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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Gene Rank Value Type Network Comparison Type green description red Filtered Interaction Map network_comparison
Results: HTML CSV LaTeX Showing element 951 to 1000 of 9634 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Rank
green
description
red
Filtered
Interaction Map
network_comparison
238 4853.29 similar to zinc finger protein 85 (zinc finger protein hpf4) (htf1). [refseq;acc:nm_145287] 4256.39 0 Low confidence 1.14024
13941.7 cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] 12677.7 High confidence 1.0997
239 201.086 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 Low confidence 1.04684
254.15 glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] 227.357 High confidence 1.11785
4853.29 similar to zinc finger protein 136. [refseq;acc:nm_145295] 4256.39 0 Low confidence 1.14024
9795.36 mto1 protein homolog (cgi-02). [swissprot;acc:q9y2z2] 8907.41 High confidence 1.09969
240 155.476 homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 162.755 1 Low confidence 1.04682
254.15 androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108] 227.357 High confidence 1.11785
4853.29 similar to dna-binding protein; zinc finger protein 253. [refseq;acc:nm_145297] 4256.39 0 Low confidence 1.14024
16326 methyltransferase like 2. [refseq;acc:nm_018396] 17946 High confidence 1.09923
241 155.476 homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] 162.755 1 Low confidence 1.04682
254.15 atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539] 227.357 High confidence 1.11785
4853.03 zinc finger protein 132. [swissprot;acc:p52740] 4256.15 0 Low confidence 1.14024
12743.3 secreted modular calcium-binding protein 1. [refseq;acc:nm_022137] 14003.7 High confidence 1.09891
242 155.476 homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] 162.755 1 Low confidence 1.04682
254.15 j domain containing protein 1. [swissprot;acc:q9ukb3] 227.357 High confidence 1.11785
4853.29 zinc finger protein 84 (zinc finger protein hpf2). [swissprot;acc:p51523] 4256.39 0 Low confidence 1.14024
13895.8 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
243 155.476 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 162.755 1 Low confidence 1.04682
254.15 sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8] 227.357 High confidence 1.11785
1373 polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361] 1251 0 1.09752
4853.62 zinc finger protein 121 (zinc finger protein 20) (fragment). [swissprot;acc:p58317] 4256.71 Low confidence 1.14023
244 155.476 homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] 162.755 1 1.04682
254.15 ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] 227.357 High confidence 1.11785
4853.87 zinc finger protein af020591. [refseq;acc:nm_014480] 4256.94 0 Low confidence 1.14023
11579.9 keratin associated protein 9.2. [refseq;acc:nm_031961] 10551.1 High confidence 1.09751
245 155.476 homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] 162.755 1 Low confidence 1.04682
202.333 small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] 226.109 High confidence 1.11751
4853.87 zinc finger protein 20 (zinc finger protein kox13) (dkfzp572p0920). [swissprot;acc:p17024] 4256.94 0 Low confidence 1.14023
13019 cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] 11867.6 High confidence 1.09702
246 155.476 homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] 162.755 1 Low confidence 1.04682
212.363 eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] 237.312 High confidence 1.11748
4853.45 zinc finger protein 11b (fragment). [swissprot;acc:q06732] 4256.55 0 Low confidence 1.14023
11573.7 keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4] 10551.6 High confidence 1.09687
247 155.476 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 162.755 1 Low confidence 1.04682
212.41 rna-binding protein. [refseq;acc:nm_019027] 237.302 High confidence 1.11719
4853.87 zinc finger protein 208. [swissprot;acc:o43345] 4256.94 0 Low confidence 1.14023
11573.7 keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184] 10551.6 High confidence 1.09687
248 155.476 retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] 162.755 1 Low confidence 1.04682
212.41 apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] 237.302 High confidence 1.11719
4853.62 zinc finger protein 136. [swissprot;acc:p52737] 4256.71 0 Low confidence 1.14023
11573.7 keratin associated protein 1.5. [refseq;acc:nm_031957] 10551.6 High confidence 1.09687
249 201.076 dual oxidase 1 precursor; nadph thyroid oxidase 1; flavoprotein nadph oxidase; nicotinamide adenine dinucleotide phosphate oxidase. [refseq;acc:nm_017434] 210.487 1 Low confidence 1.0468
212.41 ns1-associated protein 1. [refseq;acc:nm_006372] 237.302 High confidence 1.11719
4854.04 gonadotropin inducible transcription repressor-1 (giot-1). [swissprot;acc:q8taf7] 4257.1 0 Low confidence 1.14022
11573.7 keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371] 10551.6 High confidence 1.09687
250 201.051 diacylglycerol o-acyltransferase 1 (ec 2.3.1.20) (diglyceride acyltransferase) (acat related gene product 1). [swissprot;acc:o75907] 210.443 1 Low confidence 1.04671
212.41 heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] 237.302 High confidence 1.11719
4854.21 zinc finger protein 85 (zinc finger protein hpf4) (htf1). [swissprot;acc:q03923] 4257.26 0 Low confidence 1.14022
11573.7 keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966] 10551.6 High confidence 1.09687

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/