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 description Gene Value Type green Interaction Map Filtered Network Comparison Type network_comparison red
Results: HTML CSV LaTeX Showing element 501 to 550 of 9634 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Rank
description
green
Interaction Map
Filtered
network_comparison
red
126 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] 114 High confidence 1 1.21277 94
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] 17562.2 Low confidence 0 1.17872 14899.4
lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] 179.639 1 1.06707 191.688
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] 11493.8 High confidence 0 1.18216 9722.71
127 putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] 114 1 1.21277 94
scribble. [refseq;acc:nm_015356] 11814.4 Low confidence 0 1.1766 10041.1
trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] 11119.7 High confidence 1.18152 9411.34
vacuolar protein sorting 33b (hvps33b). [swissprot;acc:q9h267] 190.88 Low confidence 1 1.06705 203.678
128 60s ribosomal protein l39. [swissprot;acc:p02404] 9794.29 High confidence 0 1.18073 11564.4
associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] 114 1 1.21277 94
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] 10879.6 Low confidence 0 1.17496 9259.51
striatin. [swissprot;acc:o43815] 200.796 1 1.06618 214.085
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] 235.572 1.06609 220.969
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] 10865.5 0 1.17478 9248.93
isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252] 12058.6 High confidence 1.17945 14222.5
neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] 114 1 1.21277 94
130 enigma protein; lim domain protein. [refseq;acc:nm_005451] 17069.5 0 1.17914 14476.2
protein hspc134 (protein cda04). [swissprot;acc:q9by43] 114 1 1.21277 94
sedlin. [swissprot;acc:o14582] 13646 Low confidence 0 1.17433 16024.9
striated muscle activator of rho-dependent signaling. [refseq;acc:nm_139166] 211.529 1 1.06602 225.495
131 dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692] 9873.58 High confidence 0 1.17887 8375.43
mitochondrial 39s ribosomal protein l39 (l39mt) (mrp-l39) (mrp-l5) (pred22 protein). [swissprot;acc:q9nyk5] 5609 Low confidence 1.17013 4793.5
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] 242.562 High confidence 1 1.21228 294.053
striatin 4 (zinedin). [swissprot;acc:q9nrl3] 200.825 Low confidence 1.065 213.878
132 daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] 206.997 1.06411 220.268
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] 14027.1 0 1.17001 16411.9
rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372] 22389 High confidence 1.1754 19048
tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] 290 1 1.2069 350
133 alpha-amylase, salivary precursor (ec 3.2.1.1) (1,4-alpha-d-glucan glucanohydrolase). [swissprot;acc:p04745] 13113.5 Low confidence 0 1.16709 11236.1
alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7] 8009 High confidence 1.17537 6814
prominin-like protein 1 precursor (antigen ac133) (cd133 antigen). [swissprot;acc:o43490] 206.997 Low confidence 1 1.06411 220.268
tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] 290 High confidence 1.2069 350
134 cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187] 10489.3 0 1.17404 12314.9
dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] 290 1 1.2069 350
sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] 7893.05 Low confidence 0 1.1669 9210.38
transgelin (smooth muscle protein 22-alpha) (sm22-alpha) (ws3-10) (22 kda actin-binding protein). [swissprot;acc:q01995] 205.431 1 1.06391 218.561
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] 10489.3 High confidence 0 1.17404 12314.9
cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] 290 1 1.2069 350
neuronal protein np25. [swissprot;acc:q9ui15] 205.57 Low confidence 1.06368 218.66
phosphatidylinositol 4-kinase alpha (ec 2.7.1.67) (pi4-kinase) (ptdins-4-kinase) (pi4k-alpha). [swissprot;acc:p42356] 13250 0 1.16475 15432.9
136 cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2] 10506.8 High confidence 1.17403 12335.3
cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] 290 1 1.2069 350
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] 190.854 Low confidence 1.06362 202.996
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 13977.2 0 1.16242 12024.2
137 cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6] 10501 High confidence 1.17403 12328.5
lifeguard; kiaa0950 protein. [refseq;acc:nm_012306] 12965.5 Low confidence 1.16165 11161.3
ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] 290 High confidence 1 1.2069 350
testican-3 precursor. [swissprot;acc:q9bq16] 234.389 Low confidence 1.0635 220.395
138 likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033] 10549.4 High confidence 0 1.17397 12384.7
serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] 234.204 1 1.20493 194.372

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/