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 Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2013 to 2062 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1007 cysteine-rich protein 1 (cysteine-rich intestinal protein) (crip) (cysteine-rich heart protein) (hcrhp). [swissprot;acc:p50238] Subtracted 5706.5 6245.55 539.05
hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [refseq;acc:nm_152794] Divided 5707.73 6249.1 1.09485
1008 chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] Subtracted 2554.89 3093.78 538.89
single-minded homolog 1. [swissprot;acc:p81133] Divided 5707.73 6249.1 1.09485
1009 heparin sulfate n-deacetylase/n-sulfotransferase (ec 2.8.2.-) (n- hsst) (n-heparin sulfate sulfotransferase) (glucosaminyl n- deacetylase/n-sulfotransferase). [swissprot;acc:p52849] Subtracted 5210.58 5749.33 538.75
synapsin iii. [swissprot;acc:o14994] Divided 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]
n-deacetylase/n-sulfotransferase (heparan glucosaminyl) 3. [refseq;acc:nm_004784] Subtracted 5210.58 5749.33 538.75
1011 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] Divided 5791.82 6340.86 1.0948
n-deacetylase/n-sulfotransferase 4. [refseq;acc:nm_022569] Subtracted 5210.58 5749.33 538.75
1012 actin binding lim protein 2. [refseq;acc:nm_032432] Divided 5791.82 6340.86 1.0948
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] Subtracted 5210.58 5749.33 538.75
1013 hairy/enhancer-of-split related with yrpw motif-like. [refseq;acc:nm_014571] Divided 5791.82 6340.86 1.0948
protein cdc27hs (cell division cycle protein 27 homolog) (h-nuc). [swissprot;acc:p30260] Subtracted 5210.58 5749.33 538.75
1014 synapsin ii. [swissprot;acc:q92777] Divided 5791.82 6340.86 1.0948
uridine kinase-like 1. [swissprot;acc:q9nwz5] Subtracted 5548.78 6086.89 538.11
1015 acetyl-coa carboxylase 2 (ec 6.4.1.2) (acc-beta) [includes: biotin carboxylase (ec 6.3.4.14)]. [swissprot;acc:o00763] 7237.39 7775.21 537.82
mitochondrial ribosome recycling factor. [refseq;acc:nm_138777] Divided 5791.82 6340.86 1.0948
1016 peroxisomal targeting signal 1 receptor (peroxismore receptor 1) (peroxisomal c-terminal targeting signal import receptor) (pts1-bp) (peroxin-5) (pts1 receptor). [swissprot;acc:p50542]
rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749] Subtracted 3889.27 4426.74 537.47
1017 hairy/enhancer-of-split related with yrpw motif 2; gridlock; hes-related repressor protein 1. [refseq;acc:nm_012259] Divided 5791.82 6340.86 1.0948
rac-gamma serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-gamma) (protein kinase akt-3) (protein kinase b, gamma) (pkb gamma) (stk-2). [swissprot;acc:q9y243] Subtracted 3889.27 4426.74 537.47
1018 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]
transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [swissprot;acc:q14469] Divided 5791.82 6340.86 1.0948
1019 delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [swissprot;acc:q13011]
nicotinate-nucleotide pyrophosphorylase [carboxylating] (ec 2.4.2.19) (quinolinate phosphoribosyltransferase [decarboxylating]) (qaprtase) (qprtase). [swissprot;acc:q15274] Subtracted 5704 6241.36 537.36
1020 actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313] Divided 5791.82 6340.86 1.0948
serine/threonine protein phosphatase 6 (ec 3.1.3.16) (pp6). [swissprot;acc:o00743] Subtracted 7234.61 7771.58 536.97
1021 sporulation-induced transcript 4-associated protein. [refseq;acc:nm_018312]
synapsin i (brain protein 4.1). [swissprot;acc:p17600] Divided 5791.82 6340.86 1.0948
1022 protein kinase clk2 (ec 2.7.1.-) (cdc-like kinase 2). [swissprot;acc:p49760] 6435.94 7045.75 1.09475
tetratricopeptide repeat protein 4 (my044 protein). [swissprot;acc:o95801] Subtracted 6783.78 7320.39 536.61
1023 acetyl-coa carboxylase 1 (ec 6.4.1.2) (acc-alpha) [includes: biotin carboxylase (ec 6.3.4.14)]. [swissprot;acc:q13085] 7232.14 7768.35 536.21
protein kinase clk3 (ec 2.7.1.-) (cdc-like kinase 3). [swissprot;acc:p49761] Divided 6435.02 7044.65 1.09474
1024 cysteine-rich protein 1 (cysteine-rich intestinal protein) (crip) (cysteine-rich heart protein) (hcrhp). [swissprot;acc:p50238] 5706.5 6245.55 1.09446
topoisomerase-related function protein 4-2. [refseq;acc:nm_022447] Subtracted 4725.28 5261.06 535.78
1025 nadph:adrenodoxin oxidoreductase, mitochondrial precursor (ec 1.18.1.2) (adrenodoxin reductase) (ar) (ferredoxin-nadp(+) reductase). [swissprot;acc:p22570] 5947.53 6481.56 534.03
phosphomannomutase 2 (ec 5.4.2.8) (pmm 2). [swissprot;acc:o15305] Divided 5511.96 6031.95 1.09434
1026 limbic system-associated membrane protein precursor (lsamp). [swissprot;acc:q13449] Subtracted 5396.36 5929.41 533.05
phosphomannomutase 1 (ec 5.4.2.8) (pmm 1) (pmmh-22). [swissprot;acc:q92871] Divided 5509.89 6029.29 1.09427
1027 opioid binding protein/cell adhesion molecule precursor (obcam) (opioid-binding cell adhesion molecule) (opcml). [swissprot;acc:q14982] Subtracted 5406.5 5939.42 532.92
s-adenosylmethionine synthetase gamma form (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-ii). [swissprot;acc:p31153] Divided 6123.15 6700.05 1.09422
1028 neurotrimin precursor (hnt). [swissprot;acc:q9p121] Subtracted 5413.63 5946.46 532.83
nicotinate-nucleotide pyrophosphorylase [carboxylating] (ec 2.4.2.19) (quinolinate phosphoribosyltransferase [decarboxylating]) (qaprtase) (qprtase). [swissprot;acc:q15274] Divided 5704 6241.36 1.09421
1029 beta-catenin (pro2286). [swissprot;acc:p35222] 5635.26 6166.09 1.0942
polymerase (dna directed) sigma; topoisomerase-related function protein 4-1; polymerase (dna-directed) sigma. [refseq;acc:nm_006999] Subtracted 4726.38 5258.95 532.57
1030 casein kinase i, epsilon isoform (ec 2.7.1.-) (cki-epsilon) (ckie). [swissprot;acc:p49674] Divided 5048.33 5523.85 1.09419
electron transfer flavoprotein alpha-subunit, mitochondrial precursor (alpha-etf). [swissprot;acc:p13804] Subtracted 7919.76 8452.01 532.25
1031 membrane protein expressed in epithelial-like lung adenocarcinoma. [refseq;acc:nm_024792] Divided 6136.99 6714.98 1.09418
peroxisomal membrane protein 2 (22 kda peroxisomal membrane protein). [swissprot;acc:q9nr77] Subtracted 6437.99 6969.67 531.68

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/