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 113 to 162 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
57 kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] Divided 1631.67 2664.55 1.63302
ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] Subtracted 20911 24908.5 3997.5
58 kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] Divided 1631.67 2664.55 1.63302
ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] Subtracted 20911 24908.5 3997.5
59 anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685]
kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] Divided 1631.67 2664.55 1.63302
60 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 4489.19 2765.82 1.6231
ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] Subtracted 16771.5 12889.1 3882.4
61 beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] 6475.5 10307.5 3832
glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] Divided 4489.19 2765.82 1.6231
62 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] Subtracted 6475.5 10307.5 3832
glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] Divided 4489.19 2765.82 1.6231
63 myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7]
spermatogenesis associated 6. [refseq;acc:nm_019073] Subtracted 6475.5 10307.5 3832
64 amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]
glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] Divided 4489.19 2765.82 1.6231
65 cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] Subtracted 22515.5 18702.6 3812.9
neuralized-like. [refseq;acc:nm_004210] Divided 1657.68 2690.25 1.6229
66 a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] Subtracted 17757.5 14008 3749.5
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] Divided 1991.03 3221.38 1.61795
67 beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] 6475.5 10307.5 1.59177
raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] Subtracted 17756.5 14007.3 3749.2
68 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] Divided 6475.5 10307.5 1.59177
cyclin g2. [swissprot;acc:q16589] Subtracted 17738.6 13995.7 3742.9
69 cyclin g1 (cyclin g). [swissprot;acc:p51959] 17738.5 13995.6
spermatogenesis associated 6. [refseq;acc:nm_019073] Divided 6475.5 10307.5 1.59177
70 amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]
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] Subtracted 17738.5 13995.7 3742.8
71 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] Divided 4556.78 2945.26 1.54716
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] Subtracted 17738.5 13995.7 3742.8
72 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 13977.7 3733.2
uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] Divided 4556.79 2945.28 1.54715
73 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 2945.38 1.54711
serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] Subtracted 22268.8 18560.4 3708.4
74 homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 20446.1 24136.4 3690.3
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] Divided 4556.99 2945.8 1.54694
75 homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] Subtracted 20446.1 24136.4 3690.3
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] Divided 1920.75 2907.43 1.5137
76 homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Subtracted 20446.1 24136.4 3690.3
serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [swissprot;acc:p30154] Divided 4599.26 3058.57 1.50373
77 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Subtracted 20446.1 24136.4 3690.3
serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [swissprot;acc:p30153] Divided 4612.39 3093.6 1.49095
78 cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] 4800.81 7132.71 1.48573
homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Subtracted 20446.1 24136.4 3690.3
79 homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067]
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] Divided 3074.57 4567.51 1.48558
80 homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] Subtracted 20446.1 24136.4 3690.3
nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] Divided 4133.47 5945.32 1.43834
81 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Subtracted 20446.1 24136.4 3690.3
nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] Divided 4136.36 5943.56 1.43691

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/