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 Network Comparison Type Value Type Interaction Map red Filtered network_comparison green
Results: HTML CSV LaTeX Showing element 551 to 600 of 9634 in total
Network Comparison Type  : Divided
Value Type  : Measured
Rank
description
Interaction Map
red
Filtered
network_comparison
green
138 kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] High confidence 2755.15 1 1.31555 2094.3
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] 204.382 0 1.32026 154.804
139 60s ribosomal protein l37a. [swissprot;acc:p12751] Low confidence 5762.4 1 1.08946 6277.91
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] 147.185 0 1.29786 191.025
associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] High confidence 736.737 1.31317 561.038
potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] 2759.61 1 1.31442 2099.49
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 147.188 0 1.29775 191.013
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 1 1.31425 2100.27
ubiquitin-activating enzyme e1c (uba3 homolog, yeast); ubiquitin-activating enzyme e1c (homologous to yeast uba3). [refseq;acc:nm_003968] Low confidence 7628.44 1.08944 8310.74
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 934.726 0 1.30829 1222.89
141 brachyury protein (t protein). [swissprot;acc:o15178] Low confidence 6171.76 1 1.08897 6720.84
ccr4-not transcription complex, subunit 7 (ccr4-associated factor 1) (caf1) (btg1 binding factor 1). [swissprot;acc:q9uiv1] High confidence 1161.88 0 1.30385 891.114
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 1.29732 83.5883
small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] High confidence 4405.4 1 1.3125 5782.08
142 metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] 9276.47 1.30832 7090.37
ornithine carbamoyltransferase, mitochondrial precursor (ec 2.1.3.3) (otcase) (ornithine transcarbamylase). [swissprot;acc:p00480] Low confidence 10803 1.08837 11757.7
presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7] High confidence 874 0 1.3032 1139
solute carrier family 26, member 11. [refseq;acc:nm_173626] Low confidence 598.037 1.29177 462.96
143 3-hydroxyanthranilate 3,4-dioxygenase (ec 1.13.11.6) (3-hao) (3-hydroxyanthranilic acid dioxygenase) (3-hydroxyanthranilate oxygenase). [swissprot;acc:p46952] 10696.6 1 1.08815 11639.5
beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] High confidence 9275.1 1.30826 7089.65
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 261.105 0 1.28908 336.584
putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] High confidence 187 1.29861 144
144 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Low confidence 749.494 1.2878 965.202
beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] 7692.29 1 1.08814 8370.25
sad1/unc-84 protein-like 1. [swissprot;acc:o94901] High confidence 3349.9 1.30231 4362.61
uridine kinase-like 1. [swissprot;acc:q9nwz5] 633.433 0 1.29723 821.711
145 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] Low confidence 7693.93 1 1.08741 8366.42
likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033] High confidence 287.903 0 1.29544 372.961
lipocalin-interacting membrane receptor. [refseq;acc:nm_018113] Low confidence 553.827 1.28761 430.121
ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] High confidence 16771.5 1 1.30122 12889.1
146 adenosine deaminase (ec 3.5.4.4) (adenosine aminohydrolase). [swissprot;acc:p00813] Low confidence 1073.89 0 1.28522 835.57
associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] High confidence 11068 1 1.30082 8508.5
cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2] 291.639 0 1.29466 377.574
pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] Low confidence 10685.5 1 1.08679 11612.9
147 cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6] High confidence 292.152 0 1.29455 378.206
gaba-a receptor-associated protein. [sptrembl;acc:q9by60] Low confidence 1310 1.28372 1681.67
pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] 10684.1 1 1.08677 11611.2
putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] High confidence 11068 1.30082 8508.5
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] 293.178 0 1.29435 379.474
defender against cell death 1 (dad-1). [swissprot;acc:p46966] Low confidence 6893.42 1 1.08675 7491.39
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] 409.972 0 1.26947 322.947
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 1.29435 379.474
glycine cleavage system h protein, mitochondrial precursor. [swissprot;acc:p23434] Low confidence 745.137 1.26875 945.391
neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] High confidence 11068 1 1.30082 8508.5
pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] Low confidence 10665 1.08647 11587.2
150 metaxin 1. [swissprot;acc:q13505] High confidence 933.395 0 1.29035 723.368
protein hspc134 (protein cda04). [swissprot;acc:q9by43] 11068 1 1.30082 8508.5
serine/threonine-protein kinase plk (ec 2.7.1.-) (plk-1) (serine- threonine protein kinase 13) (stpk13). [swissprot;acc:p53350] Low confidence 7136.14 1.08628 7751.87
williams beuren syndrome chromosome region 20c isoform 1. [refseq;acc:nm_032158] 410.28 0 1.26852 323.433

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/