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 Hugo description Value Type Interaction Map Filtered network_comparison red green
Results: HTML CSV LaTeX Showing element 523 to 572 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Network Comparison Type
Hugo
description
Value Type
network_comparison
red
green
66 Divided NDUFA12 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 1.61795 1991.03 3221.38
PYGL glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] Rooted 1.35128 63.8686 47.2654
Subtracted ARAF a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] Measured 3749.5 17757.5 14008
MAP1LC3A microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Squared 63756.3 144911 81154.7
PPP2R2D uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] Ranked 56.22 187.458 243.678
TRO trophinin. [swissprot;acc:q12816] Rooted 16.623 137.446 120.823
67 Divided ARRB2 beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] Measured 1.59177 6475.5 10307.5
GNAT2 guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] Ranked 1.25805 267.14 336.075
MAGEA8 melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] Squared 1.68808 219048 129762
MYO15A myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] Rooted 1.35128 63.8686 47.2654
Subtracted ATG4B cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Squared 63739.5 144876 81136.5
GBE1 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] Rooted 16.6032 63.8686 47.2654
PPP2R2B 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 56.219 187.458 243.677
RAF1 raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] Measured 3749.2 17756.5 14007.3
68 Divided ARRB1 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] 1.59177 6475.5 10307.5
GNAZ guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] Ranked 1.25805 267.139 336.075
MAGEC1 melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] Squared 1.68808 219048 129762
PYGM glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] Rooted 1.35128 63.8686 47.2654
Subtracted CCNG2 cyclin g2. [swissprot;acc:q16589] Measured 3742.9 17738.6 13995.7
GABARAP gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] Squared 61286.4 139741 78454.6
PPP2R2C 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 56.211 187.462 243.673
PYGB glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] Rooted 16.6032 63.8686 47.2654
69 Divided GNAT1 guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488] Ranked 1.25805 267.14 336.075
MAGEA4 melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] Squared 1.68808 219048 129762
NEUROD2 neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] Rooted 1.33581 27.9136 37.2872
SPATA6 spermatogenesis associated 6. [refseq;acc:nm_019073] Measured 1.59177 6475.5 10307.5
Subtracted CCNG1 cyclin g1 (cyclin g). [swissprot;acc:p51959] 3742.9 17738.5 13995.6
NDUFA12 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 55.819 284.753 228.934
PCF11 pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] Squared 59624 178263 118639
PYGL glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] Rooted 16.6032 63.8686 47.2654
70 Divided no value melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] Squared 1.68808 219048 129762
AMPD2 amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] Measured 1.59177 6475.5 10307.5
CHD3 chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] Rooted 1.33581 27.9136 37.2872
GNAI2 guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899] Ranked 1.25804 267.142 336.074
Subtracted no value gaba-a receptor-associated protein. [sptrembl;acc:q9by60] Squared 56439.5 129597 73157.5
MYO15A myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] Rooted 16.6032 63.8686 47.2654
PPP2R1B serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [swissprot;acc:p30154] Ranked 54.054 188.688 242.742
PPP2R5E serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [swissprot;acc:q16537] Measured 3742.8 17738.5 13995.7
71 Divided no value 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] 1.54716 4556.78 2945.26
CDK2AP2 doc-1 related protein (doc-1r). [swissprot;acc:o75956] Rooted 1.33581 27.9136 37.2872
GNAI1 guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898] Ranked 1.25802 267.144 336.073
MAGEA10 melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Squared 1.68808 219048 129762
Subtracted ATG3 apg3p; pc3-96 protein. [refseq;acc:nm_022488] 56439.5 129597 73157.5
KCNIP1 kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] Ranked 53.965 265.686 319.651
PPP2R5A serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, alpha isoform (pp2a, b subunit, b' alpha isoform) (pp2a, b subunit, b56 alpha isoform) (pp2a, b subunit, pr61 alpha isoform) (pp2a, b subunit, r5 alpha isoform). [swissprot;acc:q15172] Measured 3742.8 17738.5 13995.7
PYGM glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] Rooted 16.6032 63.8686 47.2654
72 Divided GNAI3 guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754] Ranked 1.25802 267.144 336.073
MAGEB4 melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Squared 1.68808 219048 129762
NEUROD6 neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] Rooted 1.33581 27.9136 37.2872
PPP2R2D uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] Measured 1.54715 4556.79 2945.28

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
- Hugo is the HGNC identifier if it exists
- 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/