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 201 to 250 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
101 leucine zipper domain protein. [refseq;acc:nm_024589] Low confidence 221.996 238.82 1.07579
melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] High confidence 88.2482 110.265 1.24949
102 diacylglycerol kinase, theta (ec 2.7.1.107) (diglyceride kinase) (dgk- theta) (dag kinase theta). [swissprot;acc:p52824] Low confidence 229.556 213.456 1.07543
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] High confidence 88.2482 110.265 1.24949
103 trophinin. [swissprot;acc:q12816]
vacuolar protein sorting 16 (hvps16). [swissprot;acc:q9h269] Low confidence 203.948 189.652 1.07538
104 adiponectin receptor 2. [refseq;acc:nm_024551] 219.277 204.212 1.07377
homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] High confidence 252.371 202.016 1.24926
105 guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] 266.716 333.165 1.24914
transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094] Low confidence 220.497 205.364 1.07369
106 transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]
ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] High confidence 252.329 202.004 1.24913
107 homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] 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
108 disks large-associated protein 3 (dap-3) (sap90/psd-95-associated protein 3) (sapap3) (psd-95/sap90 binding protein 3) (fragment). [swissprot;acc:o95886] 197.731 212.069 1.07251
homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] High confidence 252.296 201.995 1.24902
109 guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] 266.933 333.281 1.24856
neuralized-like. [refseq;acc:nm_004210] Low confidence 232.704 216.996 1.07239
110 deltex 2. [refseq;acc:nm_020892] 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
111 deltex homolog 1; hdx-1. [refseq;acc:nm_004416] High confidence 332.925 267.274 1.24563
vacuolar protein sorting 33a (hvps33a). [swissprot;acc:q96ax1] 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
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] High confidence 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
114 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] 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
kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] High confidence 332.874 267.246 1.24557
116 guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520] 268.565 334.483 1.24545
vacuolar protein sorting 18 (hvps18). [swissprot;acc:q9p253] Low confidence 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
neuralized-like. [refseq;acc:nm_004210] High confidence 332.326 266.948 1.24491
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] 284.753 228.934 1.24382
protein-glutamine gamma-glutamyltransferase k (ec 2.3.2.13) (transglutaminase k) (tgase k) (tgk) (tg(k)) (transglutaminase 1) (epidermal tgase). [swissprot;acc:p22735] Low confidence 226.395 211.713 1.06935
119 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] High confidence 318.982 259.004 1.23157
natural resistance-associated macrophage protein 1 (nramp 1). [swissprot;acc:p49279] Low confidence 225.666 211.107 1.06897
120 potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] High confidence 269.278 327.709 1.21699
segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Low confidence 203.016 189.965 1.0687
121 cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] High confidence 269.254 327.655 1.2169
segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] Low confidence 203.007 189.985 1.06854
122 nanos (fragment). [sptrembl;acc:q8wy41] 203.66 217.479 1.06785
potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980] High confidence 269.248 327.642 1.21688
123 potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] 269.23 327.601 1.21681
segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] Low confidence 202.96 190.094 1.06768
124 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] High confidence 208.52 171.595 1.21519
natural resistance-associated macrophage protein 2 (nramp 2) (divalent metal transporter 1) (dmt1). [swissprot;acc:p49281] Low confidence 224.763 210.566 1.06742
125 b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] 213.243 227.616 1.0674
high-mobility group 20a. [refseq;acc:nm_018200] High confidence 208.588 171.778 1.21429

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/