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 4030 to 4079 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1008 eukaryotic translation initiation factor 3 subunit 8 (eif3 p110) (eif3c). [swissprot;acc:q99613] Rooted 51.2693 54.0336 1.05392
single-minded homolog 1. [swissprot;acc:p81133] Measured 5707.73 6249.1 1.09485
wd-repeat protein bing4. [swissprot;acc:o15213] Ranked 243.227 235.475 1.03292
1009 40s ribosomal protein s24 (s19). [swissprot;acc:p16632] Squared 21492.5 24677.4 1.14819
dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882] Ranked 229.116 221.823 1.03288
exportin 1; exportin-1 (required for chromosome region maintenance); exportin 1 (crm1, yeast, homolog); crm1, yeast, homolog. [refseq;acc:nm_003400] Rooted 58.8768 62.0483 1.05387
synapsin iii. [swissprot;acc:o14994] Measured 5791.82 6340.86 1.0948
1010 aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468]
nemo-like kinase; likely ortholog of mouse nemo like kinase. [refseq;acc:nm_016231] Rooted 62.0618 65.4025 1.05383
peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [swissprot;acc:q9ukg9] Ranked 217.523 210.648 1.03264
proto-oncogene tyrosine-protein kinase fes/fps (ec 2.7.1.112) (c-fes). [swissprot;acc:p07332] Squared 24025.9 27585.7 1.14817
1011 elks protein. [refseq;acc:nm_015064] Rooted 62.0618 65.4025 1.05383
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] Measured 5791.82 6340.86 1.0948
molybdenum cofactor synthesis protein 2 large subunit (molybdopterin synthase large subunit) (mpt synthase large subunit) (mocs2b) (moco1- b). [swissprot;acc:o96007] Squared 24025.9 27585.7 1.14817
retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [swissprot;acc:q08999] Ranked 217.026 210.189 1.03253
1012 actin binding lim protein 2. [refseq;acc:nm_032432] Measured 5791.82 6340.86 1.0948
anaphase-promoting complex subunit 10; anaphase-promoting complex 10. [refseq;acc:nm_014885] Squared 24025.9 27585.7 1.14817
golgi reassembly stacking protein 2; golgi reassembly stacking protein 2, 55 kda. [refseq;acc:nm_015530] Rooted 74.9231 78.9471 1.05371
retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [swissprot;acc:p28749] Ranked 217.021 210.185 1.03252
1013 60s ribosomal protein l29 (cell surface heparin binding protein hip). [swissprot;acc:p47914] Squared 24025.9 27585.7 1.14817
hairy/enhancer-of-split related with yrpw motif-like. [refseq;acc:nm_014571] Measured 5791.82 6340.86 1.0948
heparin sulfate n-deacetylase/n-sulfotransferase (ec 2.8.2.-) (n- hsst) (n-heparin sulfate sulfotransferase) (glucosaminyl n- deacetylase/n-sulfotransferase). [swissprot;acc:p52849] Rooted 58.0289 61.136 1.05354
protein bap28. [swissprot;acc:q9h583] Ranked 244.312 236.647 1.03239
1014 apoptosis antagonizing transcription factor. [refseq;acc:nm_012138] 243.045 235.422 1.03238
n-deacetylase/n-sulfotransferase (heparan glucosaminyl) 3. [refseq;acc:nm_004784] Rooted 58.0289 61.136 1.05354
proto-oncogene tyrosine-protein kinase fer (ec 2.7.1.112) (p94-fer) (c-fer). [swissprot;acc:p16591] Squared 24025.9 27585.7 1.14817
synapsin ii. [swissprot;acc:q92777] Measured 5791.82 6340.86 1.0948
1015 bai1-associated protein 1; ww domain-containing protein 3; atrophin-1 interacting protein 3. [refseq;acc:nm_004742] Ranked 221.73 228.906 1.03236
mitochondrial ribosome recycling factor. [refseq;acc:nm_138777] Measured 5791.82 6340.86 1.0948
molybdenum cofactor synthesis protein 3 (molybdopterin synthase sulfurylase) (mpt synthase sulfurylase). [swissprot;acc:o95396] Squared 24025.9 27585.7 1.14817
n-deacetylase/n-sulfotransferase 4. [refseq;acc:nm_022569] Rooted 58.0289 61.136 1.05354
1016 eukaryotic translation initiation factor 3 subunit 8 (eif3 p110) (eif3c). [swissprot;acc:q99613] Squared 15559.9 17865 1.14814
heparan sulfate n-deacetylase/n-sulfotransferase (ec 2.8.2.8) (n-hsst) (hsnst) ([heparan sulfate]-glucosamine n-sulfotransferase) (n-heparan sulfate sulfotransferase) (glucosaminyl n-deacetylase/n- sulfotransferase). [swissprot;acc:p52848] Rooted 58.0289 61.136 1.05354
importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629] Ranked 217.369 210.561 1.03233
peroxisomal targeting signal 1 receptor (peroxismore receptor 1) (peroxisomal c-terminal targeting signal import receptor) (pts1-bp) (peroxin-5) (pts1 receptor). [swissprot;acc:p50542] Measured 5791.82 6340.86 1.0948
1017 hairy/enhancer-of-split related with yrpw motif 2; gridlock; hes-related repressor protein 1. [refseq;acc:nm_012259]
orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [swissprot;acc:q9y466] Squared 29907.6 34337 1.1481
protein cdc27hs (cell division cycle protein 27 homolog) (h-nuc). [swissprot;acc:p30260] Rooted 58.0289 61.136 1.05354
target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077] Ranked 217.365 210.558 1.03233
1018 importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [swissprot;acc:o00505] 217.361 210.554
kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] Rooted 78.3617 82.5529 1.05349
peptide methionine sulfoxide reductase (ec 1.8.4.6) (protein- methionine-s-oxide reductase) (peptide met(o) reductase). [swissprot;acc:q9uj68] Squared 22827.7 26208.2 1.14809
transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [swissprot;acc:q14469] Measured 5791.82 6340.86 1.0948
1019 delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [swissprot;acc:q13011]
epidermal growth factor receptor pathway substrate 8-like protein 1 isoform c; epidermal growth factor receptor pathway substrate 8-related protein 1; eps8-related protein 1. [refseq;acc:nm_139204] Rooted 60.7786 64.0257 1.05343
phosphoserine aminotransferase (ec 2.6.1.52) (psat). [swissprot;acc:q9y617] Squared 22827.7 26208.2 1.14809
tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677] Ranked 221.302 214.409 1.03215
1020 actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313] Measured 5791.82 6340.86 1.0948
adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559] Squared 26499.7 30423.6 1.14807
dopachrome tautomerase precursor (ec 5.3.3.12) (dt) (dct) (dopachrome delta-isomerase) (tyrosinase-related protein 2) (trp-2) (trp2). [swissprot;acc:p40126] Ranked 221.28 214.409 1.03205

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/