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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Value Type Rank Filtered description Gene Network Comparison Type green Interaction Map network_comparison red
Results: HTML CSV LaTeX Showing element 501 to 550 of 19268 in total
Value Type  : Ranked
Rank
Filtered
description
Network Comparison Type
green
Interaction Map
network_comparison
red
63 1 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] Divided 336.178 High confidence 1.25973 266.865
jun dimerization protein. [refseq;acc:nm_130469] Subtracted 182.73 Low confidence 20.072 202.802
nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952] 204.309 High confidence 56.223 260.532
putative rna-binding protein 7 (rna binding motif protein 7). [swissprot;acc:q9y580] Divided 239.902 Low confidence 1.10749 265.688
64 0 early hematopoietic zinc finger. [refseq;acc:nm_015461] Subtracted 8903.28 3053.05 5850.23
hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [swissprot;acc:q16543] 11134.8 High confidence 2982.25 8152.55
selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] Divided 11356 Low confidence 1.2736 14463
similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517] 20387 High confidence 1.33563 15264
1 ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511] Subtracted 204.309 56.223 260.532
fos-related antigen 2. [swissprot;acc:p15408] 182.961 Low confidence 19.832 202.793
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] Divided 336.159 High confidence 1.25965 266.868
transcription factor jun-d. [swissprot;acc:p17535] 183.361 Low confidence 1.10552 202.709
65 0 alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7] 12943.5 1.27245 10172.1
e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409] 10406.3 High confidence 1.32502 7853.67
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Subtracted 11453 2933.17 8519.83
p28 ing5. [refseq;acc:nm_032329] 9391.47 Low confidence 3027.33 12418.8
1 guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] Divided 336.077 High confidence 1.25807 267.136
protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Subtracted 182.974 Low confidence 19.818 202.792
serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007] 243.678 High confidence 56.221 187.457
transcription factor jun-b. [swissprot;acc:p17275] Divided 183.388 Low confidence 1.10546 202.728
66 0 blocked early in transport 1 homolog (s. cerevisiae) like; golgi snare 15 kda protein. [refseq;acc:nm_016526] Subtracted 8270.5 3019.5 11290
heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174] Divided 15180 High confidence 1.32449 11461
kinesin-like protein kif13b (kinesin-like protein gakin). [swissprot;acc:q9nqt8] 10030.4 Low confidence 1.26584 7923.89
nadh-ubiquinone oxidoreductase 13 kda-b subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-b) (ci-13kd-b) (complex i subunit b13). [swissprot;acc:q16718] Subtracted 6909 High confidence 2921 9830
1 fos-related antigen 1 (fra-1). [swissprot;acc:p15407] 183.017 Low confidence 19.773 202.79
guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] Divided 336.077 High confidence 1.25807 267.136
mitochondrial tumor suppressor gene 1; transcription factor mtsg1; at2 receptor-interacting protein 1; erythroid differentiation-related gene. [refseq;acc:nm_020749] 200.783 Low confidence 1.10518 221.902
uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] Subtracted 243.678 High confidence 56.22 187.458
67 0 dynamin-like 120 kda protein, mitochondrial precursor (optic atrophy 1 gene protein). [swissprot;acc:o60313] Divided 14697.6 Low confidence 1.26309 11636.2
presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341] 14291.5 High confidence 1.32408 10793.5
protein kinase, lysine deficient 3. [refseq;acc:nm_020922] Subtracted 10324.5 Low confidence 2996 13320.5
purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491] 11823.3 High confidence 2890.74 8932.56
1 guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] Divided 336.075 1.25805 267.14
putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865] Subtracted 215.516 Low confidence 19.699 195.817
retinoblastoma-associated factor 600. [refseq;acc:nm_020765] Divided 149.799 1.10505 165.535
serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [swissprot;acc:q00005] Subtracted 243.677 High confidence 56.219 187.458
68 0 40s ribosomal protein s26. [swissprot;acc:p02383] 17098 2828.3 14269.7
fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] 12378.5 Low confidence 2929.23 9449.27
purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491] Divided 11823.3 High confidence 1.32362 8932.56
repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] 9824.6 Low confidence 1.25899 7803.58
1 60s ribosomal protein l37a. [swissprot;acc:p12751] 217.005 1.10455 239.692
guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] 336.075 High confidence 1.25805 267.139
potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Subtracted 245.308 Low confidence 19.573 225.735
serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [swissprot;acc:q9y2t4] 243.673 High confidence 56.211 187.462
69 0 collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400] Divided 10174.1 1.32051 7704.7
elongation factor ts, mitochondrial precursor (ef-ts) (ef-tsmt). [swissprot;acc:p43897] Subtracted 13464.8 2825.9 16290.7
nadh-ubiquinone oxidoreductase 13 kda-b subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-b) (ci-13kd-b) (complex i subunit b13). [swissprot;acc:q16718] 6909 Low confidence 2921 9830
transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [swissprot;acc:p23193] Divided 12610.3 1.25855 15870.7
1 guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488] 336.075 High confidence 1.25805 267.14
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] Subtracted 228.934 55.819 284.753

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/