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 530 to 579 of 8289 in total
Value Type  : Measured
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
265 wd-repeat protein wdc146. [swissprot;acc:q9c0j8] High confidence 24806.9 20369.9 1.21782
266 carboxypeptidase a1 precursor (ec 3.4.17.1). [swissprot;acc:p15085] Low confidence 8817.03 9353.9 1.06089
cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] High confidence 24806.9 20369.9 1.21782
267 choline/ethanolaminephosphotransferase. [refseq;acc:nm_006090] Low confidence 8813.83 9348.71 1.06069
ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] High confidence 14021.4 11523 1.21682
268 cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] 24473.9 20127.8 1.21593
reversion-inducing cysteine-rich protein with kazal motifs precursor (hreck) (suppressor of tumorigenicity 15) (st15). [swissprot;acc:o95980] Low confidence 8813.83 9348.71 1.06069
269 choline phosphotransferase 1; cholinephosphotransferase 1 alpha; cholinephosphotransferase 1. [refseq;acc:nm_020244] 8813.95 9348.9
u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] High confidence 4590.18 5575.52 1.21466
270 carboxypeptidase a5. [refseq;acc:nm_080385] Low confidence 8811.88 9345.51 1.06056
fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] High confidence 23640.2 19479.8 1.21358
271 carboxypeptidase b precursor (ec 3.4.17.2) (pancreas-specific protein) (pasp). [swissprot;acc:p15086] Low confidence 8811.69 9345.26 1.06055
chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] High confidence 2554.89 3093.78 1.21092
272 delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial precursor (ec 1.5.1.12) (p5c dehydrogenase). [swissprot;acc:p30038] Low confidence 11162 10526.2 1.0604
histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] High confidence 3858.52 4669.27 1.21012
273 eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] 3199.4 3870.8 1.20985
phospholipase a-2-activating protein (plap) (pla2p). [swissprot;acc:q9y263] Low confidence 11162 10526.2 1.0604
274 chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286] High confidence 3119.98 2579.49 1.20953
small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] Low confidence 7718.85 8184.75 1.06036
275 regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795] High confidence 3119.98 2579.49 1.20953
udp-glucose 4-epimerase (ec 5.1.3.2) (galactowaldenase) (udp- galactose 4-epimerase). [swissprot;acc:q14376] Low confidence 7506.19 7958.12 1.06021
276 putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] High confidence 3119.98 2579.49 1.20953
u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661] Low confidence 7762.71 8229.36 1.06011
277 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] 7900.15 8374.91 1.0601
regulator of g-protein signaling 20 (rgs20) (regulator of gz- selective protein signaling 1) (gz-selective gtpase-activating protein) (g(z)gap). [swissprot;acc:o76081] High confidence 3119.98 2579.49 1.20953
278 ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] Low confidence 7762.96 8229.42 1.06009
transcription factor lbx1. [swissprot;acc:p52954] High confidence 3119.98 2579.49 1.20953
279 dual oxidase 1 precursor; nadph thyroid oxidase 1; flavoprotein nadph oxidase; nicotinamide adenine dinucleotide phosphate oxidase. [refseq;acc:nm_017434] Low confidence 7900.92 8375.39 1.06005
mosaic protein lgn. [swissprot;acc:p81274] High confidence 3119.98 2579.49 1.20953
280 diacylglycerol o-acyltransferase 1 (ec 2.3.1.20) (diglyceride acyltransferase) (acat related gene product 1). [swissprot;acc:o75907] Low confidence 7902.9 8376.6 1.05994
regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6] High confidence 3119.98 2579.49 1.20953
281 cytochrome b-245 heavy chain (p22 phagocyte b-cytochrome) (neutrophil cytochrome b, 91 kda polypeptide) (cgd91-phox) (gp91-phox) (heme binding membrane glycoprotein gp91phox) (cytochrome b(558) beta chain) (superoxide-generating nadph oxidase heavy chain subunit). [swissprot;acc:p04839] Low confidence 7904.19 8377.38 1.05987
guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471] High confidence 3119.98 2579.49 1.20953
282 nadph oxidase, ef hand calcium-binding domain 5. [refseq;acc:nm_024505] Low confidence 7904.14 8377.35 1.05987
rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736] High confidence 3119.98 2579.49 1.20953
283 nadph oxidase 4. [refseq;acc:nm_016931] Low confidence 7904.2 8377.39 1.05987
polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] High confidence 5221.28 6314.35 1.20935
284 nadph oxidase 3; nadph oxidase catalytic subunit-like 3. [refseq;acc:nm_015718] Low confidence 7904.17 8377.37 1.05987
paxillin. [swissprot;acc:p49023] High confidence 5221.28 6314.35 1.20935
285 nadph oxidase homolog 1 (nox-1) (noh-1) (nadh/nadph mitogenic oxidase subunit p65-mox) (mitogenic oxidase 1) (mox1). [swissprot;acc:q9y5s8] Low confidence 7904.2 8377.39 1.05987
poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] High confidence 23326.5 19296.4 1.20885
286 exocyst complex component sec5. [swissprot;acc:q96kp1] 23316 19288.8 1.20878
sedlin. [swissprot;acc:o14582] Low confidence 9059.8 9601.05 1.05974
287 adiponectin receptor 2. [refseq;acc:nm_024551] 7170.39 7598.55 1.05971
poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] High confidence 23303.1 19279.5 1.2087
288 blocked early in transport 1 homolog (s. cerevisiae) like; golgi snare 15 kda protein. [refseq;acc:nm_016526] Low confidence 8155.32 8641.69 1.05964
cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] High confidence 23422.4 19380.3 1.20857
289 splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] Low confidence 7752.95 8214.32 1.05951
u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8] High confidence 4682.88 5646.19 1.20571
290 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 6885.52 7293.37 1.05923

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/