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 Network Comparison Type Value Type description green Interaction Map red Filtered network_comparison
Results: HTML CSV LaTeX Showing element 501 to 550 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Network Comparison Type
Value Type
description
green
red
network_comparison
63 Subtracted Measured spermatogenesis associated 6. [refseq;acc:nm_019073] 10307.5 6475.5 3832
Ranked nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952] 204.309 260.532 56.223
Squared serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129] 124480 189976 65496
Rooted melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] 120.823 137.446 16.623
64 Divided Measured glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] 2765.82 4489.19 1.6231
Ranked guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] 336.159 266.868 1.25965
Squared melanoma antigen, family b, 6. [refseq;acc:nm_173523] 129762 219048 1.68808
Rooted 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 47.2654 63.8686 1.35128
Subtracted Measured amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] 10307.5 6475.5 3832
Ranked 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] 204.309 260.532 56.223
Squared cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] 81169.7 144940 63770.3
Rooted melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] 120.823 137.446 16.623
65 Divided Measured neuralized-like. [refseq;acc:nm_004210] 2690.25 1657.68 1.6229
Ranked guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] 336.077 267.136 1.25807
Squared melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] 129762 219048 1.68808
Rooted glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] 47.2654 63.8686 1.35128
Subtracted Measured cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] 18702.6 22515.5 3812.9
Ranked 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] 243.678 187.457 56.221
Squared microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] 81155 144912 63757
Rooted 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] 120.823 137.446 16.623
66 Divided Measured 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] 3221.38 1991.03 1.61795
Ranked guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] 336.077 267.136 1.25807
Squared melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] 129762 219048 1.68808
Rooted glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] 47.2654 63.8686 1.35128
Subtracted Measured a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] 14008 17757.5 3749.5
Ranked uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] 243.678 187.458 56.22
Squared microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] 81154.7 144911 63756.3
Rooted trophinin. [swissprot;acc:q12816] 120.823 137.446 16.623
67 Divided Measured beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] 10307.5 6475.5 1.59177
Ranked guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] 336.075 267.14 1.25805
Squared melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] 129762 219048 1.68808
Rooted myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] 47.2654 63.8686 1.35128
Subtracted Measured raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] 14007.3 17756.5 3749.2
Ranked 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] 243.677 187.458 56.219
Squared cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 81136.5 144876 63739.5
Rooted 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 47.2654 63.8686 16.6032
68 Divided Measured beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] 10307.5 6475.5 1.59177
Ranked guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] 336.075 267.139 1.25805
Squared melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] 129762 219048 1.68808
Rooted glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] 47.2654 63.8686 1.35128
Subtracted Measured cyclin g2. [swissprot;acc:q16589] 13995.7 17738.6 3742.9
Ranked 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] 243.673 187.462 56.211
Squared gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] 78454.6 139741 61286.4
Rooted glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] 47.2654 63.8686 16.6032
69 Divided Measured spermatogenesis associated 6. [refseq;acc:nm_019073] 10307.5 6475.5 1.59177
Ranked guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488] 336.075 267.14 1.25805
Squared melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] 129762 219048 1.68808
Rooted neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] 37.2872 27.9136 1.33581
Subtracted Measured cyclin g1 (cyclin g). [swissprot;acc:p51959] 13995.6 17738.5 3742.9
Ranked 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] 228.934 284.753 55.819

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/