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 Network Comparison Type Value Type Interaction Map Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 201 to 250 of 3730 in total
Network Comparison Type  : Divided
Value Type  : Measured
Interaction Map  : High confidence
Rank
description
Filtered
green
red
network_comparison
101 cullin homolog 2 (cul-2). [swissprot;acc:q13617] 1 3225.65 2353.63 1.3705
putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7] 0 977 1442 1.47595
102 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]
presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] 1 3225.65 2353.63 1.3705
103 cullin homolog 1 (cul-1). [swissprot;acc:q13616]
transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [swissprot;acc:p51854] 0 290.667 197.333 1.47298
104 musashi 2 isoform a. [refseq;acc:nm_138962] 1 5810.79 4241.57 1.36996
nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] 0 7500.75 5106.93 1.46874
105 fos-related antigen 2. [swissprot;acc:p15408] 2208.1 3233.86 1.46454
musashi 1. [refseq;acc:nm_002442] 1 5810.79 4241.57 1.36996
106 nuclear protein ukp68. [refseq;acc:nm_024824]
tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888] 0 858.525 1251.66 1.45792
107 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] 1 5843.51 4266.04 1.36977
isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252] 0 472.605 326.677 1.4467
108 basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811] 421 292 1.44178
filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [refseq;acc:nm_001457] 1 5899.76 4366.44 1.35116
109 dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9] 0 144 100 1.44
rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] 1 5899.76 4366.44 1.35116
110 protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873]
spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813] 0 2637 1833 1.43863
111 protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] 1 5899.76 4366.44 1.35116
ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] 0 2063 2965.5 1.43747
112 lats homolog 1. [refseq;acc:nm_004690] 112.25 160 1.42539
u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] 1 5899.76 4366.44 1.35116
113 filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]
sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5] 0 112.25 160 1.42539
114 daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] 472.945 671.769 1.4204
huntingtin interacting protein c. [refseq;acc:nm_012272] 1 5807.72 4300.47 1.35048
115 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] 28492 21185 1.34491
zinc finger protein-like 1; zinc-finger protein in men1 region. [refseq;acc:nm_006782] 0 543 385 1.41039
116 alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7] 475 668 1.40632
pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] 1 28492 21185 1.34491
117 pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]
ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] 0 122 170.5 1.39754
118 methyltransferase like 2. [refseq;acc:nm_018396] 43 31 1.3871
pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] 1 28492 21185 1.34491
119 estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454] 0 460.2 633.85 1.37734
mitochondrial solute carrier protein. [refseq;acc:nm_145305] 1 28492 21185 1.34491
120 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] 6895.98 5136.78 1.34247
signal-induced proliferation-associated 1-like 1. [refseq;acc:nm_015556] 0 359.631 494.417 1.37479
121 4-aminobutyrate aminotransferase, mitochondrial precursor (ec 2.6.1.19) (gamma-amino-n-butyrate transaminase) (gaba transaminase) (gaba aminotransferase) (gaba-at) (gaba-t). [swissprot;acc:p80404] 14.3333 19.6667 1.3721
transcription factor jun-b. [swissprot;acc:p17275] 1 7488.4 5579.18 1.3422
122 high-mobility group 20a. [refseq;acc:nm_018200] 6893.53 5140.14 1.34112
sh2-b homolog; likely ortholog of mouse sh2 domain-containing putative adapter sh2-b; sh2-b gamma signaling protein; sh2-b alpha signaling protein. [refseq;acc:nm_015503] 0 78 107 1.37179
123 cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] 1 18172.1 24260.3 1.33503
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] 0 1681.3 2285.62 1.35944
124 microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] 1 18168.9 24255.7 1.33501
regulator of chromosome condensation (cell cycle regulatory protein). [swissprot;acc:p18754] 0 2399.76 3248.95 1.35386
125 microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] 1 18168.9 24255.7 1.33501
probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] 0 812.166 1095.42 1.34876

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/