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 551 to 600 of 33156 in total
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Value Type
Interaction Map
red
green
network_comparison
69 spermatogenesis associated 6. [refseq;acc:nm_019073] Measured High confidence 6475.5 10307.5 1.59177
testis-specific protein tex28. [swissprot;acc:o15482] Ranked Low confidence 259.517 235.017 1.10425
70 27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [swissprot;acc:o14653]
amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] Measured High confidence 6475.5 10307.5 1.59177
chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] Rooted 27.9136 37.2872 1.33581
guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899] Ranked 267.142 336.074 1.25804
melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] Squared 219048 129762 1.68808
phospholipase a-2-activating protein (plap) (pla2p). [swissprot;acc:q9y263] Low confidence 80538.1 64191.7 1.25465
transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] Rooted 61.9982 68.2337 1.10058
y+l amino acid transporter 1 (y(+)l-type amino acid transporter 1) (y+lat-1) (y+lat1) (monocyte amino acid permease 2) (mop-2). [swissprot;acc:q9um01] Measured 6991.78 7848.45 1.12253
71 a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] Squared 63411.7 51068.8 1.24169
cysteine-rich protein 1 (cysteine-rich intestinal protein) (crip) (cysteine-rich heart protein) (hcrhp). [swissprot;acc:p50238] Ranked 230.944 209.149 1.10421
cystine/glutamate transporter (amino acid transport system xc-) (xct) (calcium channel blocker resistance protein ccbr1). [swissprot;acc:q9upy5] Measured 6991.78 7848.45 1.12253
doc-1 related protein (doc-1r). [swissprot;acc:o75956] Rooted High confidence 27.9136 37.2872 1.33581
guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898] Ranked 267.144 336.073 1.25802
melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Squared 219048 129762 1.68808
serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007] Measured 4556.78 2945.26 1.54716
tbp-associated factor 2; taf2 rna polymerase ii, tata box binding protein (tbp)-associated factor, 150 kd; tata box binding protein (tbp)-associated factor, rna polymerase ii, b, 150kd; cofactor of initiator function, 150kd subunit. [refseq;acc:nm_003184] Rooted Low confidence 59.6397 65.6325 1.10048
72 guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754] Ranked High confidence 267.144 336.073 1.25802
melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Squared 219048 129762 1.68808
mitochondrial tumor suppressor gene 1; transcription factor mtsg1; at2 receptor-interacting protein 1; erythroid differentiation-related gene. [refseq;acc:nm_020749] Rooted Low confidence 63.1259 69.4305 1.09987
neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] High confidence 27.9136 37.2872 1.33581
raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] Squared Low confidence 63404.8 51065.9 1.24163
set and mynd domain containing 2; hskm-b protein; zinc finger, mynd domain containing 14. [refseq;acc:nm_020197] Ranked 230.944 209.149 1.10421
solute carrier family 7 (cationic amino acid transporter, y+ system), member 6. [refseq;acc:nm_003983] Measured 6991.78 7848.45 1.12253
uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] High confidence 4556.79 2945.28 1.54715
73 carboxypeptidase n 83 kda chain (carboxypeptidase n regulatory subunit) (fragment). [swissprot;acc:p22792] Squared Low confidence 63279.6 51013.1 1.24046
eukaryotic translation initiation factor 4b (eif-4b). [swissprot;acc:p23588] Measured 6991.78 7848.45 1.12253
junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] Ranked High confidence 288 362 1.25694
melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1] Squared 219048 129762 1.68808
neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] Rooted 27.9136 37.2872 1.33581
rad50-interacting protein 1. [refseq;acc:nm_021930] Low confidence 64.6594 71.0277 1.09849
serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [swissprot;acc:q00005] Measured High confidence 4556.83 2945.38 1.54711
set and mynd domain containing protein 1. [sptrembl;acc:q8nb12] Ranked Low confidence 230.944 209.149 1.10421
74 b(0,+)-type amino acid transporter 1 (b(0,+)at) (glycoprotein- associated amino acid transporter b0,+at1). [swissprot;acc:p82251] Measured 6991.78 7848.45 1.12253
diacylglycerol kinase, eta isoform 1. [refseq;acc:nm_152910] Rooted 62.2472 68.3765 1.09847
junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] Ranked High confidence 288 362 1.25694
neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] Rooted 27.9136 37.2872 1.33581
platelet glycoprotein v precursor (gpv) (cd42d). [swissprot;acc:p40197] Squared Low confidence 63279.9 51013.3 1.24046
putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865] Ranked 195.817 215.516 1.1006
serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [swissprot;acc:q9y2t4] Measured High confidence 4556.99 2945.8 1.54694
trophinin. [swissprot;acc:q12816] Squared 219048 129762 1.68808
75 b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056] Low confidence 63087.3 50932.2 1.23865
chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] Rooted High confidence 27.9136 37.2872 1.33581
diacylglycerol kinase, delta (ec 2.7.1.107) (diglyceride kinase) (dgk-delta) (dag kinase delta) (130 kda diacylglycerol kinase) (fragment). [swissprot;acc:q16760] Low confidence 62.2472 68.3765 1.09847
myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] Squared High confidence 110342 184298 1.67024
nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181] Measured 1920.75 2907.43 1.5137
nipsnap2 protein (glioblastoma amplified sequence). [swissprot;acc:o75323] Ranked Low confidence 249.709 226.944 1.10031
septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] Measured 11616 12942.3 1.11418
sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906] Ranked High confidence 288 362 1.25694

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/