularin related protein 7 (ec 3.1.3.-) (fragment). [swissprot;acc:q9y216]
nov protein homolog precursor (novh) (nephroblastoma overexpressed gene protein homolog). [swissprot;acc:p48745] High confidence 0.00001 0.00001 1
2971 dna-repair protein complementing xp-a cells (xeroderma pigmentosum group a complementing protein). [swissprot;acc:p23025]
poly(rc)-binding protein 2 (alpha-cp2) (hnrnp-e2). [swissprot;acc:q15366] Low confidence 7827.21 8047.89 1.02819
2972 poly(rc)-binding protein 1 (alpha-cp1) (hnrnp-e1) (nucleic acid binding protein sub2.3). [swissprot;acc:q15365] 7827.13 8047.73 1.02818
steroidogenic factor 1 (stf-1) (sf-1) (steroid hormone receptor ad4bp) (fushi tarazu factor homolog 1). [swissprot;acc:q13285] High confidence 0.00001 0.00001 1
2973 fructose-bisphosphate aldolase b (ec 4.1.2.13) (liver-type aldolase). [swissprot;acc:p05062]
protein c14orf122 (cgi-112). [swissprot;acc:q9y3b6] Low confidence 8323.47 8557.98 1.02817
2974 cell division protein kinase 9 (ec 2.7.1.-) (serine/threonine-protein kinase pitalre) (c-2k). [swissprot;acc:p50750] High confidence 0.00001 0.00001 1
melanotransferrin precursor (melanoma-associated antigen p97) (cd228 antigen). [swissprot;acc:p08582] Low confidence 7843.59 8064.44 1.02816
2975 general control of amino acid synthesis protein 5-like 2 (ec 2.3.1.-) (histone acetyltransferase gcn5) (hsgcn5). [swissprot;acc:q92830] 8040.27 8266.66
potassium channel tetramerisation domain containing 3; ny-ren-45 antigen. [refseq;acc:nm_016121] High confidence 0.00001 0.00001 1
2976 mo25 protein (cgi-66). [swissprot;acc:q9y376]
prefoldin subunit 4 (protein c-1). [swissprot;acc:q9nqp4] Low confidence 8124.65 8353.27 1.02814
2977 carbonic anhydrase-related protein 10 (carbonic anhydrase-related protein x) (carp x) (ca-rp x) (cerebral protein-15) (hucep-15). [swissprot;acc:q9ns85] 7818.92 8038.84 1.02813
cytochrome p450 27, mitochondrial precursor (ec 1.14.-.-) (cytochrome p-450c27/25) (sterol 26-hydroxylase) (sterol 27-hydroxylase) (vitamin d(3) 25-hydroxylase) (5-beta-cholestane-3-alpha,7-alpha,12-alpha-triol 27-hydroxylase). [swissprot;acc:q02318] High confidence 0.00001 0.00001 1
2978 integrin alpha-7 precursor. [swissprot;acc:q13683]
mrna capping enzyme (hce) (hcap1) [includes: polynucleotide 5'- triphosphatase (ec 3.1.3.33) (mrna 5'-triphosphatase) (tpase); mrna guanylyltransferase (ec 2.7.7.50) (gtp--rna guanylyltransferase) (gtase)]. [swissprot;acc:o60942] Low confidence 7994.4 8219.31 1.02813
2979 mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426] 7788.78 8007.87

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/