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 194 to 243 of 8289 in total
Value Type  : Measured
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
97 nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09] Low confidence 5811.84 6399.42 1.1011
98 presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] High confidence 2353.63 3225.65 1.3705
transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664] Low confidence 7624.8 8391.85 1.1006
99 cysteine-rich protein 1 (cysteine-rich intestinal protein) (crip) (cysteine-rich heart protein) (hcrhp). [swissprot;acc:p50238] 5752.65 6330.03 1.10037
s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991] High confidence 2353.63 3225.65 1.3705
100 f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315]
set and mynd domain containing 2; hskm-b protein; zinc finger, mynd domain containing 14. [refseq;acc:nm_020197] Low confidence 5752.65 6330.03 1.10037
101 cullin homolog 2 (cul-2). [swissprot;acc:q13617] High confidence 2353.63 3225.65 1.3705
set and mynd domain containing protein 1. [sptrembl;acc:q8nb12] Low confidence 5752.65 6330.03 1.10037
102 presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] High confidence 2353.63 3225.65 1.3705
testis-specific protein tex28. [swissprot;acc:o15482] Low confidence 5060.92 5567.34 1.10006
103 27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [swissprot;acc:o14653]
cullin homolog 1 (cul-1). [swissprot;acc:q13616] High confidence 2353.63 3225.65 1.3705
104 musashi 2 isoform a. [refseq;acc:nm_138962] 4241.57 5810.79 1.36996
ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] Low confidence 10618.8 11681.3 1.10006
105 musashi 1. [refseq;acc:nm_002442] High confidence 4241.57 5810.79 1.36996
ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] Low confidence 10585.5 11638.6 1.09949
106 nuclear protein ukp68. [refseq;acc:nm_024824] High confidence 4241.57 5810.79 1.36996
vacuolar protein sorting 18 (hvps18). [swissprot;acc:q9p253] Low confidence 7337.57 8055.84 1.09789
107 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] High confidence 4266.04 5843.51 1.36977
tumor protein p53 inducible protein 3; quinone oxidoreductase homolog; p53-induced gene 3 protein. [refseq;acc:nm_004881] Low confidence 11371 12479.2 1.09746
108 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] High confidence 4366.44 5899.76 1.35116
septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] Low confidence 10499 11515.8 1.09685
109 rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] High confidence 4366.44 5899.76 1.35116
vacuolar protein sorting 33b (hvps33b). [swissprot;acc:q9h267] Low confidence 7354.65 8065.08 1.0966
110 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 1.09572
protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] High confidence 4366.44 5899.76 1.35116
111 melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] Low confidence 11285.3 10318.5 1.0937
protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] High confidence 4366.44 5899.76 1.35116
112 hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] Low confidence 11285.3 10318.5 1.0937
u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] High confidence 4366.44 5899.76 1.35116
113 filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]
melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] Low confidence 11285.3 10318.5 1.0937
114 huntingtin interacting protein c. [refseq;acc:nm_012272] High confidence 4300.47 5807.72 1.35048
melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] Low confidence 11285.3 10318.5 1.0937
115 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] High confidence 21185 28492 1.34491
melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] Low confidence 11285.3 10318.5 1.0937
116 hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]
pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] High confidence 21185 28492 1.34491
117 melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Low confidence 11285.3 10318.5 1.0937
pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] High confidence 21185 28492 1.34491
118 necdin. [swissprot;acc:q99608] Low confidence 11285.3 10318.5 1.0937
pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] High confidence 21185 28492 1.34491
119 melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Low confidence 11285.3 10318.5 1.0937
mitochondrial solute carrier protein. [refseq;acc:nm_145305] High confidence 21185 28492 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] 5136.78 6895.98 1.34247
melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Low confidence 11285.3 10318.5 1.0937
121 melanoma antigen, family b, 6. [refseq;acc:nm_173523]
transcription factor jun-b. [swissprot;acc:p17275] High confidence 5579.18 7488.4 1.3422
122 high-mobility group 20a. [refseq;acc:nm_018200] 5140.14 6893.53 1.34112

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/