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 Network Comparison Type Value Type Rank description Interaction Map Filtered green network_comparison red
Results: HTML CSV LaTeX Showing element 501 to 550 of 66312 in total
Network Comparison Type  : Divided
Value Type  : Measured
Filtered  : 1
Rank
description
Interaction Map
green
network_comparison
red
251 kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] Low confidence 9058.09 1.06221 8527.55
tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] High confidence 7859.6 1.22477 6417.18
252 1-acyl-sn-glycerol-3-phosphate acyltransferase gamma (ec 2.3.1.51) (1- agp acyltransferase 3) (1-agpat 3) (lysophosphatidic acid acyltransferase-gamma) (lpaat-gamma) (1-acylglycerol-3-phosphate o- acyltransferase 3). [swissprot;acc:q9nrz7] Low confidence 9018.94 1.06194 8492.92
crk-like protein. [swissprot;acc:p46109] High confidence 7859.6 1.22477 6417.18
253 fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] Low confidence 8732.25 1.06188 8223.39
proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] High confidence 7859.59 1.22477 6417.18
254 dj842g6.2 (novel protein imilar to sel1l (sel-1 (suppressor of lin-12, c.elegans)-like)) (fragment). [sptrembl;acc:q9ugd3] Low confidence 8727.87 1.06179 8219.97
proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] High confidence 7859.6 1.22477 6417.18
255 proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769]
sel-1 homolog precursor (suppressor of lin-12-like protein) (sel-1l). [swissprot;acc:q9ubv2] Low confidence 8727.84 1.06179 8219.95
256 fructose-1,6-bisphosphatase (ec 3.1.3.11) (d-fructose-1,6-bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:p09467] 8723.91 1.06171 8216.87
grb2-related adaptor protein 2 (gads protein) (growth factor receptor binding protein) (grblg) (grf40 adaptor protein) (grf-40) (grb-2-like protein) (grb2l) (grbx) (p38) (hematopoietic cell-associated adaptor protein grpl) (adapter protein grid) (sh3-sh2-sh3 adaptor mona). [swissprot;acc:o75791] High confidence 7859.51 1.22476 6417.19
257 ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] 7858.12 1.22452 6417.31
synaptojanin 1 (ec 3.1.3.36) (synaptic inositol-1,4,5-trisphosphate 5- phosphatase 1). [swissprot;acc:o43426] Low confidence 8579.93 1.06157 8082.34
258 aflatoxin b1 aldehyde reductase 2 (ec 1.-.-.-) (afb1-ar 2). [swissprot;acc:o95154] 9818.95 1.06154 9249.74
homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] High confidence 7857.93 1.22449 6417.33
259 neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] 7852.52 1.22355 6417.81
oligophrenin 1. [swissprot;acc:o60890] Low confidence 6824.22 1.06152 6428.7
260 aflatoxin b1 aldehyde reductase 1 (ec 1.-.-.-) (afb1-ar 1) (aldoketoreductase 7). [swissprot;acc:o43488] 9814.59 1.06147 9246.23
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] High confidence 5193.42 1.22343 4244.95
261 adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109] Low confidence 9379.17 1.06133 8837.18
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] High confidence 5192.61 1.22255 4247.36
262 cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693] 20431.7 1.21852 24896.4
oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [swissprot;acc:q9una1] Low confidence 6834.37 1.06122 6440.08
263 oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] 7877.49 1.06106 7424.14
trs85 homolog. [swissprot;acc:q9y2l5] High confidence 20431.7 1.21852 24896.4
264 cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] 4094.57 1.2181 4987.58
diacylglycerol kinase, theta (ec 2.7.1.107) (diglyceride kinase) (dgk- theta) (dag kinase theta). [swissprot;acc:p52824] Low confidence 6786.96 1.06105 6396.44
265 synaptojanin 2 (ec 3.1.3.36) (synaptic inositol-1,4,5-trisphosphate 5- phosphatase 2) (fragment). [swissprot;acc:o15056] 8573.8 1.06098 8081.02
wd-repeat protein wdc146. [swissprot;acc:q9c0j8] High confidence 20369.9 1.21782 24806.9
266 carboxypeptidase a1 precursor (ec 3.4.17.1). [swissprot;acc:p15085] Low confidence 9353.9 1.06089 8817.03
cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] High confidence 20369.9 1.21782 24806.9
267 choline/ethanolaminephosphotransferase. [refseq;acc:nm_006090] Low confidence 9348.71 1.06069 8813.83
ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] High confidence 11523 1.21682 14021.4
268 cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] 20127.8 1.21593 24473.9
reversion-inducing cysteine-rich protein with kazal motifs precursor (hreck) (suppressor of tumorigenicity 15) (st15). [swissprot;acc:o95980] Low confidence 9348.71 1.06069 8813.83
269 choline phosphotransferase 1; cholinephosphotransferase 1 alpha; cholinephosphotransferase 1. [refseq;acc:nm_020244] 9348.9 8813.95
u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] High confidence 5575.52 1.21466 4590.18
270 carboxypeptidase a5. [refseq;acc:nm_080385] Low confidence 9345.51 1.06056 8811.88
fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] High confidence 19479.8 1.21358 23640.2
271 carboxypeptidase b precursor (ec 3.4.17.2) (pancreas-specific protein) (pasp). [swissprot;acc:p15086] Low confidence 9345.26 1.06055 8811.69
chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] High confidence 3093.78 1.21092 2554.89
272 delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial precursor (ec 1.5.1.12) (p5c dehydrogenase). [swissprot;acc:p30038] Low confidence 10526.2 1.0604 11162
histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] High confidence 4669.27 1.21012 3858.52
273 eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] 3870.8 1.20985 3199.4
phospholipase a-2-activating protein (plap) (pla2p). [swissprot;acc:q9y263] Low confidence 10526.2 1.0604 11162
274 chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286] High confidence 2579.49 1.20953 3119.98
small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] Low confidence 8184.75 1.06036 7718.85
275 regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795] High confidence 2579.49 1.20953 3119.98
udp-glucose 4-epimerase (ec 5.1.3.2) (galactowaldenase) (udp- galactose 4-epimerase). [swissprot;acc:q14376] Low confidence 7958.12 1.06021 7506.19

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/