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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Gene Rank description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 551 to 600 of 9634 in total
Value Type  : Measured
Network Comparison Type  : Divided
Rank
description
Interaction Map
Filtered
red
green
network_comparison
138 kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] High confidence 1 2755.15 2094.3 1.31555
ubiquitin-conjugating enzyme e2-17 kda 3 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 3). [swissprot;acc:p47986] 0 204.382 154.804 1.32026
139 60s ribosomal protein l37a. [swissprot;acc:p12751] Low confidence 1 5762.4 6277.91 1.08946
amiloride-sensitive cation channel 3 isoform a; testis sodium channel 1; proton-gated cation channel subunit; modulatory subunit of asic2a; amiloride-sensitive cation channel 3, testis. [refseq;acc:nm_004769] 0 147.185 191.025 1.29786
associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] High confidence 736.737 561.038 1.31317
potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] 1 2759.61 2099.49 1.31442
140 amiloride-sensitive sodium channel gamma-subunit (epithelial na+ channel gamma subunit) (gamma enac) (nonvoltage-gated sodium channel 1 gamma subunit) (scneg) (gamma nach). [swissprot;acc:p51170] Low confidence 0 147.188 191.013 1.29775
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 1 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
vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [swissprot;acc:o95670] High confidence 0 934.726 1222.89 1.30829
141 brachyury protein (t protein). [swissprot;acc:o15178] Low confidence 1 6171.76 6720.84 1.08897
ccr4-not transcription complex, subunit 7 (ccr4-associated factor 1) (caf1) (btg1 binding factor 1). [swissprot;acc:q9uiv1] High confidence 0 1161.88 891.114 1.30385
sarcoplasmic/endoplasmic reticulum calcium atpase 1 (ec 3.6.3.8) (calcium pump 1) (serca1) (sr ca(2+)-atpase 1) (calcium-transporting atpase sarcoplasmic reticulum type, fast twitch skeletal muscle isoform) (endoplasmic reticulum class 1/2 ca(2+) atpase). [swissprot;acc:o14983] Low confidence 108.441 83.5883 1.29732
small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] High confidence 1 4405.4 5782.08 1.3125
142 metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] 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
presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7] High confidence 0 874 1139 1.3032
solute carrier family 26, member 11. [refseq;acc:nm_173626] Low confidence 598.037 462.96 1.29177
143 3-hydroxyanthranilate 3,4-dioxygenase (ec 1.13.11.6) (3-hao) (3-hydroxyanthranilic acid dioxygenase) (3-hydroxyanthranilate oxygenase). [swissprot;acc:p46952] 1 10696.6 11639.5 1.08815
beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] High confidence 9275.1 7089.65 1.30826
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] Low confidence 0 261.105 336.584 1.28908
putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] High confidence 187 144 1.29861
144 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Low confidence 749.494 965.202 1.2878
beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] 1 7692.29 8370.25 1.08814
sad1/unc-84 protein-like 1. [swissprot;acc:o94901] High confidence 3349.9 4362.61 1.30231
uridine kinase-like 1. [swissprot;acc:q9nwz5] 0 633.433 821.711 1.29723
145 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] Low confidence 1 7693.93 8366.42 1.08741
likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033] High confidence 0 287.903 372.961 1.29544
lipocalin-interacting membrane receptor. [refseq;acc:nm_018113] Low confidence 553.827 430.121 1.28761
ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] High confidence 1 16771.5 12889.1 1.30122
146 adenosine deaminase (ec 3.5.4.4) (adenosine aminohydrolase). [swissprot;acc:p00813] Low confidence 0 1073.89 835.57 1.28522
associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] High confidence 1 11068 8508.5 1.30082
cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2] 0 291.639 377.574 1.29466
pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] Low confidence 1 10685.5 11612.9 1.08679
147 cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6] High confidence 0 292.152 378.206 1.29455
gaba-a receptor-associated protein. [sptrembl;acc:q9by60] Low confidence 1310 1681.67 1.28372
pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] 1 10684.1 11611.2 1.08677
putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] High confidence 11068 8508.5 1.30082
148 associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463]
cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187] 0 293.178 379.474 1.29435
defender against cell death 1 (dad-1). [swissprot;acc:p46966] Low confidence 1 6893.42 7491.39 1.08675
williams beuren syndrome critical region 20a isoform 2; nol1/nop2/sun gene family member; williams-beuren syndrome critical region protein 20 copy a; williams beuren syndrome chromosome region 20. [refseq;acc:nm_018044] 0 409.972 322.947 1.26947
149 cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329] High confidence 293.178 379.474 1.29435
glycine cleavage system h protein, mitochondrial precursor. [swissprot;acc:p23434] Low confidence 745.137 945.391 1.26875
neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] High confidence 1 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
150 metaxin 1. [swissprot;acc:q13505] High confidence 0 933.395 723.368 1.29035
protein hspc134 (protein cda04). [swissprot;acc:q9by43] 1 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
williams beuren syndrome chromosome region 20c isoform 1. [refseq;acc:nm_032158] 0 410.28 323.433 1.26852

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/