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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Gene Rank Interaction Map Value Type description Network Comparison Type green Filtered red network_comparison
Results: HTML CSV LaTeX Showing element 501 to 550 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
Network Comparison Type
green
red
network_comparison
63 Squared melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Divided 129762 219048 1.68808
serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129] Subtracted 124480 189976 65496
Rooted 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] Divided 31.7576 43.4554 1.36835
melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Subtracted 120.823 137.446 16.623
64 Measured amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] 10307.5 6475.5 3832
glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] Divided 2765.82 4489.19 1.6231
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] Subtracted 204.309 260.532 56.223
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] Divided 336.159 266.868 1.25965
Squared cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Subtracted 81169.7 144940 63770.3
melanoma antigen, family b, 6. [refseq;acc:nm_173523] Divided 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
melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Subtracted 120.823 137.446 16.623
65 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
neuralized-like. [refseq;acc:nm_004210] Divided 2690.25 1657.68 1.6229
Ranked guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] 336.077 267.136 1.25807
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] Subtracted 243.678 187.457 56.221
Squared melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Divided 129762 219048 1.68808
microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] Subtracted 81155 144912 63757
Rooted glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] Divided 47.2654 63.8686 1.35128
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 120.823 137.446 16.623
66 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
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 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
uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] Subtracted 243.678 187.458 56.22
Squared melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] Divided 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] Subtracted 81154.7 144911 63756.3
Rooted glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] Divided 47.2654 63.8686 1.35128
trophinin. [swissprot;acc:q12816] Subtracted 120.823 137.446 16.623
67 Measured beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] Divided 10307.5 6475.5 1.59177
raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] Subtracted 14007.3 17756.5 3749.2
Ranked guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] Divided 336.075 267.14 1.25805
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] Subtracted 243.677 187.458 56.219
Squared cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 81136.5 144876 63739.5
melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] Divided 129762 219048 1.68808
Rooted 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] Subtracted 47.2654 63.8686 16.6032
myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] Divided 1.35128
68 Measured beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] 10307.5 6475.5 1.59177
cyclin g2. [swissprot;acc:q16589] Subtracted 13995.7 17738.6 3742.9
Ranked guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] Divided 336.075 267.139 1.25805
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] Subtracted 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
melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] Divided 129762 219048 1.68808
Rooted glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] Subtracted 47.2654 63.8686 16.6032
glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] Divided 1.35128
69 Measured cyclin g1 (cyclin g). [swissprot;acc:p51959] Subtracted 13995.6 17738.5 3742.9
spermatogenesis associated 6. [refseq;acc:nm_019073] Divided 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
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] Subtracted 228.934 284.753 55.819
Squared melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] Divided 129762 219048 1.68808
pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] Subtracted 118639 178263 59624

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/