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 Filtered Value Type Network Comparison Type Interaction Map description green red network_comparison
Results: HTML CSV LaTeX Showing element 501 to 550 of 19268 in total
Value Type  : Ranked
Rank
Filtered
Network Comparison Type
Interaction Map
description
green
red
network_comparison
63 1 Divided High confidence guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] 336.178 266.865 1.25973
Low confidence putative rna-binding protein 7 (rna binding motif protein 7). [swissprot;acc:q9y580] 239.902 265.688 1.10749
Subtracted High confidence 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] 204.309 260.532 56.223
Low confidence jun dimerization protein. [refseq;acc:nm_130469] 182.73 202.802 20.072
64 0 Divided High confidence similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517] 20387 15264 1.33563
Low confidence selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] 11356 14463 1.2736
Subtracted High confidence hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [swissprot;acc:q16543] 11134.8 8152.55 2982.25
Low confidence early hematopoietic zinc finger. [refseq;acc:nm_015461] 8903.28 5850.23 3053.05
1 Divided High confidence guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] 336.159 266.868 1.25965
Low confidence transcription factor jun-d. [swissprot;acc:p17535] 183.361 202.709 1.10552
Subtracted High confidence 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] 204.309 260.532 56.223
Low confidence fos-related antigen 2. [swissprot;acc:p15408] 182.961 202.793 19.832
65 0 Divided High confidence e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409] 10406.3 7853.67 1.32502
Low confidence alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7] 12943.5 10172.1 1.27245
Subtracted High confidence oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] 11453 8519.83 2933.17
Low confidence p28 ing5. [refseq;acc:nm_032329] 9391.47 12418.8 3027.33
1 Divided High confidence guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] 336.077 267.136 1.25807
Low confidence transcription factor jun-b. [swissprot;acc:p17275] 183.388 202.728 1.10546
Subtracted High confidence 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] 243.678 187.457 56.221
Low confidence protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] 182.974 202.792 19.818
66 0 Divided High confidence heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174] 15180 11461 1.32449
Low confidence kinesin-like protein kif13b (kinesin-like protein gakin). [swissprot;acc:q9nqt8] 10030.4 7923.89 1.26584
Subtracted High confidence 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 9830 2921
Low confidence blocked early in transport 1 homolog (s. cerevisiae) like; golgi snare 15 kda protein. [refseq;acc:nm_016526] 8270.5 11290 3019.5
1 Divided High confidence guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] 336.077 267.136 1.25807
Low confidence mitochondrial tumor suppressor gene 1; transcription factor mtsg1; at2 receptor-interacting protein 1; erythroid differentiation-related gene. [refseq;acc:nm_020749] 200.783 221.902 1.10518
Subtracted High confidence uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] 243.678 187.458 56.22
Low confidence fos-related antigen 1 (fra-1). [swissprot;acc:p15407] 183.017 202.79 19.773
67 0 Divided High confidence presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341] 14291.5 10793.5 1.32408
Low confidence dynamin-like 120 kda protein, mitochondrial precursor (optic atrophy 1 gene protein). [swissprot;acc:o60313] 14697.6 11636.2 1.26309
Subtracted High confidence purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491] 11823.3 8932.56 2890.74
Low confidence protein kinase, lysine deficient 3. [refseq;acc:nm_020922] 10324.5 13320.5 2996
1 Divided High confidence guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] 336.075 267.14 1.25805
Low confidence retinoblastoma-associated factor 600. [refseq;acc:nm_020765] 149.799 165.535 1.10505
Subtracted High confidence 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] 243.677 187.458 56.219
Low confidence putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865] 215.516 195.817 19.699
68 0 Divided High confidence purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491] 11823.3 8932.56 1.32362
Low confidence repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] 9824.6 7803.58 1.25899
Subtracted High confidence 40s ribosomal protein s26. [swissprot;acc:p02383] 17098 14269.7 2828.3
Low confidence fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] 12378.5 9449.27 2929.23
1 Divided High confidence guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] 336.075 267.139 1.25805
Low confidence 60s ribosomal protein l37a. [swissprot;acc:p12751] 217.005 239.692 1.10455
Subtracted High confidence 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] 243.673 187.462 56.211
Low confidence potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] 245.308 225.735 19.573
69 0 Divided High confidence collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400] 10174.1 7704.7 1.32051
Low confidence transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [swissprot;acc:p23193] 12610.3 15870.7 1.25855
Subtracted High confidence elongation factor ts, mitochondrial precursor (ef-ts) (ef-tsmt). [swissprot;acc:p43897] 13464.8 16290.7 2825.9
Low confidence 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 9830 2921
1 Divided High confidence guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488] 336.075 267.14 1.25805
Low confidence testis-specific protein tex28. [swissprot;acc:o15482] 235.017 259.517 1.10425

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/