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

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/