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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


Navigation/Query Panel:
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 1477 to 1526 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
739 cellular modulator of immune recognition. [refseq;acc:nm_145021] Divided 5768.32 6434.78 1.11554
splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [swissprot;acc:q15459] Subtracted 5248.07 5901.72 653.65
740 syntaxin 7. [swissprot;acc:o15400] 5580.97 6233.52 652.55
vacuolar atp synthase 21 kda proteolipid subunit (ec 3.6.3.14) (hatpl). [swissprot;acc:q99437] Divided 5768.32 6434.78 1.11554
741 gamma-sarcoglycan (gamma-sg) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q13326]
sipl protein. [refseq;acc:nm_018269] Subtracted 6522.94 7175.18 652.24
742 ataxin 2 related protein isoform a; ataxin-2 domain protein. [refseq;acc:nm_007245] 4864.66 5514.87 650.21
eukaryotic translation initiation factor 3 subunit 4 (eif-3 delta) (eif3 p44) (eif-3 rna-binding subunit) (eif3 p42) (eif3g). [swissprot;acc:o75821] Divided 4131.04 4607.9 1.11543
743 ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] Subtracted 4864.66 5514.87 650.21
eukaryotic translation initiation factor 3 subunit 10 (eif-3 theta) (eif3 p167) (eif3 p180) (eif3 p185) (eif3a). [swissprot;acc:q14152] Divided 4131.04 4607.9 1.11543
744 c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545] Subtracted 9903.22 9253.79 649.43
cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857] Divided 12515.4 11221.1 1.11535
745 b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [refseq;acc:nm_181844] Subtracted 9899.79 9251.2 648.59
neuroepithelial cell transforming gene 1; guanine nucleotide regulatory protein (oncogene); rho guanine nucleotide exchange factor (gef) 8. [refseq;acc:nm_005863] Divided 4086.6 4557.68 1.11527
746 pas domain containing serine/threonine kinase; pas-serine/threonine kinase. [refseq;acc:nm_015148] Subtracted 9899.73 9251.16 648.57
rho guanine nucleotide exchange factor 3; rhogef protein; 59.8 kda protein; exchange factor found in platelets and leukemic and neuronal tissues, xpln. [refseq;acc:nm_019555] Divided 4086.6 4557.68 1.11527
747 b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [swissprot;acc:p41182] Subtracted 9899.73 9251.16 648.57
down-regulated in metastasis. [refseq;acc:nm_014503] Divided 4086.6 4557.68 1.11527
748 ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812] 12503.3 11212 1.11517
zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623] Subtracted 9899.73 9251.16 648.57
749 atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7] 3432.96 4081.21 648.25
ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [swissprot;acc:q99447] Divided 4565.34 5085.92 1.11403
750 c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363] Subtracted 9895.77 9248.18 647.59
myosin light chain 1, skeletal muscle isoform (mlc1f) (a1 catalytic) (alkali). [swissprot;acc:p05976] Divided 4565.34 5085.92 1.11403
751 cathepsin b precursor (ec 3.4.22.1) (cathepsin b1) (app secretase). [swissprot;acc:p07858] Subtracted 6513.45 7161 647.55
myosin light chain 1, slow-twitch muscle b/ventricular isoform (mlc1sb) (alkali). [swissprot;acc:p08590] Divided 4565.34 5085.92 1.11403
752 cerebral cell adhesion molecule. [refseq;acc:nm_016174] Subtracted 9596.59 10241.9 645.31
nadh-ubiquinone oxidoreductase 13 kda-a subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-a) (ci-13kd-a). [swissprot;acc:o75380] Divided 4565.34 5085.92 1.11403
753 dna damage binding protein 1 (damage-specific dna binding protein 1) (ddb p127 subunit) (ddba) (uv-damaged dna-binding protein 1) (uv-ddb 1) (xeroderma pigmentosum group e complementing protein) (xpce) (x- associated protein 1) (xap-1). [swissprot;acc:q16531] Subtracted 6194.15 6839.37 645.22
myosin light chain 1, slow-twitch muscle a isoform (mlc1sa) (alkali). [swissprot;acc:p14649] Divided 4565.34 5085.92 1.11403
754 myosin light chain 1, embryonic muscle/atrial isoform (pro1957). [swissprot;acc:p12829]
propionyl-coa carboxylase beta chain, mitochondrial precursor (ec 6.4.1.3) (pccase beta subunit) (propanoyl-coa:carbon dioxide ligase beta subunit). [swissprot;acc:p05166] Subtracted 6194.15 6839.37 645.22
755 nucleolar rna-associated protein alpha isoform. [refseq;acc:nm_022917] Divided 4079.81 4545.01 1.11402
transcription initiation factor iib (general transcription factor tfiib) (s300-ii). [swissprot;acc:q00403] Subtracted 4651.88 5296.78 644.9
756 thyroid receptor interacting protein 3 (trip-3) (fragment). [swissprot;acc:q15649]
topoisomerase-related function protein 4-2. [refseq;acc:nm_022447] Divided 4725.28 5261.06 1.11339
757 nhp2-like protein 1 (high mobility group-like nuclear protein 2 homolog 1) ([u4/u6.u5] tri-snrnp 15.5 kda protein) (otk27). [swissprot;acc:p55769] Subtracted 4651.88 5296.78 644.9
signal recognition particle 68 kda protein (srp68). [swissprot;acc:q9uhb9] Divided 5622.89 6260.02 1.11331
758 dna polymerase epsilon subunit b (ec 2.7.7.7) (dna polymerase ii subunit b). [swissprot;acc:p56282] 3760.3 4185.82 1.11316
nuclear fragile x mental retardation protein interacting protein 1; nuclear fragile x mental retardation intercating protein 1; nuclear fragile x mental retardation protein-interacting protein 1. [refseq;acc:nm_012345] Subtracted 4651.88 5296.78 644.9
759 6-phosphofructokinase, type c (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme c) (pfk-c) (6-phosphofructokinase, platelet type). [swissprot;acc:q01813] Divided 4254.62 4736.03 1.11315
phosphoglycerate kinase, testis specific (ec 2.7.2.3). [swissprot;acc:p07205] Subtracted 6597.56 7240.64 643.08
760 atpase, h+ transporting, lysosomal 38kda, v0 subunit d isoform 2. [refseq;acc:nm_152565] Divided 5870.2 6533.39 1.11298
gamma enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (neural enolase) (nse) (enolase 2). [swissprot;acc:p09104] Subtracted 6597.98 7241 643.02
761 beta enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (skeletal muscle enolase) (mse) (enolase 3). [swissprot;acc:p13929]
translation initiation factor if-2. [swissprot;acc:o60841] Divided 5811.51 6467.62 1.1129
762 alpha enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (non- neural enolase) (nne) (enolase 1) (phosphopyruvate hydratase). [swissprot;acc:p06733] Subtracted 6597.98 7241 643.02
pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278] Divided 6231.31 6933.9 1.11275
763 6-phosphofructokinase, muscle type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme a) (pfk-a) (phosphofructokinase-m). [swissprot;acc:p08237] 4250.54 4729.67 1.11272
phosphoglycerate kinase 1 (ec 2.7.2.3) (primer recognition protein 2) (prp 2). [swissprot;acc:p00558] Subtracted 6598.37 7241.32 642.95

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/