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.


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Gene Rank description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1051 to 1100 of 66312 in total
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
Interaction Map
red
green
network_comparison
66 mitochondrial tumor suppressor gene 1; transcription factor mtsg1; at2 receptor-interacting protein 1; erythroid differentiation-related gene. [refseq;acc:nm_020749] Ranked Divided Low confidence 221.902 200.783 1.10518
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 High confidence 1991.03 3221.38 1.61795
septin 10 isoform 1. [refseq;acc:nm_144710] Squared Low confidence 74803.9 94281 1.26038
son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583] Measured 4900.7 5555.81 1.13368
trophinin. [swissprot;acc:q12816] Rooted Subtracted High confidence 137.446 120.823 16.623
uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] Ranked 187.458 243.678 56.22
67 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] Rooted 63.8686 47.2654 16.6032
beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] Measured Divided 6475.5 10307.5 1.59177
brachyury protein (t protein). [swissprot;acc:o15178] Rooted Low confidence 61.687 68.2003 1.10559
cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Squared Subtracted High confidence 144876 81136.5 63739.5
glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926] Rooted Low confidence 52.3425 45.0567 7.2858
guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] Ranked Divided High confidence 267.14 336.075 1.25805
hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] Measured Low confidence 12176.9 13781.8 1.1318
jumonji domain containing 1; zinc finger protein; testis-specific protein a. [refseq;acc:nm_018433] Subtracted 1927.68 2959.19 1031.51
melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] Squared Divided High confidence 219048 129762 1.68808
myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] Rooted 63.8686 47.2654 1.35128
pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] Squared Subtracted Low confidence 52172 64605 12433
putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865] Ranked 195.817 215.516 19.699
raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] Measured High confidence 17756.5 14007.3 3749.2
retinoblastoma-associated factor 600. [refseq;acc:nm_020765] Ranked Divided Low confidence 165.535 149.799 1.10505
septin 6. [swissprot;acc:q14141] Squared 74378.4 93531.9 1.25751
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 Subtracted High confidence 187.458 243.677 56.219
68 60s ribosomal protein l37a. [swissprot;acc:p12751] Divided Low confidence 239.692 217.005 1.10455
Rooted Subtracted 57.2649 64.3669 7.102
beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] Measured Divided High confidence 6475.5 10307.5 1.59177
cyclin g2. [swissprot;acc:q16589] Subtracted 17738.6 13995.7 3742.9
gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] Squared 139741 78454.6 61286.4
glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] Rooted 63.8686 47.2654 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 267.139 336.075 1.25805
melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] Squared 219048 129762 1.68808
pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] Subtracted Low confidence 52168.6 64594.5 12425.9
potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Ranked 225.735 245.308 19.573
putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] Measured Divided 19498.1 17265.4 1.12932
ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] Rooted 55.9786 61.8641 1.10514
retinoblastoma-associated factor 600. [refseq;acc:nm_020765] Squared 27909.1 35068.7 1.25653
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 High confidence 187.462 243.673 56.211
trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [swissprot;acc:p35030] Measured Low confidence 1972.65 2998.1 1025.45
69 a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] Squared 63411.7 51068.8 12342.9
amino acid transporter xat2; likely ortholog of mouse aspartate/glutamate transporter 1 (agt1). [refseq;acc:nm_138817] Measured Divided 6991.78 7848.45 1.12253
amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410] Rooted 60.7884 67.1136 1.10405
cyclin g1 (cyclin g). [swissprot;acc:p51959] Measured Subtracted High confidence 17738.5 13995.6 3742.9
delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial precursor (ec 1.5.1.12) (p5c dehydrogenase). [swissprot;acc:p30038] Squared Divided Low confidence 80538.1 64191.7 1.25465
glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] Rooted Subtracted High confidence 63.8686 47.2654 16.6032
guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488] Ranked Divided 267.14 336.075 1.25805
melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] Squared 219048 129762 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 284.753 228.934 55.819
Rooted Low confidence 59.0909 66.1317 7.0408
neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] Divided High confidence 27.9136 37.2872 1.33581
pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] Squared Subtracted 178263 118639 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/