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 2051 to 2100 of 33156 in total
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Value Type
Interaction Map
red
green
network_comparison
257 cln3 protein (battenin) (batten disease protein). [swissprot;acc:q13286] Rooted Low confidence 68.3669 72.2396 1.05665
dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656] Ranked High confidence 200.691 179.88 1.11569
glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840] Squared Low confidence 53244.4 48813.4 1.09077
huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] High confidence 15482.3 20162.4 1.30229
synaptojanin 1 (ec 3.1.3.36) (synaptic inositol-1,4,5-trisphosphate 5- phosphatase 1). [swissprot;acc:o43426] Measured Low confidence 8082.34 8579.93 1.06157
tropomyosin alpha 3 chain (tropomyosin 3) (tropomyosin gamma). [swissprot;acc:p06753] Ranked 201.316 192.404 1.04632
258 adp-ribosylation factor guanine nucleotide factor 6; hepatocellular carcinoma-associated antigen 67. [refseq;acc:nm_015310] Squared 50448.8 46264.1 1.09045
aflatoxin b1 aldehyde reductase 2 (ec 1.-.-.-) (afb1-ar 2). [swissprot;acc:o95154] Measured 9249.74 9818.95 1.06154
homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] High confidence 6417.33 7857.93 1.22449
huntingtin interacting protein 1 (hip-i). [swissprot;acc:o00291] Squared 76438 58889.7 1.29799
max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] Ranked 227.999 204.366 1.11564
thrombospondin 3 precursor. [swissprot;acc:p49746] Rooted 51.6132 45.8422 1.12589
tropomyosin 1 alpha chain (alpha-tropomyosin). [swissprot;acc:p09493] Ranked Low confidence 201.304 192.427 1.04613
ubiquitin-conjugating enzyme e2 g1 (ec 6.3.2.19) (ubiquitin-protein ligase g1) (ubiquitin carrier protein g1) (e217k) (ubc7). [swissprot;acc:q99462] Rooted 70.3765 74.3627 1.05664
259 goodpasture antigen-binding protein (ec 2.7.1.37) (gpbp) (collagen type iv alpha 3 binding protein) (star-related lipid transfer protein 11) (stard11) (start domain-containing protein 11). [swissprot;acc:q9y5p4] Squared High confidence 76360.8 58841.7 1.29773
max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] Ranked 227.999 204.37 1.11562
neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] Measured 6417.81 7852.52 1.22355
oligophrenin 1. [swissprot;acc:o60890] Low confidence 6428.7 6824.22 1.06152
parafibromin. [refseq;acc:nm_024529] Rooted 67.6012 71.4286 1.05662
trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] Ranked 211.794 202.482 1.04599
trs85 homolog. [swissprot;acc:q9y2l5] Squared 50448.8 46264.1 1.09045
tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] Rooted High confidence 58.2964 65.5926 1.12516
260 aflatoxin b1 aldehyde reductase 1 (ec 1.-.-.-) (afb1-ar 1) (aldoketoreductase 7). [swissprot;acc:o43488] Measured Low confidence 9246.23 9814.59 1.06147
ankyrin repeat domain protein 7 (testis-specific protein tsa806). [swissprot;acc:q92527] Ranked 216.855 207.34 1.04589
c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] High confidence 219.421 196.978 1.11394
calcineurin b subunit isoform 1 (protein phosphatase 2b regulatory subunit 1) (protein phosphatase 3 regulatory subunit b alpha isoform 1). [swissprot;acc:p06705] Rooted Low confidence 67.4201 71.2324 1.05655
huntingtin interacting protein 1 related (hip1-related) (hip 12). [swissprot;acc:o75146] Squared High confidence 76296.4 58801.6 1.29752
leukemia-associated protein with a cxxc domain. [sptrembl;acc:q8nfu7] Low confidence 50448.8 46264.1 1.09045
multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] Rooted High confidence 59.0951 66.4332 1.12417
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Measured 4244.95 5193.42 1.22343
261 adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109] Low confidence 8837.18 9379.17 1.06133
ba526d8.2 (novel protein similar to kiaa1074). [sptrembl;acc:q9h560] Ranked 216.845 207.333 1.04588
heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042] High confidence 219.421 196.978 1.11394
pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [swissprot;acc:p11498] Squared 48127.9 62245.6 1.29334
ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] Rooted 62.3337 70.0738 1.12417
sec7 homolog; adp-ribosylation factor guanine nucleotide-exchange factor 6. [refseq;acc:nm_012455] Squared Low confidence 50448.8 46264.1 1.09045
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Measured High confidence 4247.36 5192.61 1.22255
trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] Rooted Low confidence 67.7274 71.5408 1.05631
262 ariadne-1 protein homolog (ari-1) (ubiquitin-conjugating enzyme e2- binding protein 1) (ubch7-binding protein) (ubcm4-interacting protein) (hhari) (h7-ap2) (hussy-27) (mop-6). [swissprot;acc:q9y4x5] Squared 56512.1 51843.6 1.09005
breast cancer antigen ny-br-1. [refseq;acc:nm_052997] Ranked 216.842 207.332 1.04587
cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693] Measured High confidence 24896.4 20431.7 1.21852
heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041] Ranked 219.421 196.978 1.11394
neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] Squared 26157.6 20236.2 1.29261
oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [swissprot;acc:q9una1] Measured Low confidence 6440.08 6834.37 1.06122
polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] Rooted High confidence 59.4073 66.7002 1.12276
udp-glucose 4-epimerase (ec 5.1.3.2) (galactowaldenase) (udp- galactose 4-epimerase). [swissprot;acc:q14376] Low confidence 70.6152 74.5839 1.0562
263 adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306] Squared High confidence 26157.6 20236.2 1.29261
coiled-coil protein bicd2; homolog of drosophila bicaudal d. [refseq;acc:nm_015250] Rooted Low confidence 70.75 74.7143 1.05603
heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043] Ranked High confidence 219.421 196.978 1.11394
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Measured Low confidence 7424.14 7877.49 1.06106

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/