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 Network Comparison Type Gene Value Type description Interaction Map red green Filtered network_comparison
Results: HTML CSV LaTeX Showing element 551 to 600 of 16578 in total
Value Type  : Measured
Filtered  : 1
Rank
Network Comparison Type
description
Interaction Map
red
green
network_comparison
138 Subtracted step ii splicing factor slu7. [refseq;acc:nm_006425] Low confidence 9870.83 10591.9 721.07
tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [swissprot;acc:q13625] High confidence 15182.5 13277.9 1904.6
139 Divided 60s ribosomal protein l37a. [swissprot;acc:p12751] Low confidence 5762.4 6277.91 1.08946
potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] High confidence 2759.61 2099.49 1.31442
Subtracted cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493] 12780.7 10876.4 1904.3
vacuolar protein sorting 18 (hvps18). [swissprot;acc:q9p253] Low confidence 7337.57 8055.84 718.27
140 Divided 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] High confidence 2760.28 2100.27 1.31425
ubiquitin-activating enzyme e1c (uba3 homolog, yeast); ubiquitin-activating enzyme e1c (homologous to yeast uba3). [refseq;acc:nm_003968] Low confidence 7628.44 8310.74 1.08944
Subtracted asparagine synthetase [glutamine-hydrolyzing] (ec 6.3.5.4) (glutamine- dependent asparagine synthetase) (ts11 cell cycle control protein). [swissprot;acc:p08243] 9818 10529.5 711.5
homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] High confidence 2597.5 698.5 1899
141 Divided brachyury protein (t protein). [swissprot;acc:o15178] Low confidence 6171.76 6720.84 1.08897
small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] High confidence 4405.4 5782.08 1.3125
Subtracted hbs1-like. [refseq;acc:nm_006620] 2597.5 698.5 1899
vacuolar protein sorting 33b (hvps33b). [swissprot;acc:q9h267] Low confidence 7354.65 8065.08 710.43
142 Divided metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] High confidence 9276.47 7090.37 1.30832
ornithine carbamoyltransferase, mitochondrial precursor (ec 2.1.3.3) (otcase) (ornithine transcarbamylase). [swissprot;acc:p00480] Low confidence 10803 11757.7 1.08837
Subtracted a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] 10392.7 9683.56 709.14
transcription factor jun-d. [swissprot;acc:p17535] High confidence 5638.2 7523.39 1885.19
143 Divided 3-hydroxyanthranilate 3,4-dioxygenase (ec 1.13.11.6) (3-hao) (3-hydroxyanthranilic acid dioxygenase) (3-hydroxyanthranilate oxygenase). [swissprot;acc:p46952] Low confidence 10696.6 11639.5 1.08815
beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] High confidence 9275.1 7089.65 1.30826
Subtracted cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240] 15427.2 13572.8 1854.4
raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] Low confidence 10391.8 9682.99 708.81
144 Divided beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] 7692.29 8370.25 1.08814
sad1/unc-84 protein-like 1. [swissprot;acc:o94901] High confidence 3349.9 4362.61 1.30231
Subtracted bcl2-related ovarian killer. [refseq;acc:nm_032515] Low confidence 4955.33 5659.35 704.02
nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] High confidence 4133.47 5945.32 1811.85
145 Divided beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] Low confidence 7693.93 8366.42 1.08741
ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] High confidence 16771.5 12889.1 1.30122
Subtracted carboxypeptidase n 83 kda chain (carboxypeptidase n regulatory subunit) (fragment). [swissprot;acc:p22792] Low confidence 10374.8 9672.48 702.32
nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] High confidence 4136.36 5943.56 1807.2
146 Divided associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] 11068 8508.5 1.30082
pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] Low confidence 10685.5 11612.9 1.08679
Subtracted platelet glycoprotein v precursor (gpv) (cd42d). [swissprot;acc:p40197] 10374.8 9672.51 702.29
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] High confidence 2671 871 1800
147 Divided pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] Low confidence 10684.1 11611.2 1.08677
putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] High confidence 11068 8508.5 1.30082
Subtracted protein x 0004. [refseq;acc:nm_016301] 2671 871 1800
similar to atp/gtp-binding protein. [sptrembl;acc:q8nem8] Low confidence 9385.4 10086.4 701
148 Divided associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] High confidence 11068 8508.5 1.30082
defender against cell death 1 (dad-1). [swissprot;acc:p46966] Low confidence 6893.42 7491.39 1.08675
Subtracted symplekin. [swissprot;acc:q92797] High confidence 15213.4 13418.1 1795.3
trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648] Low confidence 9385.4 10086.4 701
149 Divided neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] High confidence 11068 8508.5 1.30082
pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] Low confidence 10665 11587.2 1.08647
Subtracted b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056] 10348.7 9656.36 692.34
trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648] High confidence 11736.6 13531.9 1795.3
150 Divided protein hspc134 (protein cda04). [swissprot;acc:q9by43] 11068 8508.5 1.30082
serine/threonine-protein kinase plk (ec 2.7.1.-) (plk-1) (serine- threonine protein kinase 13) (stpk13). [swissprot;acc:p53350] Low confidence 7136.14 7751.87 1.08628
Subtracted 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] 7206.99 7896.81 689.82
small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] High confidence 4172.91 5954.48 1781.57

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/