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

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/