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 red Filtered Interaction Map network_comparison green
Results: HTML CSV LaTeX Showing element 951 to 1000 of 9634 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Rank
description
red
Filtered
Interaction Map
network_comparison
green
238 rd protein. [swissprot;acc:p18615] 227.357 1 High confidence 1.11785 254.15
similar to zinc finger protein 85 (zinc finger protein hpf4) (htf1). [refseq;acc:nm_145287] 4256.39 0 Low confidence 1.14024 4853.29
239 dual oxidase 2 precursor; dual oxidase-like domains 2; nicotinamide adenine dinucleotide phosphate oxidase; flavoprotein nadph oxidase; nadph thyroid oxidase 2; nadh/nadph thyroid oxidase p138-tox; nadph oxidase/peroxidase duox2. [refseq;acc:nm_014080] 210.504 1 1.04684 201.086
glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] 227.357 High confidence 1.11785 254.15
mto1 protein homolog (cgi-02). [swissprot;acc:q9y2z2] 8907.41 0 1.09969 9795.36
similar to zinc finger protein 136. [refseq;acc:nm_145295] 4256.39 Low confidence 1.14024 4853.29
240 androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108] 227.357 1 High confidence 1.11785 254.15
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 162.755 Low confidence 1.04682 155.476
methyltransferase like 2. [refseq;acc:nm_018396] 17946 0 High confidence 1.09923 16326
similar to dna-binding protein; zinc finger protein 253. [refseq;acc:nm_145297] 4256.39 Low confidence 1.14024 4853.29
241 atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539] 227.357 1 High confidence 1.11785 254.15
homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] 162.755 Low confidence 1.04682 155.476
secreted modular calcium-binding protein 1. [refseq;acc:nm_022137] 14003.7 0 High confidence 1.09891 12743.3
zinc finger protein 132. [swissprot;acc:p52740] 4256.15 Low confidence 1.14024 4853.03
242 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 15260.6 High confidence 1.09822 13895.8
homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] 162.755 1 Low confidence 1.04682 155.476
j domain containing protein 1. [swissprot;acc:q9ukb3] 227.357 High confidence 1.11785 254.15
zinc finger protein 84 (zinc finger protein hpf2). [swissprot;acc:p51523] 4256.39 0 Low confidence 1.14024 4853.29
243 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 162.755 1 1.04682 155.476
polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361] 1251 0 High confidence 1.09752 1373
sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8] 227.357 1 1.11785 254.15
zinc finger protein 121 (zinc finger protein 20) (fragment). [swissprot;acc:p58317] 4256.71 0 Low confidence 1.14023 4853.62
244 ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] 227.357 1 High confidence 1.11785 254.15
homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] 162.755 Low confidence 1.04682 155.476
keratin associated protein 9.2. [refseq;acc:nm_031961] 10551.1 0 High confidence 1.09751 11579.9
zinc finger protein af020591. [refseq;acc:nm_014480] 4256.94 Low confidence 1.14023 4853.87
245 cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] 11867.6 High confidence 1.09702 13019
homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] 162.755 1 Low confidence 1.04682 155.476
small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] 226.109 High confidence 1.11751 202.333
zinc finger protein 20 (zinc finger protein kox13) (dkfzp572p0920). [swissprot;acc:p17024] 4256.94 0 Low confidence 1.14023 4853.87
246 eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] 237.312 1 High confidence 1.11748 212.363
homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] 162.755 Low confidence 1.04682 155.476
keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4] 10551.6 0 High confidence 1.09687 11573.7
zinc finger protein 11b (fragment). [swissprot;acc:q06732] 4256.55 Low confidence 1.14023 4853.45
247 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 162.755 1 1.04682 155.476
keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184] 10551.6 0 High confidence 1.09687 11573.7
rna-binding protein. [refseq;acc:nm_019027] 237.302 1 1.11719 212.41
zinc finger protein 208. [swissprot;acc:o43345] 4256.94 0 Low confidence 1.14023 4853.87
248 apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] 237.302 1 High confidence 1.11719 212.41
keratin associated protein 1.5. [refseq;acc:nm_031957] 10551.6 0 1.09687 11573.7
retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] 162.755 1 Low confidence 1.04682 155.476
zinc finger protein 136. [swissprot;acc:p52737] 4256.71 0 1.14023 4853.62
249 dual oxidase 1 precursor; nadph thyroid oxidase 1; flavoprotein nadph oxidase; nicotinamide adenine dinucleotide phosphate oxidase. [refseq;acc:nm_017434] 210.487 1 1.0468 201.076
gonadotropin inducible transcription repressor-1 (giot-1). [swissprot;acc:q8taf7] 4257.1 0 1.14022 4854.04
keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371] 10551.6 High confidence 1.09687 11573.7
ns1-associated protein 1. [refseq;acc:nm_006372] 237.302 1 1.11719 212.41
250 diacylglycerol o-acyltransferase 1 (ec 2.3.1.20) (diglyceride acyltransferase) (acat related gene product 1). [swissprot;acc:o75907] 210.443 Low confidence 1.04671 201.051
heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] 237.302 High confidence 1.11719 212.41
keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966] 10551.6 0 1.09687 11573.7
zinc finger protein 85 (zinc finger protein hpf4) (htf1). [swissprot;acc:q03923] 4257.26 Low confidence 1.14022 4854.21

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/