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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Filtered Value Type Rank Gene description green Interaction Map Network Comparison Type network_comparison red
Results: HTML CSV LaTeX Showing element 501 to 550 of 19268 in total
Filtered  : 0
Value Type  : Ranked
Rank
description
green
Interaction Map
Network Comparison Type
network_comparison
red
126 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 Divided 1.17872 14899.4
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 Subtracted 1825.6 12314.9
putative protein-tyrosine phosphatase tpte (ec 3.1.3.48). [swissprot;acc:p56180] 14123.3 Low confidence 1822.2 15945.5
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 Divided 1.18216 9722.71
127 ccr4-not transcription complex, subunit 7 (ccr4-associated factor 1) (caf1) (btg1 binding factor 1). [swissprot;acc:q9uiv1] 13530.6 Subtracted 1798.6 11732
dna helicase homolog (fragment). [sptrembl;acc:q9y645] 18475.5 Low confidence 1814.7 16660.8
scribble. [refseq;acc:nm_015356] 11814.4 Divided 1.1766 10041.1
trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] 11119.7 High confidence 1.18152 9411.34
128 60s ribosomal protein l39. [swissprot;acc:p02404] 9794.29 1.18073 11564.4
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] 10879.6 Low confidence 1.17496 9259.51
lifeguard; kiaa0950 protein. [refseq;acc:nm_012306] 12965.5 Subtracted 1804.2 11161.3
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 1771.09 9722.71
129 60s ribosomal protein l39. [swissprot;acc:p02404] 9794.29 1770.11 11564.4
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] 10865.5 Low confidence Divided 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
piwi-like 2; miwi like. [refseq;acc:nm_018068] 15008.1 Low confidence Subtracted 1801.4 13206.7
130 enigma protein; lim domain protein. [refseq;acc:nm_005451] 17069.5 High confidence Divided 1.17914 14476.2
potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] 13174.5 Subtracted 1748.2 14922.7
scribble. [refseq;acc:nm_015356] 11814.4 Low confidence 1773.3 10041.1
sedlin. [swissprot;acc:o14582] 13646 Divided 1.17433 16024.9
131 dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692] 9873.58 High confidence 1.17887 8375.43
integral membrane protein cii-3b. [sptrembl;acc:o75609] 13204.2 Subtracted 1747.4 14951.6
mitochondrial 39s ribosomal protein l39 (l39mt) (mrp-l39) (mrp-l5) (pred22 protein). [swissprot;acc:q9nyk5] 5609 Low confidence Divided 1.17013 4793.5
transcription factor bteb4 (basic transcription element binding- protein 4) (bte-binding protein 4) (krueppel-like factor 16) (novel sp1-like zinc finger transcription factor 2) (transcription factor nslp2). [swissprot;acc:q9bxk1] 13277.6 Subtracted 1762.2 15039.8
132 glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712] 10962.4 1754.1 12716.5
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 Divided 1.17001 16411.9
myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] 12622.8 High confidence Subtracted 1739.8 10883
rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372] 22389 Divided 1.1754 19048
133 alpha-amylase, salivary precursor (ec 3.2.1.1) (1,4-alpha-d-glucan glucanohydrolase). [swissprot;acc:p04745] 13113.5 Low confidence 1.16709 11236.1
alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7] 8009 High confidence 1.17537 6814
mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [refseq;acc:nm_022362] 15405.6 Subtracted 1739.2 17144.8
potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] 13174.5 Low confidence 1748.2 14922.7
134 cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187] 10489.3 High confidence Divided 1.17404 12314.9
maspin precursor (protease inhibitor 5). [swissprot;acc:p36952] 15123 Low confidence Subtracted 1730 16853
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 13890.3 High confidence 1732.7 12157.6
sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] 7893.05 Low confidence Divided 1.1669 9210.38
135 bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132] 10603.2 High confidence Subtracted 1732.09 8871.11
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 Divided 1.17404 12314.9
phosphatidylinositol 4-kinase alpha (ec 2.7.1.67) (pi4-kinase) (ptdins-4-kinase) (pi4k-alpha). [swissprot;acc:p42356] 13250 Low confidence 1.16475 15432.9
serpin b11. [swissprot;acc:q96p15] 15123 Subtracted 1730 16853
136 cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2] 10506.8 High confidence Divided 1.17403 12335.3
cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452] 15123 Low confidence Subtracted 1730 16853
polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393] 11028.8 High confidence 1730.6 12759.4
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 13977.2 Low confidence Divided 1.16242 12024.2
137 cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6] 10501 High confidence 1.17403 12328.5
homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099] 21041 Low confidence Subtracted 1727 19314
lifeguard; kiaa0950 protein. [refseq;acc:nm_012306] 12965.5 Divided 1.16165 11161.3
maspin precursor (protease inhibitor 5). [swissprot;acc:p36952] 15123 High confidence Subtracted 1730 16853
138 beta tubulin 1, class vi. [refseq;acc:nm_030773] 14503.8 Low confidence 1709.5 12794.3
likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033] 10549.4 High confidence Divided 1.17397 12384.7

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/