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 501 to 550 of 9634 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Rank
description
Interaction Map
Filtered
red
green
network_comparison
126 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] High confidence 1 94 114 1.21277
bromodomain adjacent to zinc finger domain protein 1a (atp-utilizing chromatin assembly and remodeling factor 1) (hacf1) (atp-dependent chromatin remodelling protein) (williams syndrome transcription factor-related chromatin remodeling factor 180) (wcrf180) (hwalp1) (chrac subunit acf1) (hspc317). [swissprot;acc:q9nrl2] Low confidence 0 14899.4 17562.2 1.17872
lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] 1 191.688 179.639 1.06707
ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858] High confidence 0 9722.71 11493.8 1.18216
127 putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] 1 94 114 1.21277
scribble. [refseq;acc:nm_015356] Low confidence 0 10041.1 11814.4 1.1766
trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] High confidence 9411.34 11119.7 1.18152
vacuolar protein sorting 33b (hvps33b). [swissprot;acc:q9h267] Low confidence 1 203.678 190.88 1.06705
128 60s ribosomal protein l39. [swissprot;acc:p02404] High confidence 0 11564.4 9794.29 1.18073
associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] 1 94 114 1.21277
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] Low confidence 0 9259.51 10879.6 1.17496
striatin. [swissprot;acc:o43815] 1 214.085 200.796 1.06618
129 goodpasture antigen-binding protein (ec 2.7.1.37) (gpbp) (collagen type iv alpha 3 binding protein) (star-related lipid transfer protein 11) (stard11) (start domain-containing protein 11). [swissprot;acc:q9y5p4] 220.969 235.572 1.06609
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] 0 9248.93 10865.5 1.17478
isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252] High confidence 14222.5 12058.6 1.17945
neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] 1 94 114 1.21277
130 enigma protein; lim domain protein. [refseq;acc:nm_005451] 0 14476.2 17069.5 1.17914
protein hspc134 (protein cda04). [swissprot;acc:q9by43] 1 94 114 1.21277
sedlin. [swissprot;acc:o14582] Low confidence 0 16024.9 13646 1.17433
striated muscle activator of rho-dependent signaling. [refseq;acc:nm_139166] 1 225.495 211.529 1.06602
131 dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692] High confidence 0 8375.43 9873.58 1.17887
mitochondrial 39s ribosomal protein l39 (l39mt) (mrp-l39) (mrp-l5) (pred22 protein). [swissprot;acc:q9nyk5] Low confidence 4793.5 5609 1.17013
son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583] High confidence 1 294.053 242.562 1.21228
striatin 4 (zinedin). [swissprot;acc:q9nrl3] Low confidence 213.878 200.825 1.065
132 daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] 220.268 206.997 1.06411
mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476] 0 16411.9 14027.1 1.17001
rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372] High confidence 19048 22389 1.1754
tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] 1 350 290 1.2069
133 alpha-amylase, salivary precursor (ec 3.2.1.1) (1,4-alpha-d-glucan glucanohydrolase). [swissprot;acc:p04745] Low confidence 0 11236.1 13113.5 1.16709
alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7] High confidence 6814 8009 1.17537
prominin-like protein 1 precursor (antigen ac133) (cd133 antigen). [swissprot;acc:o43490] Low confidence 1 220.268 206.997 1.06411
tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] High confidence 350 290 1.2069
134 cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187] 0 12314.9 10489.3 1.17404
dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] 1 350 290 1.2069
sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] Low confidence 0 9210.38 7893.05 1.1669
transgelin (smooth muscle protein 22-alpha) (sm22-alpha) (ws3-10) (22 kda actin-binding protein). [swissprot;acc:q01995] 1 218.561 205.431 1.06391
135 cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329] High confidence 0 12314.9 10489.3 1.17404
cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] 1 350 290 1.2069
neuronal protein np25. [swissprot;acc:q9ui15] Low confidence 218.66 205.57 1.06368
phosphatidylinositol 4-kinase alpha (ec 2.7.1.67) (pi4-kinase) (ptdins-4-kinase) (pi4k-alpha). [swissprot;acc:p42356] 0 15432.9 13250 1.16475
136 cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2] High confidence 12335.3 10506.8 1.17403
cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] 1 350 290 1.2069
high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339] Low confidence 202.996 190.854 1.06362
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 0 12024.2 13977.2 1.16242
137 cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6] High confidence 12328.5 10501 1.17403
lifeguard; kiaa0950 protein. [refseq;acc:nm_012306] Low confidence 11161.3 12965.5 1.16165
ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] High confidence 1 350 290 1.2069
testican-3 precursor. [swissprot;acc:q9bq16] Low confidence 220.395 234.389 1.0635
138 likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033] High confidence 0 12384.7 10549.4 1.17397
serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] 1 194.372 234.204 1.20493

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/