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 4908 to 4957 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
614 rac-beta serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-beta) (protein kinase akt-2) (protein kinase b, beta) (pkb beta). [swissprot;acc:p31751] Rooted Subtracted 50.2317 55.0025 4.7708
solute carrier family 4 (anion exchanger), member 1, adaptor protein; kidney anion exchanger adaptor protein; kanadaptin; lung cancer oncogene 3. [refseq;acc:nm_018158] Measured Divided 11222.2 9948.93 1.12798
thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762] Subtracted 5480.24 6222.04 741.8
tyrosyl-trna synthetase (ec 6.1.1.1) (tyrosyl--trna ligase) (tyrrs). [swissprot;acc:p54577] Ranked 232.468 245.048 12.58
ubiquitin-conjugating enzyme e2 n (ec 6.3.2.19) (ubiquitin-protein ligase n) (ubiquitin carrier protein n) (ubc13) (bendless-like ubiquitin conjugating enzyme). [swissprot;acc:q16781] Squared 27949.8 32471.7 4521.9
615 3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325] Measured 5480.24 6222.04 741.8
40s ribosomal protein s15a. [swissprot;acc:p39027] Rooted 50.5463 45.7763 4.77
coatomer gamma subunit (gamma-coat protein) (gamma-cop). [swissprot;acc:q9y678] Squared Divided 51527.6 43689.1 1.17942
cyclin-dependent kinases regulatory subunit 2 (cks-2). [swissprot;acc:p33552] Measured 11222.2 9948.93 1.12798
dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864] Ranked Subtracted 241.907 229.35 12.557
ga binding protein beta-2 chain (gabp-beta-2 subunit) (transcription factor e4tf1-47) (gapbp-2) (nuclear respiratory factor-2 subunit gamma). [swissprot;acc:q06545] Rooted Divided 57.2007 61.7615 1.07973
hepatitis c virus core-binding protein 6; cervical cancer oncogene 3. [refseq;acc:nm_023934] Squared Subtracted 27407.7 31927.7 4520
homeobox protein hox-b9 (hox-2e) (hox-2.5). [swissprot;acc:p17482] Ranked Divided 214.257 202.132 1.05999
616 1-acyl-sn-glycerol-3-phosphate acyltransferase gamma (ec 2.3.1.51) (1- agp acyltransferase 3) (1-agpat 3) (lysophosphatidic acid acyltransferase-gamma) (lpaat-gamma) (1-acylglycerol-3-phosphate o- acyltransferase 3). [swissprot;acc:q9nrz7] Rooted Subtracted 73.9102 78.6514 4.7412
catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [refseq;acc:nm_003798] Measured Divided 11222.2 9948.93 1.12798
coatomer zeta-1 subunit (zeta-1 coat protein) (zeta-1 cop) (cgi-120) (hspc181). [swissprot;acc:q9y3c3] Squared 51527.6 43689.1 1.17942
dc11 protein. [refseq;acc:nm_020186] Subtracted 27407.7 31927.7 4520
homeobox protein hox-a9 (hox-1g). [swissprot;acc:p31269] Ranked Divided 214.257 202.132 1.05999
mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] Subtracted 177.698 190.24 12.542
nadh-ubiquinone oxidoreductase 23 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-23kd) (ci-23kd) (tyky subunit). [swissprot;acc:o00217] Rooted Divided 57.2007 61.7615 1.07973
transforming protein rhoa (h12). [swissprot;acc:p06749] Measured Subtracted 5480.24 6222.04 741.8
617 adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109] Rooted 76.0455 80.7777 4.7322
amyloid beta precursor protein-binding protein 1; amyloid protein-binding protein 1. [refseq;acc:nm_003905] Squared 27407.7 31927.7 4520
carboxypeptidase b precursor. [refseq;acc:nm_020361] Ranked 177.698 190.239 12.541
coatomer delta subunit (delta-coat protein) (delta-cop) (archain). [swissprot;acc:p48444] Squared Divided 51527.6 43689.1 1.17942
dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576] Measured 5162.52 5822.47 1.12783
elongation of very long chain fatty acids protein 1 (cgi-88). [swissprot;acc:q9bw60] Rooted 57.2008 61.7614 1.07973
homeobox protein hox-c9 (hox-3b). [swissprot;acc:p31274] Ranked 214.257 202.135 1.05997
splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] Measured Subtracted 4532.73 5269.33 736.6
618 5-aminolevulinic acid synthase, erythroid-specific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-e). [swissprot;acc:p22557] Squared 27407.7 31927.7 4520
dna mismatch repair protein mlh3 (mutl protein homolog 3). [swissprot;acc:q9uhc1] Measured 6327.86 7064.13 736.27
gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [swissprot;acc:q99928] Ranked Divided 214.256 202.139 1.05994
myc proto-oncogene protein (c-myc). [swissprot;acc:p01106] Rooted 57.208 61.7592 1.07956
nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [swissprot;acc:q13232] Measured 7878.27 8879.08 1.12703
peptidyl-prolyl cis-trans isomerase e (ec 5.2.1.8) (ppiase e) (rotamase e) (cyclophilin e) (cyclophilin 33). [swissprot;acc:q9unp9] Squared 51527.6 43689.1 1.17942
plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872] Ranked Subtracted 177.699 190.24 12.541
synapsin iii. [swissprot;acc:o14994] Rooted 60.0129 64.7371 4.7242
619 aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468]
coatomer zeta-2 subunit (zeta-2 coat protein) (zeta-2 cop). [swissprot;acc:q9p299] Squared Divided 51527.6 43689.1 1.17942
dendritic cell protein. [refseq;acc:nm_006360] Rooted 63.847 68.8873 1.07894
forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488] Ranked 214.256 202.139 1.05994
nucleolar protein nop56 (nucleolar protein 5a). [swissprot;acc:o00567] Measured 3879.99 4371.24 1.12661
ornithine decarboxylase (ec 4.1.1.17) (odc). [swissprot;acc:p11926] Subtracted 6811.2 7547.35 736.15
ubiquitin-activating enzyme e1c (uba3 homolog, yeast); ubiquitin-activating enzyme e1c (homologous to yeast uba3). [refseq;acc:nm_003968] Squared 27407.7 31927.7 4520
vam6/vps39-like protein (hvam6p). [swissprot;acc:q96jc1] Ranked 206.274 218.792 12.518
620 aminoadipate-semialdehyde synthase; lysine-ketoglutarate reductase /saccharopine dehydrogenase; lysine-2-oxoglutarate reductase; aminoadipic semialdehyde synthase. [refseq;acc:nm_005763] Measured 6807.78 7543.28 735.5
ferritin heavy chain (ferritin h subunit). [swissprot;acc:p02794] Divided 6227.87 7012.9 1.12605
gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [swissprot;acc:q8n1c3] Ranked 214.256 202.14 1.05994
hairy/enhancer-of-split related with yrpw motif 1 (hairy and enhancer of split related-1) (hesr-1) (cardiovascular helix-loop-helix factor 2) (hes-related repressor protein 2 herp2). [swissprot;acc:q9y5j3] Rooted Subtracted 60.0129 64.7371 4.7242
homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356] Squared Divided 32208.8 37986.6 1.17939

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/