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.


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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 5330 to 5379 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
2665 proto-oncogene tyrosine-protein kinase fer (ec 2.7.1.112) (p94-fer) (c-fer). [swissprot;acc:p16591] Divided 204.768 204.549 1.00107
2666 molybdenum cofactor synthesis protein 2 large subunit (molybdopterin synthase large subunit) (mpt synthase large subunit) (mocs2b) (moco1- b). [swissprot;acc:o96007] Subtracted 0.219
thioredoxin domain containing; thioredoxin-related transmembrane protein; thioredoxin domain-containing. [refseq;acc:nm_030755] Divided 210.136 209.911 1.00107
2667 anaphase-promoting complex subunit 10; anaphase-promoting complex 10. [refseq;acc:nm_014885] Subtracted 204.768 204.549 0.219
molybdenum cofactor synthesis protein 3 (molybdopterin synthase sulfurylase) (mpt synthase sulfurylase). [swissprot;acc:o95396] Divided 1.00107
2668 60s ribosomal protein l29 (cell surface heparin binding protein hip). [swissprot;acc:p47914] Subtracted 0.219
fuse binding protein 3 (fragment). [sptrembl;acc:q92946] Divided 217.176 216.944 1.00107
2669 glycerol-3-phosphate dehydrogenase [nad+], cytoplasmic (ec 1.1.1.8) (gpd-c) (gpdh-c). [swissprot;acc:p21695] 214.575 214.354 1.00103
proto-oncogene tyrosine-protein kinase fer (ec 2.7.1.112) (p94-fer) (c-fer). [swissprot;acc:p16591] Subtracted 204.768 204.549 0.219
2670 molybdenum cofactor synthesis protein 3 (molybdopterin synthase sulfurylase) (mpt synthase sulfurylase). [swissprot;acc:o95396]
transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116] Divided 144.391 144.538 1.00102
2671 rad9 homolog; cell cycle checkpoint control protein; rad9 homolog (s. pombe). [refseq;acc:nm_004584] Subtracted 216.372 216.588 0.216
similar to glucosamine-phosphate n-acetyltransferase (hypothetical protein flj33258). [sptrembl;acc:q96ek6] Divided 216.288 216.067 1.00102
2672 branched-chain amino acid aminotransferase, cytosolic (ec 2.6.1.42) (bcat(c)) (eca39 protein). [swissprot;acc:p54687] 210.957 210.741
Subtracted 0.216
2673 28s ribosomal protein s26, mitochondrial precursor (mrp-s26) (mrp- s13). [swissprot;acc:q9byn8] 214.893 215.108 0.215
rad9 homolog; cell cycle checkpoint control protein; rad9 homolog (s. pombe). [refseq;acc:nm_004584] Divided 216.372 216.588 1.001
2674 enhancer of rudimentary homolog. [swissprot;acc:q14259] Subtracted 214.893 215.108 0.215
glutamine synthetase (ec 6.3.1.2) (glutamate--ammonia ligase). [swissprot;acc:p15104] Divided 203.151 202.948 1.001
2675 28s ribosomal protein s26, mitochondrial precursor (mrp-s26) (mrp- s13). [swissprot;acc:q9byn8] 214.893 215.108
glutamine synthetase (ec 6.3.1.2) (glutamate--ammonia ligase). [swissprot;acc:p15104] Subtracted 203.151 202.948 0.203
2676 enhancer of rudimentary homolog. [swissprot;acc:q14259] Divided 214.893 215.108 1.001
proteasome subunit beta type 7 precursor (ec 3.4.25.1) (proteasome subunit z) (macropain chain z) (multicatalytic endopeptidase complex chain z). [swissprot;acc:q99436] Subtracted 219.829 219.629 0.2
2677 leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] Divided 144.412 144.553 1.00098
nuclease sensitive element binding protein 1 (y box binding protein-1) (y-box transcription factor) (yb-1) (ccaat-binding transcription factor i subunit a) (cbf-a) (enhancer factor i subunit a) (efi-a) (dna-binding protein b) (dbpb). [swissprot;acc:p16991] Subtracted 208.438 208.635 0.197
2678 dna-binding protein a (cold shock domain protein a) (single-strand dna binding protein nf-gmb). [swissprot;acc:p16989]
ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211] Divided 144.411 144.552 1.00098
2679 anaphase-promoting complex subunit 2; anaphase-promoting complex 2. [refseq;acc:nm_013366] 190.142 189.959 1.00096
germ cell specific y-box binding protein; contrin. [refseq;acc:nm_015982] Subtracted 208.438 208.635 0.197
2680 transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112] Divided 144.422 144.56 1.00096
ubiquitin-specific protease otubain 2. [refseq;acc:nm_023112] Subtracted 203.592 203.787 0.195
2681 branched-chain amino acid aminotransferase, mitochondrial precursor (ec 2.6.1.42) (bcat(m)) (placental protein 18) (pp18). [swissprot;acc:o15382] 210.939 210.755 0.184
ubiquitin-specific protease otubain 2. [refseq;acc:nm_023112] Divided 203.592 203.787 1.00096
2682 anaphase-promoting complex subunit 2; anaphase-promoting complex 2. [refseq;acc:nm_013366] Subtracted 190.142 189.959 0.183
transforming protein n-ras. [swissprot;acc:p01111] Divided 144.427 144.564 1.00095
2683 atp-citrate synthase (ec 2.3.3.8) (atp-citrate (pro-s-)-lyase) (citrate cleavage enzyme). [swissprot;acc:p53396] Subtracted 213.792 213.619 0.173
nuclease sensitive element binding protein 1 (y box binding protein-1) (y-box transcription factor) (yb-1) (ccaat-binding transcription factor i subunit a) (cbf-a) (enhancer factor i subunit a) (efi-a) (dna-binding protein b) (dbpb). [swissprot;acc:p16991] Divided 208.438 208.635 1.00095
2684 dna-binding protein a (cold shock domain protein a) (single-strand dna binding protein nf-gmb). [swissprot;acc:p16989]
peroxisomal 3,2-trans-enoyl-coa isomerase (ec 5.3.3.8) (dodecenoyl-coa delta-isomerase) (d3,d2-enoyl-coa isomerase) (dbi-related protein 1) (drs-1) (hepatocellular carcinoma-associated antigen 88). [swissprot;acc:o75521] Subtracted 194.557 194.392 0.165
2685 germ cell specific y-box binding protein; contrin. [refseq;acc:nm_015982] Divided 208.438 208.635 1.00095
signal recognition particle 54 kda protein (srp54). [swissprot;acc:p13624] Subtracted 215.545 215.384 0.161
2686 arp2/3 complex 34 kda subunit (p34-arc) (actin-related protein 2/3 complex subunit 2). [swissprot;acc:o15144] 225.081 225.232 0.151
proteasome subunit beta type 7 precursor (ec 3.4.25.1) (proteasome subunit z) (macropain chain z) (multicatalytic endopeptidase complex chain z). [swissprot;acc:q99436] Divided 219.829 219.629 1.00091
2687 branched-chain amino acid aminotransferase, mitochondrial precursor (ec 2.6.1.42) (bcat(m)) (placental protein 18) (pp18). [swissprot;acc:o15382] 210.939 210.755 1.00087
transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116] Subtracted 144.391 144.538 0.147
2688 aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [swissprot;acc:p55087] 188.191 188.046 0.145
peroxisomal 3,2-trans-enoyl-coa isomerase (ec 5.3.3.8) (dodecenoyl-coa delta-isomerase) (d3,d2-enoyl-coa isomerase) (dbi-related protein 1) (drs-1) (hepatocellular carcinoma-associated antigen 88). [swissprot;acc:o75521] Divided 194.557 194.392 1.00085
2689 aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181] Subtracted 188.193 188.048 0.145
atp-citrate synthase (ec 2.3.3.8) (atp-citrate (pro-s-)-lyase) (citrate cleavage enzyme). [swissprot;acc:p53396] Divided 213.792 213.619 1.00081
2690 aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [swissprot;acc:p55087] 188.191 188.046 1.00077

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/