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 6258 to 6307 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
783 aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [swissprot;acc:p55087] Rooted Subtracted 82.3421 86.4631 4.121
coactosin-like protein. [swissprot;acc:q14019] Squared 24418 28453.7 4035.7
cytochrome b5 reductase b5r.2. [refseq;acc:nm_016229] Measured 6289.72 6911.96 622.24
hepatitis c virus core-binding protein 6; cervical cancer oncogene 3. [refseq;acc:nm_023934] Squared Divided 27407.7 31927.7 1.16492
phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941] Rooted 62.2361 58.3858 1.06595
translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598] Ranked 224.385 235.131 1.04789
vacuolar atp synthase subunit b, brain isoform (ec 3.6.3.14) (v-atpase b2 subunit) (vacuolar proton pump b isoform 2) (endomembrane proton pump 58 kda subunit) (ho57). [swissprot;acc:p21281] Measured 5874.78 6533.37 1.1121
784 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] Rooted Subtracted 82.3408 86.4617 4.1209
cytochrome b5 reductase 1 (b5r.1). [refseq;acc:nm_016243] Measured 6289.72 6911.96 622.24
dc11 protein. [refseq;acc:nm_020186] Squared Divided 27407.7 31927.7 1.16492
dna repair protein rad52 homolog. [swissprot;acc:p43351] Rooted 62.2361 58.3858 1.06595
hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [swissprot;acc:p51858] Ranked Subtracted 231.734 222.222 9.512
polyglutamine binding protein 1; nuclear protein containing ww domain 38 kd. [refseq;acc:nm_005710] Divided 224.385 235.131 1.04789
uracil-dna glycosylase, mitochondrial precursor (ec 3.2.2.-) (udg). [swissprot;acc:p13051] Squared Subtracted 24418 28453.7 4035.7
vacuolar atp synthase subunit e (ec 3.6.3.14) (v-atpase e subunit) (vacuolar proton pump e subunit) (v-atpase 31 kda subunit) (p31). [swissprot;acc:p36543] Measured Divided 5874.77 6533.36 1.1121
785 amyloid beta precursor protein-binding protein 1; amyloid protein-binding protein 1. [refseq;acc:nm_003905] Squared 27407.7 31927.7 1.16492
aquaporin 5. [swissprot;acc:p55064] Rooted Subtracted 82.3414 86.4623 4.1209
clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675] Divided 62.2332 58.3925 1.06577
hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [swissprot;acc:q9y5r4] Measured 4997 5557.17 1.1121
nadh-cytochrome b5 reductase (ec 1.6.2.2) (b5r). [swissprot;acc:p00387] Subtracted 6289.72 6911.96 622.24
neuroepithelial cell transforming gene 1; guanine nucleotide regulatory protein (oncogene); rho guanine nucleotide exchange factor (gef) 8. [refseq;acc:nm_005863] Ranked Divided 244.447 233.508 1.04685
probable glutamyl-trna(gln) amidotransferase subunit b, mitochondrial precursor (ec 6.3.5.-) (glu-adt subunit b) (cytochrome oxidase assembly factor pet112 homolog). [swissprot;acc:o75879] Squared Subtracted 24418 28453.7 4035.7
pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [refseq;acc:nm_138574] Ranked 231.734 222.222 9.512
786 14.5 kda translational inhibitor protein (p14.5) (uk114 antigen homolog). [swissprot;acc:p52758] Squared 25739.7 29768.2 4028.5
40s ribosomal protein s9. [swissprot;acc:p46781] Rooted Divided 52.0101 48.813 1.0655
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 1.16492
arginine/serine-rich splicing factor 10 (transformer-2-beta) (htra2- beta) (transformer 2 protein homolog) (silica-induced protein 41) (ra301). [swissprot;acc:q15815] Measured Subtracted 6499.89 7121.77 621.88
lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [swissprot;acc:p30301] Rooted 82.3406 86.4614 4.1208
probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196] Ranked 231.734 222.222 9.512
pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [swissprot;acc:p11498] Measured Divided 9304.83 10347.3 1.11204
rho guanine nucleotide exchange factor 3; rhogef protein; 59.8 kda protein; exchange factor found in platelets and leukemic and neuronal tissues, xpln. [refseq;acc:nm_019555] Ranked 244.447 233.508 1.04685
787 aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [swissprot;acc:p29972] Rooted Subtracted 82.3212 86.4383 4.1171
biotin--protein ligase (ec 6.3.4.-) (biotin apo-protein ligase) [includes: biotin--[methylmalonyl-coa-carboxyltransferase] ligase (ec 6.3.4.9); biotin--[propionyl-coa-carboxylase [atp-hydrolyzing]] ligase (ec 6.3.4.10) (holocarboxylase synthetase) (hcs); biotin--[methylcrotonoyl-coa-carboxylase] ligase (ec 6.3.4.11); biotin--[acetyl-coa-carboxylase] ligase (ec 6.3.4.15)]. [swissprot;acc:p50747] Squared 24183.6 28211.1 4027.5
coatomer alpha subunit (alpha-coat protein) (alpha-cop) (hepcop) (hep-cop) [contains: xenin (xenopsin-related peptide); proxenin]. [swissprot;acc:p53621] Measured 9720.64 9099.1 621.54
down-regulated in metastasis. [refseq;acc:nm_014503] Ranked Divided 244.447 233.508 1.04685
rw1 protein (fragment). [swissprot;acc:q92545] Subtracted 231.734 222.222 9.512
uba/ubx 33.3 kda protein. [swissprot;acc:q04323] Rooted Divided 64.5489 68.7769 1.0655
ubiquitin-activating enzyme e1c (uba3 homolog, yeast); ubiquitin-activating enzyme e1c (homologous to yeast uba3). [refseq;acc:nm_003968] Squared 27407.7 31927.7 1.16492
vacuolar proton translocating atpase 116 kda subunit a isoform 2 (v-atpase 116-kda isoform a2) (tj6). [swissprot;acc:q9y487] Measured 5890.49 6547.9 1.11161
788 ero1-like. [refseq;acc:nm_014584] Rooted 64.5489 68.7769 1.0655
eukaryotic translation initiation factor 3 subunit 9 (eif-3 eta) (eif3 p116) (eif3 p110) (eif3b). [swissprot;acc:p55884] Subtracted 52.7523 56.8686 4.1163
hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] Ranked Divided 138.705 132.538 1.04653
histone deacetylase 9 (hd9) (hd7b) (hd7). [swissprot;acc:q9ukv0] Squared Subtracted 28579.3 32606.8 4027.5
loh1cr12. [refseq;acc:nm_058169] Ranked 230.087 220.579 9.508
transformer-2 protein homolog (tra-2 alpha). [swissprot;acc:q13595] Measured 6472.38 7092.65 620.27
ubiquitin-activating enzyme e1 (a1s9 protein). [swissprot;acc:p22314] Squared Divided 27407.7 31927.7 1.16492
vacuolar proton translocating atpase 116 kda subunit a isoform 3 (v- atpase 116-kda isoform a3) (osteoclastic proton pump 116 kda subunit) (oc-116 kda) (oc116) (t-cell immune regulator 1) (t cell immune response cdna7 protein) (tirc7). [swissprot;acc:q13488] Measured 5890.41 6547.81 1.11161
789 40s ribosomal protein sa (p40) (34/67 kda laminin receptor) (colon carcinoma laminin-binding protein) (nem/1chd4) (multidrug resistance- associated protein mgr1-ag). [swissprot;acc:p08865] Ranked 224.244 234.511 1.04578
atpase, h+ transporting, lysosomal v0 subunit a isoform 4; vacuolar proton pump 116 kda accessory subunit; vacuolar proton pump, subunit 2; h(+)-transporting two-sector atpase, noncatalytic accessory protein 1b; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1b; renal tubular acidosis; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 2 (38kd). [refseq;acc:nm_020632] Measured 5890.59 6547.99 1.1116
calcium-binding mitochondrial carrier protein aralar1 (solute carrier family 25, member 12). [swissprot;acc:o75746] Squared 27407.7 31927.7 1.16492

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/