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 red green 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
red
green
network_comparison
63 1 Divided High confidence guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] 266.865 336.178 1.25973
Low confidence putative rna-binding protein 7 (rna binding motif protein 7). [swissprot;acc:q9y580] 265.688 239.902 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] 260.532 204.309 56.223
Low confidence jun dimerization protein. [refseq;acc:nm_130469] 202.802 182.73 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] 15264 20387 1.33563
Low confidence selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] 14463 11356 1.2736
Subtracted High confidence hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [swissprot;acc:q16543] 8152.55 11134.8 2982.25
Low confidence early hematopoietic zinc finger. [refseq;acc:nm_015461] 5850.23 8903.28 3053.05
1 Divided High confidence guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] 266.868 336.159 1.25965
Low confidence transcription factor jun-d. [swissprot;acc:p17535] 202.709 183.361 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] 260.532 204.309 56.223
Low confidence fos-related antigen 2. [swissprot;acc:p15408] 202.793 182.961 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] 7853.67 10406.3 1.32502
Low confidence alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7] 10172.1 12943.5 1.27245
Subtracted High confidence oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] 8519.83 11453 2933.17
Low confidence p28 ing5. [refseq;acc:nm_032329] 12418.8 9391.47 3027.33
1 Divided High confidence guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] 267.136 336.077 1.25807
Low confidence transcription factor jun-b. [swissprot;acc:p17275] 202.728 183.388 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] 187.457 243.678 56.221
Low confidence protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] 202.792 182.974 19.818
66 0 Divided High confidence heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174] 11461 15180 1.32449
Low confidence kinesin-like protein kif13b (kinesin-like protein gakin). [swissprot;acc:q9nqt8] 7923.89 10030.4 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] 9830 6909 2921
Low confidence blocked early in transport 1 homolog (s. cerevisiae) like; golgi snare 15 kda protein. [refseq;acc:nm_016526] 11290 8270.5 3019.5
1 Divided High confidence guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] 267.136 336.077 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] 221.902 200.783 1.10518
Subtracted High confidence uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] 187.458 243.678 56.22
Low confidence fos-related antigen 1 (fra-1). [swissprot;acc:p15407] 202.79 183.017 19.773
67 0 Divided High confidence presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341] 10793.5 14291.5 1.32408
Low confidence dynamin-like 120 kda protein, mitochondrial precursor (optic atrophy 1 gene protein). [swissprot;acc:o60313] 11636.2 14697.6 1.26309
Subtracted High confidence purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491] 8932.56 11823.3 2890.74
Low confidence protein kinase, lysine deficient 3. [refseq;acc:nm_020922] 13320.5 10324.5 2996
1 Divided High confidence guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] 267.14 336.075 1.25805
Low confidence retinoblastoma-associated factor 600. [refseq;acc:nm_020765] 165.535 149.799 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] 187.458 243.677 56.219
Low confidence putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865] 195.817 215.516 19.699
68 0 Divided High confidence purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491] 8932.56 11823.3 1.32362
Low confidence repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] 7803.58 9824.6 1.25899
Subtracted High confidence 40s ribosomal protein s26. [swissprot;acc:p02383] 14269.7 17098 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] 9449.27 12378.5 2929.23
1 Divided High confidence guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] 267.139 336.075 1.25805
Low confidence 60s ribosomal protein l37a. [swissprot;acc:p12751] 239.692 217.005 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] 187.462 243.673 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] 225.735 245.308 19.573
69 0 Divided High confidence collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400] 7704.7 10174.1 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] 15870.7 12610.3 1.25855
Subtracted High confidence elongation factor ts, mitochondrial precursor (ef-ts) (ef-tsmt). [swissprot;acc:p43897] 16290.7 13464.8 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] 9830 6909 2921
1 Divided High confidence guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488] 267.14 336.075 1.25805
Low confidence testis-specific protein tex28. [swissprot;acc:o15482] 259.517 235.017 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/