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 Value Type description 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
Value Type
description
red
green
network_comparison
763 Squared lifeguard; kiaa0950 protein. [refseq;acc:nm_012306] 21186.4 24698.3 1.16576
Rooted tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [swissprot;acc:q01658] 60.3269 64.3387 1.0665
764 Measured 6-phosphofructokinase, liver type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme b) (pfk-b). [swissprot;acc:p17858] 4250.18 4729.12 1.11269
Ranked u4/u6-associated rna splicing factor. [refseq;acc:nm_004698] 222.082 211.707 1.04901
Squared sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772] 21186.4 24698.3 1.16576
Rooted cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520] 63.5181 67.7402 1.06647
765 Measured polymerase (dna directed) sigma; topoisomerase-related function protein 4-1; polymerase (dna-directed) sigma. [refseq;acc:nm_006999] 4726.38 5258.95 1.11268
Ranked hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [swissprot;acc:q9y5r4] 229.045 218.343 1.04901
Squared sterol regulatory element binding protein-1 (srebp-1) (sterol regulatory element-binding transcription factor 1). [swissprot;acc:p36956] 21186.4 24698.3 1.16576
Rooted transforming protein rhoc (h9). [swissprot;acc:p08134] 63.5181 67.7402 1.06647
766 Measured ubiquitin-conjugating enzyme e2 variant 1 isoform b; dna-binding protein. [refseq;acc:nm_003349] 6691.93 7445.09 1.11255
Ranked protein tara (trio-associated repeat on actin) (hrihfb2122). [swissprot;acc:q9h2d6] 213.804 224.226 1.04875
Squared atp synthase gamma chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p36542] 24509.4 28571.6 1.16574
Rooted thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762] 63.5181 67.7402 1.06647
767 Measured utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [swissprot;acc:q16851] 6691.21 7444.22 1.11254
Ranked rho interacting protein 3. [refseq;acc:nm_015134] 213.803 224.224 1.04874
Squared atp synthase oligomycin sensitivity conferral protein, mitochondrial precursor (ec 3.6.3.14) (oscp). [swissprot;acc:p48047] 24509.4 28571.6 1.16574
Rooted 3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325] 63.5181 67.7402 1.06647
768 Measured 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] 6690.44 7443.29 1.11253
Ranked dnaj homolog subfamily b member 4 (heat shock 40 kda protein 1 homolog) (heat shock protein 40 homolog) (hsp40 homolog). [swissprot;acc:q9udy4] 210.946 221.225 1.04873
Squared eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] 12108.4 14114.6 1.16569
Rooted transforming protein rhoa (h12). [swissprot;acc:p06749] 63.5181 67.7402 1.06647
769 Measured 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] 5873.77 6532.44 1.11214
Ranked cab2. [refseq;acc:nm_033419] 210.946 221.225 1.04873
Squared n-acetylglutamate synthase. [refseq;acc:nm_153006] 20943 24412.8 1.16568
Rooted 60s ribosomal protein l39. [swissprot;acc:p02404] 55.6817 59.3786 1.06639
770 Measured 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] 5874.74 6533.34 1.11211
Ranked dnaj homolog subfamily b member 5 (heat shock protein hsp40-3) (heat shock protein cognate 40) (hsc40) (hsp40-2). [swissprot;acc:o75953] 210.946 221.225 1.04873
Squared fibulin-2 precursor. [swissprot;acc:p98095] 45189.6 52666.2 1.16545
Rooted 60s ribosomal protein l18a. [swissprot;acc:q02543] 55.6817 59.3786 1.06639
771 Measured apoptosis inhibitor 5; fibroblast growth factor 2-interacting factor 2; api5-like 1. [refseq;acc:nm_006595] 5874.74 6533.34 1.11211
Ranked 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] 210.946 221.225 1.04873
Squared glutaminyl-trna synthase (glutamine-hydrolyzing)-like 1. [refseq;acc:nm_018292] 24418 28453.7 1.16528
Rooted 40s ribosomal protein s19. [swissprot;acc:p39019] 55.6817 59.3786 1.06639
772 Measured sec13-related protein. [swissprot;acc:p55735] 5874.76 6533.36 1.11211
Ranked eukaryotic peptide chain release factor subunit 1 (erf1) (eukaryotic release factor 1) (tb3-1) (c11 protein). [swissprot;acc:p46055] 210.946 221.225 1.04873
Squared fatty-acid amide hydrolase (ec 3.1.-.-) (oleamide hydrolase) (anandamide amidohydrolase). [swissprot;acc:o00519] 24418 28453.7 1.16528
Rooted 60s ribosomal protein l31. [swissprot;acc:p12947] 55.6817 59.3786 1.06639
773 Measured 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] 5874.74 6533.34 1.11211
Ranked suppressor of actin mutations 2-like isoform b; dj1033b10.5. [refseq;acc:nm_022553] 210.946 221.225 1.04873
Squared coactosin-like protein. [swissprot;acc:q14019] 24418 28453.7 1.16528
Rooted serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] 127.967 120.003 1.06637
774 Measured yeast sec31p homolog. [refseq;acc:nm_014933] 5874.76 6533.36 1.11211
Ranked multiple coagulation factor deficiency 2; neural stem cell derived neuronal survival protein; multiple coagulation factor deficiency protein 2. [refseq;acc:nm_139279] 225.996 215.535 1.04854
Squared uracil-dna glycosylase, mitochondrial precursor (ec 3.2.2.-) (udg). [swissprot;acc:p13051] 24418 28453.7 1.16528
Rooted 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] 65.3248 69.648 1.06618
775 Measured 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] 5874.74 6533.33 1.11211
Ranked histone deacetylase 2 (hd2). [swissprot;acc:q92769] 226.003 215.541 1.04854
Squared 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] 24418 28453.7 1.16528
Rooted clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610] 62.2385 58.38 1.06609

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/