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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Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 7114 to 7163 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1779 conserved oligomeric golgi complex component 3 (vesicle docking protein sec34 homolog) (p94). [swissprot;acc:q96jb2] Measured 5386.37 5744.89 1.06656
dna-repair protein complementing xp-g cells (xeroderma pigmentosum group g complementing protein) (dna excision repair protein ercc-5). [swissprot;acc:p28715] Squared 11731 12903.2 1.09992
pre-b-cell leukemia transcription factor-1 (homeobox protein pbx1) (homeobox protein prl). [swissprot;acc:p40424] Ranked 206.332 203.874 1.01206
1780 germ cell-less. [refseq;acc:nm_022471] 206.335 203.877
nuclear factor (erythroid-derived 2)-like 3; nf-e2-related factor 3. [refseq;acc:nm_004289] Rooted 71.372 73.6197 1.03149
proteasome subunit beta type 6 precursor (ec 3.4.25.1) (proteasome delta chain) (macropain delta chain) (multicatalytic endopeptidase complex delta chain) (proteasome subunit y). [swissprot;acc:p28072] Squared 29473.4 32415 1.09981
similar to actin-related protein 3-beta. [sptrembl;acc:q96bt2] Measured 5386.37 5744.89 1.06656
1781 arp2/3 complex 41 kda subunit (p41-arc) (actin-related protein 2/3 complex subunit 1b). [swissprot;acc:o15143]
phosphoglycerate kinase, testis specific (ec 2.7.2.3). [swissprot;acc:p07205] Rooted 67.1463 69.2594 1.03147
pre-b-cell leukemia transcription factor-3 (homeobox protein pbx3). [swissprot;acc:p40426] Ranked 206.332 203.874 1.01206
proteasome subunit alpha type 1 (ec 3.4.25.1) (proteasome component c2) (macropain subunit c2) (multicatalytic endopeptidase complex subunit c2) (proteasome nu chain) (30 kda prosomal protein) (pros-30). [swissprot;acc:p25786] Squared 28410 31244.9 1.09979
1782 60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429] 13245.8 14566.6 1.09971
hyporthetical protein mgc27169. [refseq;acc:nm_176782] Ranked 206.332 203.874 1.01206
rna-binding region containing protein 1 (hsrnaseb) (ssdna binding protein seb4) (cll-associated antigen kw-5). [swissprot;acc:q9h0z9] Rooted 62.1036 64.058 1.03147
zinc finger protein 198 (fused in myeloproliferative disorders protein) (rearranged in atypical myeloproliferative disorder protein). [swissprot;acc:q9ubw7] Measured 5386.37 5744.89 1.06656
1783 60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1] Squared 13244.1 14564.4 1.09969
actin-like protein 3 (actin-related protein 3) (actin-2). [swissprot;acc:p32391] Measured 5386.37 5744.89 1.06656
gamma enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (neural enolase) (nse) (enolase 2). [swissprot;acc:p09104] Rooted 67.1494 69.2625 1.03147
homeobox protein meis1. [swissprot;acc:o00470] Ranked 206.332 203.874 1.01206
1784 40s ribosomal protein s16. [swissprot;acc:p17008] Squared 13244.1 14564.4 1.09969
arp2/3 complex 21 kda subunit (p21-arc) (actin-related protein 2/3 complex subunit 3). [swissprot;acc:o15145] Measured 5386.37 5744.89 1.06656
beta enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (skeletal muscle enolase) (mse) (enolase 3). [swissprot;acc:p13929] Rooted 67.1494 69.2625 1.03147
homeobox protein meis2 (meis1-related protein 1). [swissprot;acc:o14770] Ranked 206.332 203.874 1.01206
1785 bag-family molecular chaperone regulator-2. [swissprot;acc:o95816]
nardilysin precursor (ec 3.4.24.61) (n-arginine dibasic convertase) (nrd convertase) (nrd-c). [swissprot;acc:o43847] Measured 5386.37 5744.89 1.06656
phosphoglycerate kinase 1 (ec 2.7.2.3) (primer recognition protein 2) (prp 2). [swissprot;acc:p00558] Rooted 67.1523 69.2654 1.03147
set domain and mariner transposase fusion gene. [refseq;acc:nm_006515] Squared 19340.3 21267.5 1.09965
1786 actin-related protein 2/3 complex subunit 1a (sop2-like protein). [swissprot;acc:q92747] Measured 5386.37 5744.89 1.06656
cd209 antigen-like; putative type ii membrane protein. [refseq;acc:nm_014257] Squared 19340.3 21267.5 1.09965
pre-b-cell leukemia transcription factor-2 (homeobox protein pbx2) (g17 protein). [swissprot;acc:p40425] Ranked 206.332 203.874 1.01206
proteasome subunit alpha type 6 (ec 3.4.25.1) (proteasome iota chain) (macropain iota chain) (multicatalytic endopeptidase complex iota chain) (27 kda prosomal protein) (pros-27) (p27k). [swissprot;acc:p34062] Rooted 63.6258 65.628 1.03147
1787 alpha enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (non- neural enolase) (nne) (enolase 1) (phosphopyruvate hydratase). [swissprot;acc:p06733] 67.1494 69.2625
interferon-related developmental regulator 2 (skmc15 protein). [swissprot;acc:q12894] Measured 5386.48 5744.78 1.06652
low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734] Squared 19340.3 21267.5 1.09965
pre-b-cell leukemia transcription factor 4. [refseq;acc:nm_025245] Ranked 206.332 203.874 1.01206
1788 arp2/3 complex 16 kda subunit (p16-arc) (actin-related protein 2/3 complex subunit 5). [swissprot;acc:o15511] Measured 5386.49 5744.76 1.06651
branched-chain amino acid aminotransferase, mitochondrial precursor (ec 2.6.1.42) (bcat(m)) (placental protein 18) (pp18). [swissprot;acc:o15382] Rooted 63.9873 65.9937 1.03136
cd209 antigen; dendritic cell-specific icam3-grabbing nonintegrin. [refseq;acc:nm_021155] Squared 19340.3 21267.5 1.09965
homeobox protein meis3 (meis1-related protein 2) (fragment). [swissprot;acc:q99687] Ranked 206.332 203.874 1.01206
1789 enthoprotin; epsin 4; clathrin interacting protein localized in the trans-golgi region. [refseq;acc:nm_014666] Squared 24761.4 27226.6 1.09956
ribonuclease hi large subunit (ec 3.1.26.-) (rnase hi large subunit) (rnase h(35)) (ribonuclease h2) (rnase h2). [swissprot;acc:o75792] Ranked 210.997 213.539 1.01205
serine/threonine protein kinase 12 (ec 2.7.1.37) (aurora- and ipl1- like midbody-associated protein 1) (aim-1) (aurora/ipl1-related kinase 2) (aurora-related kinase 2) (stk-1) (aurora-b). [swissprot;acc:q96gd4] Measured 5839.72 6227.33 1.06637
t-complex associated-testis-expressed 1-like (protein 91/23). [swissprot;acc:p51808] Rooted 85.2289 82.6464 1.03125
1790 dna topoisomerase ii, alpha isozyme (ec 5.99.1.3). [swissprot;acc:p11388] Ranked 203.759 201.349 1.01197
double-strand break repair protein mre11a (mre11 homolog 1). [swissprot;acc:p49959] Rooted 85.2289 82.6464 1.03125
f-actin capping protein alpha-1 subunit (capz alpha-1). [swissprot;acc:p52907] Squared 30558.1 33599.6 1.09953
kinesin-like protein kif23 (mitotic kinesin-like protein-1) (kinesin- like protein 5). [swissprot;acc:q02241] Measured 5839.72 6227.33 1.06637
1791 bifunctional aminoacyl-trna synthetase [includes: glutamyl-trna synthetase (ec 6.1.1.17) (glutamate--trna ligase); prolyl-trna synthetase (ec 6.1.1.15) (proline--trna ligase)]. [swissprot;acc:p07814] Rooted 60.4164 62.3011 1.0312
elav-like protein 3 (hu-antigen c) (huc) (paraneoplastic cerebellar degeneration-associated antigen) (paraneoplastic limbic encephalitis antigen 21). [swissprot;acc:q14576] Ranked 217.866 215.295 1.01194
probable dimethyladenosine transferase (ec 2.1.1.-) (s- adenosylmethionine-6-n',n'-adenosyl(rrna) dimethyltransferase) (18s rrna dimethylase). [swissprot;acc:q9unq2] Squared 21739.2 23895.5 1.09919

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/