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 1168 to 1217 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
146 xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] Measured Subtracted 2671 871 1800
147 cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] Rooted 41.6851 28.9509 12.7342
forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] Divided 42.0574 50.4237 1.19893
hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] Squared Subtracted 55630.4 76083.7 20453.3
lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461] Ranked 239.32 267.842 28.522
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Divided 50.7983 42.3003 1.2009
protein x 0004. [refseq;acc:nm_016301] Measured Subtracted 2671 871 1800
putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] Divided 11068 8508.5 1.30082
ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] Squared 103496 146848 1.41888
148 associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] Measured 11068 8508.5 1.30082
filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [refseq;acc:nm_001457] Ranked Subtracted 226.582 198.444 28.138
forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] Rooted Divided 42.0577 50.424 1.19892
potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980] Subtracted 41.6879 28.9554 12.7325
ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] Squared Divided 103496 146848 1.41888
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] Subtracted 70011 49783 20228
sad1/unc-84 protein-like 1. [swissprot;acc:o94901] Ranked Divided 296.677 247.559 1.19841
symplekin. [swissprot;acc:q92797] Measured Subtracted 15213.4 13418.1 1795.3
149 anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] Squared Divided 103496 146848 1.41888
atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] Ranked 142 170 1.19718
forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] Rooted 42.0684 50.4323 1.19882
metaxin 1. [swissprot;acc:q13505] Squared Subtracted 60401.6 79875.7 19474.1
neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] Measured Divided 11068 8508.5 1.30082
potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] Rooted Subtracted 41.6969 28.9696 12.7273
rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] Ranked 226.582 198.444 28.138
trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648] Measured 11736.6 13531.9 1795.3
150 amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410] Rooted 42.2825 54.9687 12.6862
enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [swissprot;acc:p30084] Squared 57913.5 76336.3 18422.8
myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] Ranked Divided 55 46 1.19565
pre-mrna cleavage complex ii protein clp1. [swissprot;acc:q92989] Squared 121200 85473.4 1.41799
protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] Ranked Subtracted 226.582 198.444 28.138
protein hspc134 (protein cda04). [swissprot;acc:q9by43] Measured Divided 11068 8508.5 1.30082
serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] Rooted 63.5827 53.0856 1.19774
small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Measured Subtracted 4172.91 5954.48 1781.57
151 chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] Rooted Divided 38.8223 46.4975 1.1977
deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] Squared 250303 354894 1.41786
epoxide hydrolase 1 (ec 3.3.2.3) (microsomal epoxide hydrolase) (epoxide hydratase). [swissprot;acc:p07099] Subtracted 87971.9 69563.1 18408.8
homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] Rooted 50.3065 62.9788 12.6723
myosin vc (myosin 5c). [swissprot;acc:q9nqx4] Ranked Divided 55 46 1.19565
pre-mrna cleavage complex ii protein clp1. [swissprot;acc:q92989] Measured Subtracted 14830.5 13050.3 1780.2
protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] Ranked 226.582 198.444 28.138
sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489] Measured Divided 4578.09 5939.91 1.29746
152 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] Subtracted 5136.78 6895.98 1759.2
luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] Rooted Divided 55.2859 65.9288 1.19251
melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] Measured 23693.7 18263 1.29736
myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] Ranked 55 46 1.19565
oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] Squared Subtracted 73995.1 56003.7 17991.4
septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] Divided 90226 126939 1.4069
u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] Ranked Subtracted 226.582 198.444 28.138
ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] Rooted 50.3247 62.9892 12.6645
153 chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286] Ranked Divided 249.663 298.263 1.19466

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/