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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 425 to 474 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
description
Network Comparison Type
Interaction Map
red
green
network_comparison
107 eap30 subunit of ell complex. [refseq;acc:nm_007241] Subtracted High confidence 209.299 249.187 39.888
homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] Divided 252.309 201.998 1.24907
mouse mammary turmor virus receptor homolog 1. [refseq;acc:nm_152832] Low confidence 227.429 211.97 1.07293
vacuolar protein sorting 16 (hvps16). [swissprot;acc:q9h269] Subtracted 203.948 189.652 14.296
108 disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6] 197.752 212.031 14.279
disks large-associated protein 3 (dap-3) (sap90/psd-95-associated protein 3) (sapap3) (psd-95/sap90 binding protein 3) (fragment). [swissprot;acc:o95886] Divided 197.731 212.069 1.07251
homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] High confidence 252.296 201.995 1.24902
liv-1 protein, estrogen regulated. [refseq;acc:nm_012319] Subtracted 209.299 249.187 39.888
109 cellular repressor of e1a-stimulated genes. [refseq;acc:nm_003851] Low confidence 197.762 212.013 14.251
glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329] High confidence 209.299 249.187 39.888
guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] Divided 266.933 333.281 1.24856
neuralized-like. [refseq;acc:nm_004210] Low confidence 232.704 216.996 1.07239
110 cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836] Subtracted 197.763 212.011 14.248
deltex 2. [refseq;acc:nm_020892] Divided High confidence 333.144 267.393 1.2459
disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6] Low confidence 197.752 212.031 1.07221
gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747] Subtracted High confidence 209.299 249.187 39.888
111 deltex homolog 1; hdx-1. [refseq;acc:nm_004416] Divided 332.925 267.274 1.24563
disks large-associated protein 1 (dap-1) (guanylate kinase-associated protein) (hgkap) (sap90/psd-95-associated protein 1) (sapap1) (psd- 95/sap90 binding protein 1). [swissprot;acc:o14490] Subtracted Low confidence 197.779 211.983 14.204
glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259] High confidence 209.299 249.187 39.888
vacuolar protein sorting 33a (hvps33a). [swissprot;acc:q96ax1] Divided Low confidence 203.914 190.189 1.07217
112 cellular repressor of e1a-stimulated genes. [refseq;acc:nm_003851] 197.762 212.013 1.07206
disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [swissprot;acc:q9y2h0] Subtracted 197.779 211.983 14.204
dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] High confidence 275.754 235.908 39.846
t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492] Divided 332.874 267.246 1.24557
113 cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836] Low confidence 197.763 212.011 1.07205
kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] High confidence 332.874 267.246 1.24557
natural resistance-associated macrophage protein 2 (nramp 2) (divalent metal transporter 1) (dmt1). [swissprot;acc:p49281] Subtracted Low confidence 224.763 210.566 14.197
serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] High confidence 194.372 234.204 39.832
114 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] Low confidence 58 44 14
b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] High confidence 229.818 267.265 37.447
disks large-associated protein 1 (dap-1) (guanylate kinase-associated protein) (hgkap) (sap90/psd-95-associated protein 1) (sapap1) (psd- 95/sap90 binding protein 1). [swissprot;acc:o14490] Divided Low confidence 197.779 211.983 1.07182
kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] High confidence 332.874 267.246 1.24557
115 disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [swissprot;acc:q9y2h0] Low confidence 197.779 211.983 1.07182
histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] Subtracted High confidence 277.546 240.461 37.085
kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] Divided 332.874 267.246 1.24557
mitochondrial solute carrier protein. [refseq;acc:nm_145305] Subtracted Low confidence 58 44 14
116 guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520] Divided High confidence 268.565 334.483 1.24545
high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339] Subtracted 208.52 171.595 36.925
testican-3 precursor. [swissprot;acc:q9bq16] Low confidence 220.395 234.389 13.994
vacuolar protein sorting 18 (hvps18). [swissprot;acc:q9p253] Divided 204.161 190.791 1.07008
117 coagulation factor xiii a chain precursor (ec 2.3.2.13) (protein- glutamine gamma-glutamyltransferase a chain) (transglutaminase a chain). [swissprot;acc:p00488] 226.395 211.713 1.06935
high-mobility group 20a. [refseq;acc:nm_018200] Subtracted High confidence 208.588 171.778 36.81
neuralized-like. [refseq;acc:nm_004210] Divided 332.326 266.948 1.24491
striated muscle activator of rho-dependent signaling. [refseq;acc:nm_139166] Subtracted Low confidence 225.495 211.529 13.966
118 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 High confidence 284.753 228.934 1.24382
odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] Subtracted 274.027 237.79 36.237
protein-glutamine gamma-glutamyltransferase k (ec 2.3.2.13) (transglutaminase k) (tgase k) (tgk) (tg(k)) (transglutaminase 1) (epidermal tgase). [swissprot;acc:p22735] Divided Low confidence 226.395 211.713 1.06935
testican-1 precursor (spock protein). [swissprot;acc:q08629] Subtracted 220.254 234.111 13.857
119 adiponectin receptor 2. [refseq;acc:nm_024551] High confidence 281.582 246.371 35.211
nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181] Divided 318.982 259.004 1.23157

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/