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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Gene Rank description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 3051 to 3100 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
763 putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [swissprot;acc:q9y5n5] Ranked 228.78 218.091 1.04901
tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [swissprot;acc:q01658] Rooted 60.3269 64.3387 1.0665
764 6-phosphofructokinase, liver type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme b) (pfk-b). [swissprot;acc:p17858] Measured 4250.18 4729.12 1.11269
cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520] Rooted 63.5181 67.7402 1.06647
sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772] Squared 21186.4 24698.3 1.16576
u4/u6-associated rna splicing factor. [refseq;acc:nm_004698] Ranked 222.082 211.707 1.04901
765 hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [swissprot;acc:q9y5r4] 229.045 218.343
polymerase (dna directed) sigma; topoisomerase-related function protein 4-1; polymerase (dna-directed) sigma. [refseq;acc:nm_006999] Measured 4726.38 5258.95 1.11268
sterol regulatory element binding protein-1 (srebp-1) (sterol regulatory element-binding transcription factor 1). [swissprot;acc:p36956] Squared 21186.4 24698.3 1.16576
transforming protein rhoc (h9). [swissprot;acc:p08134] Rooted 63.5181 67.7402 1.06647
766 atp synthase gamma chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p36542] Squared 24509.4 28571.6 1.16574
protein tara (trio-associated repeat on actin) (hrihfb2122). [swissprot;acc:q9h2d6] Ranked 213.804 224.226 1.04875
thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762] Rooted 63.5181 67.7402 1.06647
ubiquitin-conjugating enzyme e2 variant 1 isoform b; dna-binding protein. [refseq;acc:nm_003349] Measured 6691.93 7445.09 1.11255
767 3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325] Rooted 63.5181 67.7402 1.06647
atp synthase oligomycin sensitivity conferral protein, mitochondrial precursor (ec 3.6.3.14) (oscp). [swissprot;acc:p48047] Squared 24509.4 28571.6 1.16574
rho interacting protein 3. [refseq;acc:nm_015134] Ranked 213.803 224.224 1.04874
utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [swissprot;acc:q16851] Measured 6691.21 7444.22 1.11254
768 dnaj homolog subfamily b member 4 (heat shock 40 kda protein 1 homolog) (heat shock protein 40 homolog) (hsp40 homolog). [swissprot;acc:q9udy4] Ranked 210.946 221.225 1.04873
eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] Squared 12108.4 14114.6 1.16569
transforming protein rhoa (h12). [swissprot;acc:p06749] Rooted 63.5181 67.7402 1.06647
ubiquitin-conjugating enzyme e2 variant 2; 1 alpha,25-dihydroxyvitamin d3-inducible; enterocyte differentiation promoting factor; methyl methanesulfonate sensitive 2, s. cerevisiae, homolog of. [refseq;acc:nm_003350] Measured 6690.44 7443.29 1.11253
769 60s ribosomal protein l39. [swissprot;acc:p02404] Rooted 55.6817 59.3786 1.06639
cab2. [refseq;acc:nm_033419] Ranked 210.946 221.225 1.04873
n-acetylglutamate synthase. [refseq;acc:nm_153006] Squared 20943 24412.8 1.16568
vacuolar atp synthase subunit f (ec 3.6.3.14) (v-atpase f subunit) (vacuolar proton pump f subunit) (v-atpase 14 kda subunit). [swissprot;acc:q16864] Measured 5873.77 6532.44 1.11214
770 60s ribosomal protein l18a. [swissprot;acc:q02543] Rooted 55.6817 59.3786 1.06639
dnaj homolog subfamily b member 5 (heat shock protein hsp40-3) (heat shock protein cognate 40) (hsc40) (hsp40-2). [swissprot;acc:o75953] Ranked 210.946 221.225 1.04873
fibulin-2 precursor. [swissprot;acc:p98095] Squared 45189.6 52666.2 1.16545
vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [swissprot;acc:o95670] Measured 5874.74 6533.34 1.11211
771 40s ribosomal protein s19. [swissprot;acc:p39019] Rooted 55.6817 59.3786 1.06639
apoptosis inhibitor 5; fibroblast growth factor 2-interacting factor 2; api5-like 1. [refseq;acc:nm_006595] Measured 5874.74 6533.34 1.11211
dnaj homolog subfamily b member 1 (heat shock 40 kda protein 1) (heat shock protein 40) (hsp40) (dnaj protein homolog 1) (hdj-1). [swissprot;acc:p25685] Ranked 210.946 221.225 1.04873
glutaminyl-trna synthase (glutamine-hydrolyzing)-like 1. [refseq;acc:nm_018292] Squared 24418 28453.7 1.16528
772 60s ribosomal protein l31. [swissprot;acc:p12947] Rooted 55.6817 59.3786 1.06639
eukaryotic peptide chain release factor subunit 1 (erf1) (eukaryotic release factor 1) (tb3-1) (c11 protein). [swissprot;acc:p46055] Ranked 210.946 221.225 1.04873
fatty-acid amide hydrolase (ec 3.1.-.-) (oleamide hydrolase) (anandamide amidohydrolase). [swissprot;acc:o00519] Squared 24418 28453.7 1.16528
sec13-related protein. [swissprot;acc:p55735] Measured 5874.76 6533.36 1.11211
773 coactosin-like protein. [swissprot;acc:q14019] Squared 24418 28453.7 1.16528
serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] Rooted 127.967 120.003 1.06637
suppressor of actin mutations 2-like isoform b; dj1033b10.5. [refseq;acc:nm_022553] Ranked 210.946 221.225 1.04873
vacuolar atp synthase subunit g 3 (ec 3.6.3.14) (v-atpase g subunit 3) (vacuolar proton pump g subunit 3) (v-atpase 13 kda subunit 3). [swissprot;acc:q96lb4] Measured 5874.74 6533.34 1.11211
774 dolichol-phosphate mannosyltransferase (ec 2.4.1.83) (dolichol- phosphate mannose synthase) (dolichyl-phosphate beta-d- mannosyltransferase) (mannose-p-dolichol synthase) (mpd synthase) (dpm synthase). [swissprot;acc:o60762] Rooted 65.3248 69.648 1.06618
multiple coagulation factor deficiency 2; neural stem cell derived neuronal survival protein; multiple coagulation factor deficiency protein 2. [refseq;acc:nm_139279] Ranked 225.996 215.535 1.04854
uracil-dna glycosylase, mitochondrial precursor (ec 3.2.2.-) (udg). [swissprot;acc:p13051] Squared 24418 28453.7 1.16528
yeast sec31p homolog. [refseq;acc:nm_014933] Measured 5874.76 6533.36 1.11211
775 clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610] Rooted 62.2385 58.38 1.06609
histone deacetylase 2 (hd2). [swissprot;acc:q92769] Ranked 226.003 215.541 1.04854
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 24418 28453.7 1.16528
vacuolar atp synthase subunit g 1 (ec 3.6.3.14) (v-atpase g subunit 1) (vacuolar proton pump g subunit 1) (v-atpase 13 kda subunit 1) (vacuolar atp synthase subunit m16). [swissprot;acc:o75348] Measured 5874.74 6533.33 1.11211

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/