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 501 to 550 of 19268 in total
Value Type  : Ranked
Rank
description
Network Comparison Type
Interaction Map
Filtered
red
green
network_comparison
63 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] Subtracted High confidence 1 260.532 204.309 56.223
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Divided 0 8519.83 11453 1.34428
putative rna-binding protein 7 (rna binding motif protein 7). [swissprot;acc:q9y580] Low confidence 1 265.688 239.902 1.10749
spir-2 protein (fragment). [sptrembl;acc:q8wwl2] Subtracted High confidence 0 18662.8 15627 3035.8
64 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] 1 260.532 204.309 56.223
early hematopoietic zinc finger. [refseq;acc:nm_015461] Low confidence 0 5850.23 8903.28 3053.05
fos-related antigen 2. [swissprot;acc:p15408] 1 202.793 182.961 19.832
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] Divided High confidence 266.868 336.159 1.25965
hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [swissprot;acc:q16543] Subtracted 0 8152.55 11134.8 2982.25
selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] Divided Low confidence 14463 11356 1.2736
similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517] High confidence 15264 20387 1.33563
transcription factor jun-d. [swissprot;acc:p17535] Low confidence 1 202.709 183.361 1.10552
65 alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7] 0 10172.1 12943.5 1.27245
e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409] High confidence 7853.67 10406.3 1.32502
guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] 1 267.136 336.077 1.25807
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Subtracted 0 8519.83 11453 2933.17
p28 ing5. [refseq;acc:nm_032329] Low confidence 12418.8 9391.47 3027.33
protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] 1 202.792 182.974 19.818
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] High confidence 187.457 243.678 56.221
transcription factor jun-b. [swissprot;acc:p17275] Divided Low confidence 202.728 183.388 1.10546
66 blocked early in transport 1 homolog (s. cerevisiae) like; golgi snare 15 kda protein. [refseq;acc:nm_016526] Subtracted 0 11290 8270.5 3019.5
fos-related antigen 1 (fra-1). [swissprot;acc:p15407] 1 202.79 183.017 19.773
guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] Divided High confidence 267.136 336.077 1.25807
heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174] 0 11461 15180 1.32449
kinesin-like protein kif13b (kinesin-like protein gakin). [swissprot;acc:q9nqt8] Low confidence 7923.89 10030.4 1.26584
mitochondrial tumor suppressor gene 1; transcription factor mtsg1; at2 receptor-interacting protein 1; erythroid differentiation-related gene. [refseq;acc:nm_020749] 1 221.902 200.783 1.10518
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 High confidence 0 9830 6909 2921
uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] 1 187.458 243.678 56.22
67 dynamin-like 120 kda protein, mitochondrial precursor (optic atrophy 1 gene protein). [swissprot;acc:o60313] Divided Low confidence 0 11636.2 14697.6 1.26309
guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] High confidence 1 267.14 336.075 1.25805
presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341] 0 10793.5 14291.5 1.32408
protein kinase, lysine deficient 3. [refseq;acc:nm_020922] Subtracted Low confidence 13320.5 10324.5 2996
purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491] High confidence 8932.56 11823.3 2890.74
putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865] Low confidence 1 195.817 215.516 19.699
retinoblastoma-associated factor 600. [refseq;acc:nm_020765] Divided 165.535 149.799 1.10505
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 High confidence 187.458 243.677 56.219
68 40s ribosomal protein s26. [swissprot;acc:p02383] 0 14269.7 17098 2828.3
60s ribosomal protein l37a. [swissprot;acc:p12751] Divided Low confidence 1 239.692 217.005 1.10455
fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] Subtracted 0 9449.27 12378.5 2929.23
guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] Divided High confidence 1 267.139 336.075 1.25805
potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Subtracted Low confidence 225.735 245.308 19.573
purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491] Divided High confidence 0 8932.56 11823.3 1.32362
repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] Low confidence 7803.58 9824.6 1.25899
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] Subtracted High confidence 1 187.462 243.673 56.211
69 collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400] Divided 0 7704.7 10174.1 1.32051
elongation factor ts, mitochondrial precursor (ef-ts) (ef-tsmt). [swissprot;acc:p43897] Subtracted 16290.7 13464.8 2825.9
guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488] Divided 1 267.14 336.075 1.25805
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 Low confidence 0 9830 6909 2921
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] High confidence 1 284.753 228.934 55.819
putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:q96hn2] Low confidence 195.851 215.424 19.573

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/