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 2225 to 2274 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1113 phosphoglycerate mutase 1 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme b) (pgam-b) (bpg-dependent pgam 1). [swissprot;acc:p18669] Divided 5910.54 6440.58 1.08968
xylulokinase homolog; xylulokinase (h. influenzae) homolog. [refseq;acc:nm_005108] Subtracted 5950.27 6465.72 515.45
1114 cad protein [includes: glutamine-dependent carbamoyl-phosphate synthase (ec 6.3.5.5); aspartate carbamoyltransferase (ec 2.1.3.2); dihydroorotase (ec 3.5.2.3)]. [swissprot;acc:p27708] 6021.21 6536.45 515.24
phosphoglycerate mutase 2 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme m) (pgam-m) (bpg-dependent pgam 2) (muscle-specific phosphoglycerate mutase). [swissprot;acc:p15259] Divided 5910.54 6440.58 1.08968
1115 5-methyltetrahydrofolate--homocysteine methyltransferase (ec 2.1.1.13) (methionine synthase, vitamin-b12 dependent) (ms). [swissprot;acc:q99707] 5795.13 6314.19 1.08957
tumor necrosis factor, alpha-induced protein 1, endothelial (b12 protein). [swissprot;acc:q13829] Subtracted 5840.65 6355.84 515.19
1116 dynactin complex 50 kda subunit (50 kda dynein-associated polypeptide) (dynamitin) (dctn-50) (dynactin 2). [swissprot;acc:q13561] Divided 5322.16 5798.38 1.08948
polymerase delta-interacting protein 1; tnfaip1-like. [refseq;acc:nm_178863] Subtracted 5840.77 6355.89 515.12
1117 adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236] Divided 5322.16 5798.38 1.08948
mitogen-activated protein kinase kinase kinase 7 (ec 2.7.1.-) (transforming growth factor-beta-activated kinase 1) (tgf-beta- activated kinase 1). [swissprot;acc:o43318] Subtracted 6001.16 6515.9 514.74
1118 adp,atp carrier protein, heart/skeletal muscle isoform t1 (adp/atp translocase 1) (adenine nucleotide translocator 1) (ant 1). [swissprot;acc:p12235] Divided 5322.16 5798.38 1.08948
tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] Subtracted 3658.76 3144.39 514.37
1119 adp,atp carrier protein, fibroblast isoform (adp/atp translocase 2) (adenine nucleotide translocator 2) (ant 2). [swissprot;acc:p05141] Divided 5322.16 5798.38 1.08948
orphan nuclear receptor hmr (early response protein nak1) (tr3 orphan receptor). [swissprot;acc:p22736] Subtracted 6230.49 6744.5 514.01
1120 heat shock factor binding protein 1. [swissprot;acc:o75506] Divided 5915.42 6443.77 1.08932
nuclear hormone receptor nor-1 (neuron-derived orphan receptor 1) (mitogen induced nuclear orphan receptor). [swissprot;acc:q92570] Subtracted 6230.38 6744.35 513.97
1121 nucleolar protein nop5 (nucleolar protein 5) (nop58) (hspc120). [swissprot;acc:q9y2x3] Divided 4338.49 4725.86 1.08929
orphan nuclear receptor nurr1 (immediate-early response protein not) (transcriptionally inducible nuclear receptor). [swissprot;acc:p43354] Subtracted 6229.16 6742.79 513.63
1122 importin alpha-6 subunit (karyopherin alpha-5 subunit). [swissprot;acc:o15131] 5792.08 6305.67 513.59
isocitrate dehydrogenase [nadp], mitochondrial precursor (ec 1.1.1.42) (oxalosuccinate decarboxylase) (idh) (nadp+-specific icdh) (idp) (icd-m). [swissprot;acc:p48735] Divided 7937.72 8646.38 1.08928
1123 argininosuccinate lyase (ec 4.3.2.1) (arginosuccinase) (asal). [swissprot;acc:p04424] 5857.48 6380.4 1.08927
interleukin enhancer-binding factor 1 (cellular transcription factor ilf-1). [swissprot;acc:q01167] Subtracted 5651.07 6164.55 513.48
1124 suppressor of cytokine signaling 1 (socs-1) (jak-binding protein) (jab) (stat induced stat inhibitor 1) (ssi-1) (tec-interacting protein 3) (tip-3). [swissprot;acc:o15524] 5946.33 6459.79 513.46
transducin-like enhancer protein 2 (esg2). [swissprot;acc:q04725] Divided 6288.27 6846.97 1.08885
1125 glia maturation factor gamma (gmf-gamma). [swissprot;acc:o60234] Subtracted 5946.33 6459.79 513.46
transducin-like enhancer protein 1 (esg1). [swissprot;acc:q04724] Divided 6287.07 6845.28 1.08879
1126 asc-1 complex subunit p100. [refseq;acc:nm_032204] Subtracted 5946.33 6459.79 513.46
importin alpha-6 subunit (karyopherin alpha-5 subunit). [swissprot;acc:o15131] Divided 5792.08 6305.67 1.08867
1127 fk506-binding protein 1a (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (12 kda fkbp) (fkbp-12) (immunophilin fkbp12). [swissprot;acc:p20071] Subtracted 5946.33 6459.79 513.46
yip1 interacting factor homolog; yip1p-interacting factor; putative rab5-interacting protein; putative transmembrane protein 54tmp. [refseq;acc:nm_020470] Divided 5790.65 6303.92 1.08864
1128 voltage-gated potassium channel beta-3 subunit (k+ channel beta-3 subunit) (kv-beta-3). [swissprot;acc:o43448] 6303.94
Subtracted 513.29
1129 choline o-acetyltransferase (ec 2.3.1.6) (choactase) (choline acetylase) (chat). [swissprot;acc:p28329] 5790.66 6303.95
voltage-gated potassium channel beta-1 subunit (k+ channel beta-1 subunit) (kv-beta-1). [swissprot;acc:q14722] Divided 5790.65 6303.92 1.08864
1130 methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial precursor (ec 1.2.1.27) (mmsdh). [swissprot;acc:q02252] Subtracted 5790.67 6303.95 513.28
similar to putative transmembrane protein; homolog of yeast golgi membrane protein yif1p (yip1p-interacting factor). [refseq;acc:nm_033557] Divided 5790.65 6303.92 1.08864
1131 aflatoxin b1 aldehyde reductase 2 (ec 1.-.-.-) (afb1-ar 2). [swissprot;acc:o95154]
voltage-gated potassium channel beta-2 subunit (k+ channel beta-2 subunit) (kv-beta-2) (hkvbeta2). [swissprot;acc:q13303] Subtracted 6303.93 513.28
1132 aflatoxin b1 aldehyde reductase 1 (ec 1.-.-.-) (afb1-ar 1) (aldoketoreductase 7). [swissprot;acc:o43488]
alpha/beta hydrolase domain containing protein 3; lung alpha/beta hydrolase 3. [refseq;acc:nm_138340] Divided 6303.92 1.08864
1133 golgi membrane protein sb140; smooth muscle cell associated protein 5. [refseq;acc:nm_030799]
yip1 interacting factor homolog; yip1p-interacting factor; putative rab5-interacting protein; putative transmembrane protein 54tmp. [refseq;acc:nm_020470] Subtracted 513.27
1134 alpha/beta hydrolase domain containing protein 1 isoform 2; lung alpha/beta hydrolase protein 1. [refseq;acc:nm_152870] Divided 1.08864
voltage-gated potassium channel beta-1 subunit (k+ channel beta-1 subunit) (kv-beta-1). [swissprot;acc:q14722] Subtracted 513.27
1135 methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial precursor (ec 1.2.1.27) (mmsdh). [swissprot;acc:q02252] Divided 5790.67 6303.95 1.08864
similar to putative transmembrane protein; homolog of yeast golgi membrane protein yif1p (yip1p-interacting factor). [refseq;acc:nm_033557] Subtracted 5790.65 6303.92 513.27
1136 10 kda heat shock protein, mitochondrial (hsp10) (10 kda chaperonin) (cpn10). [swissprot;acc:q04984] Divided 1.08864
aflatoxin b1 aldehyde reductase 2 (ec 1.-.-.-) (afb1-ar 2). [swissprot;acc:o95154] Subtracted 513.27
1137 alpha/beta hydrolase domain containing protein 3; lung alpha/beta hydrolase 3. [refseq;acc:nm_138340]
rab acceptor 1 (prenylated); prenylated rab acceptor 1. [refseq;acc:nm_006423] Divided 1.08864

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/