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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Value Type Rank Gene Network Comparison Type Interaction Map green description red Filtered network_comparison
Results: HTML CSV LaTeX Showing element 101 to 150 of 25824 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
Network Comparison Type
green
description
red
network_comparison
51 Divided 1390.33 neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] 779.167 1.78438
Subtracted 19479.8 fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] 23640.2 4160.4
52 Divided 1390.33 chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] 779.167 1.78438
Subtracted 19380.3 cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] 23422.4 4042.1
53 Divided 1390.33 cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519] 779.167 1.78438
Subtracted 19296.4 poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] 23326.5 4030.1
54 Divided 2651.88 deltex 2. [refseq;acc:nm_020892] 1618.84 1.63814
Subtracted 19288.8 exocyst complex component sec5. [swissprot;acc:q96kp1] 23316 4027.2
55 Divided 2662.12 deltex homolog 1; hdx-1. [refseq;acc:nm_004416] 1629.21 1.63399
Subtracted 19279.5 poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] 23303.1 4023.6
56 Divided 2664.55 t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492] 1631.67 1.63302
Subtracted 24908.5 ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] 20911 3997.5
57 Divided 2664.55 kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] 1631.67 1.63302
Subtracted 24908.5 ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] 20911 3997.5
58 Divided 2664.55 kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] 1631.67 1.63302
Subtracted 24908.5 ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] 20911 3997.5
59 Divided 2664.55 kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] 1631.67 1.63302
Subtracted 24908.5 anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] 20911 3997.5
60 Divided 2765.82 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 4489.19 1.6231
Subtracted 12889.1 ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] 16771.5 3882.4
61 Divided 2765.82 glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] 4489.19 1.6231
Subtracted 10307.5 beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] 6475.5 3832
62 Divided 2765.82 glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] 4489.19 1.6231
Subtracted 10307.5 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] 6475.5 3832
63 Divided 2765.82 myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] 4489.19 1.6231
Subtracted 10307.5 spermatogenesis associated 6. [refseq;acc:nm_019073] 6475.5 3832
64 Divided 2765.82 glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] 4489.19 1.6231
Subtracted 10307.5 amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] 6475.5 3832
65 Divided 2690.25 neuralized-like. [refseq;acc:nm_004210] 1657.68 1.6229
Subtracted 18702.6 cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] 22515.5 3812.9
66 Divided 3221.38 nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09] 1991.03 1.61795
Subtracted 14008 a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] 17757.5 3749.5
67 Divided 10307.5 beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] 6475.5 1.59177
Subtracted 14007.3 raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] 17756.5 3749.2
68 Divided 10307.5 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] 6475.5 1.59177
Subtracted 13995.7 cyclin g2. [swissprot;acc:q16589] 17738.6 3742.9
69 Divided 10307.5 spermatogenesis associated 6. [refseq;acc:nm_019073] 6475.5 1.59177
Subtracted 13995.6 cyclin g1 (cyclin g). [swissprot;acc:p51959] 17738.5 3742.9
70 Divided 10307.5 amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] 6475.5 1.59177
Subtracted 13995.7 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] 17738.5 3742.8
71 Divided 2945.26 serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007] 4556.78 1.54716
Subtracted 13995.7 serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, alpha isoform (pp2a, b subunit, b' alpha isoform) (pp2a, b subunit, b56 alpha isoform) (pp2a, b subunit, pr61 alpha isoform) (pp2a, b subunit, r5 alpha isoform). [swissprot;acc:q15172] 17738.5 3742.8
72 Divided 2945.28 uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] 4556.79 1.54715
Subtracted 13977.7 b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056] 17710.9 3733.2
73 Divided 2945.38 serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [swissprot;acc:q00005] 4556.83 1.54711
Subtracted 18560.4 serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] 22268.8 3708.4
74 Divided 2945.8 serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [swissprot;acc:q9y2t4] 4556.99 1.54694
Subtracted 24136.4 homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 20446.1 3690.3
75 Divided 2907.43 nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181] 1920.75 1.5137
Subtracted 24136.4 homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] 20446.1 3690.3

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/