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 580 to 629 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
145 ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] Measured 16771.5 12889.1 1.30122
146 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] 11068 8508.5 1.30082
huntingtin interacting protein c. [refseq;acc:nm_012272] Rooted 55.0737 66.0298 1.19894
kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193] Ranked 265.632 319.531 1.20291
ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] Squared 103496 146848 1.41888
147 forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] Rooted 42.0574 50.4237 1.19893
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Ranked 50.7983 42.3003 1.2009
putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] Measured 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
forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] Rooted 42.0577 50.424 1.19892
ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] Squared 103496 146848 1.41888
sad1/unc-84 protein-like 1. [swissprot;acc:o94901] Ranked 296.677 247.559 1.19841
149 anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] Squared 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
neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] Measured 11068 8508.5 1.30082
150 myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] Ranked 55 46 1.19565
pre-mrna cleavage complex ii protein clp1. [swissprot;acc:q92989] Squared 121200 85473.4 1.41799
protein hspc134 (protein cda04). [swissprot;acc:q9by43] Measured 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
151 chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] 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
myosin vc (myosin 5c). [swissprot;acc:q9nqx4] Ranked 55 46 1.19565
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 4578.09 5939.91 1.29746
152 luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] Rooted 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
septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] Squared 90226 126939 1.4069
153 chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286] Ranked 249.663 298.263 1.19466
hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] Measured 23693.7 18263 1.29736
luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] Rooted 55.297 65.9236 1.19217
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] Squared 70011 49783 1.40632
154 eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] Rooted 43.5479 51.5473 1.18369
melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] Measured 23693.7 18263 1.29736
regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795] Ranked 249.663 298.263 1.19466
t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] Squared 42788.3 60162.6 1.40605
155 cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240] 126408 89940.5 1.40546
melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] Measured 23693.7 18263 1.29736
putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] Ranked 249.663 298.263 1.19466
small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] Rooted 55.7423 65.6839 1.17835
156 melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] Measured 23693.7 18263 1.29736
regulator of g-protein signaling 20 (rgs20) (regulator of gz- selective protein signaling 1) (gz-selective gtpase-activating protein) (g(z)gap). [swissprot;acc:o76081] Ranked 249.663 298.263 1.19466
septin 10 isoform 1. [refseq;acc:nm_144710] Squared 89578.7 125883 1.40528
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] Rooted 56.3447 66.124 1.17356
157 brain protein 44. [swissprot;acc:o95563] Squared 89182.8 125229 1.40418
eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] Rooted 52.7582 61.9123 1.17351
hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Measured 23693.7 18263 1.29736
transcription factor lbx1. [swissprot;acc:p52954] Ranked 249.663 298.263 1.19466
158 breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] Rooted 56.3507 66.1252 1.17346

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/