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

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/