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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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 [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered green red 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
Network Comparison Type
green
red
network_comparison
63 myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] Measured Divided 2765.82 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 Subtracted 204.309 260.532 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 Divided 47.2654 63.8686 1.35128
amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] Measured Subtracted 10307.5 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 Divided 2765.82 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 Subtracted 120.823 137.446 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 Divided 47.2654 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 Subtracted 120.823 137.446 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 Divided 2690.25 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 Subtracted 243.678 187.457 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 Divided 47.2654 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] Subtracted 81154.7 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 Divided 3221.38 1991.03 1.61795
trophinin. [swissprot;acc:q12816] Rooted Subtracted 120.823 137.446 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 Divided 10307.5 6475.5 1.59177
cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Squared Subtracted 81136.5 144876 63739.5
guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] Ranked Divided 336.075 267.14 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 Subtracted 14007.3 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 Divided 10307.5 6475.5 1.59177
cyclin g2. [swissprot;acc:q16589] Subtracted 13995.7 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 Subtracted 243.673 187.462 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 Divided 336.075 267.14 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 Subtracted 228.934 284.753 55.819
neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] Rooted Divided 37.2872 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/