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 Interaction Map Network Comparison Type Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 451 to 500 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
226 cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] High confidence 239.991 269.238 1.12187
lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [swissprot;acc:q9uju2] Low confidence 208.289 198.538 1.04911
227 c1 domain-containing phosphatase and tensin-like protein isoform 2; putative protein tyrosine phosphatase; c1 domain-containing phosphatase and tensin-like protein; tensin 2. [refseq;acc:nm_015319] 216.404 206.277 1.04909
thrombospondin 3 precursor. [swissprot;acc:p49746] High confidence 239.99 269.234 1.12186
228 sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489] 226.411 202.088 1.12036
u1 small nuclear ribonucleoprotein a (u1 snrnp a protein). [swissprot;acc:p09012] Low confidence 202.727 193.31 1.04871
229 breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] High confidence 226.401 202.094 1.12028
toll-like receptor 2 precursor (toll/interleukin 1 receptor-like protein 4). [swissprot;acc:o60603] Low confidence 207.926 198.276 1.04867
230 cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291] High confidence 239.35 267.915 1.11934
jm1 protein. [refseq;acc:nm_014008] Low confidence 216.308 206.292 1.04855
231 likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] High confidence 239.336 267.881 1.11927
mitochondrial import inner membrane translocase subunit tim23. [swissprot;acc:o14925] Low confidence 220.722 210.645 1.04784
232 ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511] 214.032 204.284 1.04772
smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527] High confidence 239.336 267.879 1.11926
233 lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461] 239.32 267.842 1.11918
nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952] Low confidence 209.649 200.129 1.04757
234 chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] High confidence 287.41 256.835 1.11905
cytochrome p450 51a1 (ec 1.14.13.70) (cypli) (p450li) (sterol 14-alpha demethylase) (lanosterol 14-alpha demethylase) (ldm) (p450-14dm). [swissprot;acc:q16850] Low confidence 208.851 199.38 1.0475
235 phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439] High confidence 227.357 254.15 1.11785
u2 small nuclear ribonucleoprotein b". [swissprot;acc:p08579] Low confidence 202.654 193.53 1.04715
236 peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936] 212.056 202.524 1.04707
pp3111 protein. [refseq;acc:nm_022156] High confidence 227.357 254.15 1.11785
237 single-minded homolog 1. [swissprot;acc:p81133] Low confidence 212.056 202.524 1.04707
syntaxin 18. [swissprot;acc:q9p2w9] High confidence 227.357 254.15 1.11785
238 nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] Low confidence 200.699 191.678 1.04706
rd protein. [swissprot;acc:p18615] High confidence 227.357 254.15 1.11785
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] Low confidence 210.504 201.086 1.04684
glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] High confidence 227.357 254.15 1.11785
240 androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108]
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Low confidence 162.755 155.476 1.04682
241 atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539] High confidence 227.357 254.15 1.11785
homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] Low confidence 162.755 155.476 1.04682
242 homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444]
j domain containing protein 1. [swissprot;acc:q9ukb3] High confidence 227.357 254.15 1.11785
243 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Low confidence 162.755 155.476 1.04682
sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8] High confidence 227.357 254.15 1.11785
244 ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5]
homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Low confidence 162.755 155.476 1.04682
245 homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067]
small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] High confidence 226.109 202.333 1.11751
246 eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] 237.312 212.363 1.11748
homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] Low confidence 162.755 155.476 1.04682
247 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]
rna-binding protein. [refseq;acc:nm_019027] High confidence 237.302 212.41 1.11719
248 apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576]
retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] Low confidence 162.755 155.476 1.04682
249 dual oxidase 1 precursor; nadph thyroid oxidase 1; flavoprotein nadph oxidase; nicotinamide adenine dinucleotide phosphate oxidase. [refseq;acc:nm_017434] 210.487 201.076 1.0468
ns1-associated protein 1. [refseq;acc:nm_006372] High confidence 237.302 212.41 1.11719
250 diacylglycerol o-acyltransferase 1 (ec 2.3.1.20) (diglyceride acyltransferase) (acat related gene product 1). [swissprot;acc:o75907] Low confidence 210.443 201.051 1.04671
heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] High confidence 237.302 212.41 1.11719

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/