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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Gene Rank Value Type green red description Network Comparison Type Interaction Map Filtered network_comparison
Results: HTML CSV LaTeX Showing element 501 to 550 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
green
red
description
Network Comparison Type
network_comparison
63 Squared 124480 189976 serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129] Subtracted 65496
129762 219048 melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Divided 1.68808
Rooted 31.7576 43.4554 kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193] 1.36835
120.823 137.446 melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Subtracted 16.623
64 Measured 2765.82 4489.19 glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] Divided 1.6231
10307.5 6475.5 amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] Subtracted 3832
Ranked 204.309 260.532 ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511] 56.223
336.159 266.868 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] Divided 1.25965
Squared 81169.7 144940 cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Subtracted 63770.3
129762 219048 melanoma antigen, family b, 6. [refseq;acc:nm_173523] Divided 1.68808
Rooted 47.2654 63.8686 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 1.35128
120.823 137.446 melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Subtracted 16.623
65 Measured 2690.25 1657.68 neuralized-like. [refseq;acc:nm_004210] Divided 1.6229
18702.6 22515.5 cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] Subtracted 3812.9
Ranked 243.678 187.457 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] 56.221
336.077 267.136 guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] Divided 1.25807
Squared 81155 144912 microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] Subtracted 63757
129762 219048 melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Divided 1.68808
Rooted 47.2654 63.8686 glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] 1.35128
120.823 137.446 melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1] Subtracted 16.623
66 Measured 3221.38 1991.03 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 1.61795
14008 17757.5 a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] Subtracted 3749.5
Ranked 243.678 187.458 uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] 56.22
336.077 267.136 guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] Divided 1.25807
Squared 81154.7 144911 microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Subtracted 63756.3
129762 219048 melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] Divided 1.68808
Rooted 47.2654 63.8686 glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] 1.35128
120.823 137.446 trophinin. [swissprot;acc:q12816] Subtracted 16.623
67 Measured 10307.5 6475.5 beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] Divided 1.59177
14007.3 17756.5 raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] Subtracted 3749.2
Ranked 243.677 187.458 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] 56.219
336.075 267.14 guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] Divided 1.25805
Squared 81136.5 144876 cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Subtracted 63739.5
129762 219048 melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] Divided 1.68808
Rooted 47.2654 63.8686 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] Subtracted 16.6032
myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] Divided 1.35128
68 Measured 10307.5 6475.5 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] 1.59177
13995.7 17738.6 cyclin g2. [swissprot;acc:q16589] Subtracted 3742.9
Ranked 243.673 187.462 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] 56.211
336.075 267.139 guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] Divided 1.25805
Squared 78454.6 139741 gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] Subtracted 61286.4
129762 219048 melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] Divided 1.68808
Rooted 47.2654 63.8686 glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] Subtracted 16.6032
glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] Divided 1.35128
69 Measured 10307.5 6475.5 spermatogenesis associated 6. [refseq;acc:nm_019073] 1.59177
13995.6 17738.5 cyclin g1 (cyclin g). [swissprot;acc:p51959] Subtracted 3742.9
Ranked 228.934 284.753 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] 55.819
336.075 267.14 guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488] Divided 1.25805
Squared 118639 178263 pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] Subtracted 59624
129762 219048 melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] Divided 1.68808

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/