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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Network Comparison Type Rank Gene description Value Type Interaction Map red Filtered green network_comparison
Results: HTML CSV LaTeX Showing element 3680 to 3729 of 66312 in total
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Value Type
Interaction Map
red
green
network_comparison
460 ubiquitin-conjugating enzyme e2 variant 1 isoform b; dna-binding protein. [refseq;acc:nm_003349] Squared High confidence 29547.4 35683.5 1.20767
461 40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880] Rooted 50.6156 46.2239 1.09501
amyloid beta precursor protein-binding protein 1; amyloid protein-binding protein 1. [refseq;acc:nm_003905] Low confidence 72.6285 75.9695 1.046
grb2-related adaptor protein. [swissprot;acc:q13588] Measured High confidence 5986.65 6865.68 1.14683
huntingtin interacting protein c. [refseq;acc:nm_012272] Ranked Low confidence 201.429 194.776 1.03416
insulin-degrading enzyme (ec 3.4.24.56) (insulysin) (insulinase) (insulin protease). [swissprot;acc:p14735] Squared 49247 46248 1.06485
krueppel-like factor 5 (intestinal-enriched krueppel-like factor) (colon krueppel-like factor) (transcription factor bteb2) (basic transcription element binding protein 2) (bte-binding protein 2) (gc box binding protein 2). [swissprot;acc:q13887] Ranked High confidence 223.648 207.62 1.0772
pr-domain zinc finger protein 12. [swissprot;acc:q9h4q4] Measured Low confidence 8864.55 9309.3 1.05017
utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [swissprot;acc:q16851] Squared High confidence 29544.1 35678.3 1.20763
462 40s ribosomal protein s3. [swissprot;acc:p23396] Rooted 50.6274 46.236 1.09498
g10 protein homolog (edg-2). [swissprot;acc:p41223] Low confidence 71.7173 75.0143 1.04597
large neutral amino acids transporter small subunit 1 (l-type amino acid transporter 1) (4f2 light chain) (4f2 lc) (4f2lc) (cd98 light chain) (integral membrane protein e16) (hlat1). [swissprot;acc:q01650] Ranked 201.466 194.819 1.03412
mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390] High confidence 254.434 236.224 1.07709
pr-domain zinc finger protein 7. [swissprot;acc:q9nqw5] Measured Low confidence 8864.53 9309.27 1.05017
ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858] High confidence 11383.2 9926.61 1.14674
ring1 and yy1 binding protein; ring1 interactor rybp; yy1 and e4tf1 associated factor 1; apoptin-associating protein 1. [refseq;acc:nm_012234] Squared Low confidence 40888.1 38402 1.06474
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] High confidence 29540.4 35672.6 1.20759
463 aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [swissprot;acc:p55087] Measured Low confidence 8844.87 9288.13 1.05011
atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1] High confidence 3720.18 4264.46 1.1463
calcium-transporting atpase type 2c, member 1 (ec 3.6.3.8) (atpase 2c1) (atp-dependent ca(2+) pump pmr1) (hussy-28). [swissprot;acc:p98194] Squared 25533.3 30810.8 1.20669
dna-directed rna polymerases iii 39 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c39 subunit). [swissprot;acc:q9h1d9] Ranked 238.921 257.327 1.07704
paired mesoderm homeobox protein 1 (prx-1) (paired related homeobox protein 1) (homeobox protein phox1). [swissprot;acc:p54821] Low confidence 194.41 201.036 1.03408
rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749] Rooted High confidence 50.2317 55.0025 1.09498
stip1 homology and u-box containing protein 1; serologically defined colon cancer antigen 7; carboxy terminus of hsp70p-interacting protein; heat shock protein a binding protein 2 (c-terminal). [refseq;acc:nm_005861] Low confidence 72.0791 75.3921 1.04596
yy1 associated factor 2. [refseq;acc:nm_005748] Squared 40888.1 38402 1.06474
464 ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [sptrembl;acc:q96lh6] Ranked High confidence 210.578 226.764 1.07686
histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] Measured 4858.96 5568.85 1.1461
homeobox protein prh (hematopoietically expressed homeobox) (homeobox protein hex). [swissprot;acc:q03014] Squared 54726.7 45358.5 1.20654
pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] Measured Low confidence 7847.59 8240.61 1.05008
rac-gamma serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-gamma) (protein kinase akt-3) (protein kinase b, gamma) (pkb gamma) (stk-2). [swissprot;acc:q9y243] Rooted High confidence 50.2317 55.0025 1.09498
ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] Squared Low confidence 51553.8 54890.2 1.06472
rna polymerase ii elongation factor ell2. [swissprot;acc:o00472] Ranked 198.618 205.369 1.03399
rna-binding protein. [refseq;acc:nm_019027] Rooted 71.0964 74.3634 1.04595
465 apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] 71.0968 74.3631 1.04594
c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] Ranked 207.812 200.994 1.03392
deltex 2. [refseq;acc:nm_020892] Squared 43977.9 41304.5 1.06472
neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] Ranked High confidence 248.152 267.226 1.07686
rac-beta serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-beta) (protein kinase akt-2) (protein kinase b, beta) (pkb beta). [swissprot;acc:p31751] Rooted 50.2317 55.0025 1.09498
serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [swissprot;acc:q16537] Measured Low confidence 7580.97 7960.37 1.05005
transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094] High confidence 3847.31 4409.22 1.14605
trna isopentenylpyrophosphate transferase. [refseq;acc:nm_017646] Squared 25310.2 30537 1.20651
466 adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306] Ranked 248.152 267.226 1.07686
heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042] Low confidence 207.812 200.994 1.03392
lu1 protein. [refseq;acc:nm_032512] Squared 46292.3 43478.2 1.06472
probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] High confidence 25513.6 30779.5 1.2064
rna 3'-terminal phosphate cyclase-like protein (hspc338). [swissprot;acc:q9y2p8] Rooted Low confidence 71.0763 74.3418 1.04594
transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] Measured High confidence 3847.31 4409.22 1.14605
vav-3 protein. [swissprot;acc:q9ukw4] Rooted 66.089 72.3555 1.09482
yippee-like protein 2 (digeorge syndrome-related protein fksg4). [swissprot;acc:q96qa6] Measured Low confidence 8941.56 9388.99 1.05004
467 40s ribosomal protein s5. [swissprot;acc:p46782] Rooted High confidence 50.4649 46.1093 1.09446

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/