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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene Value Type Interaction Map Network Comparison Type description Filtered green network_comparison red
Results: HTML CSV LaTeX Showing element 501 to 550 of 19268 in total
Value Type  : Ranked
Rank
Interaction Map
Network Comparison Type
description
Filtered
green
network_comparison
red
63 Low confidence Divided 60s ribosomal protein l37a. [swissprot;acc:p12751] 0 15783.5 1.27551 12374.3
putative rna-binding protein 7 (rna binding motif protein 7). [swissprot;acc:q9y580] 1 239.902 1.10749 265.688
Subtracted dynamin-like 120 kda protein, mitochondrial precursor (optic atrophy 1 gene protein). [swissprot;acc:o60313] 0 14697.6 3061.4 11636.2
jun dimerization protein. [refseq;acc:nm_130469] 1 182.73 20.072 202.802
64 High confidence Divided guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] 336.159 1.25965 266.868
similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517] 0 20387 1.33563 15264
Subtracted 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] 1 204.309 56.223 260.532
hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [swissprot;acc:q16543] 0 11134.8 2982.25 8152.55
Low confidence Divided selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] 11356 1.2736 14463
transcription factor jun-d. [swissprot;acc:p17535] 1 183.361 1.10552 202.709
Subtracted early hematopoietic zinc finger. [refseq;acc:nm_015461] 0 8903.28 3053.05 5850.23
fos-related antigen 2. [swissprot;acc:p15408] 1 182.961 19.832 202.793
65 High confidence Divided e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409] 0 10406.3 1.32502 7853.67
guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] 1 336.077 1.25807 267.136
Subtracted oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] 0 11453 2933.17 8519.83
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] 1 243.678 56.221 187.457
Low confidence Divided alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7] 0 12943.5 1.27245 10172.1
transcription factor jun-b. [swissprot;acc:p17275] 1 183.388 1.10546 202.728
Subtracted p28 ing5. [refseq;acc:nm_032329] 0 9391.47 3027.33 12418.8
protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] 1 182.974 19.818 202.792
66 High confidence Divided guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] 336.077 1.25807 267.136
heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174] 0 15180 1.32449 11461
Subtracted 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 2921 9830
uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] 1 243.678 56.22 187.458
Low confidence Divided kinesin-like protein kif13b (kinesin-like protein gakin). [swissprot;acc:q9nqt8] 0 10030.4 1.26584 7923.89
mitochondrial tumor suppressor gene 1; transcription factor mtsg1; at2 receptor-interacting protein 1; erythroid differentiation-related gene. [refseq;acc:nm_020749] 1 200.783 1.10518 221.902
Subtracted blocked early in transport 1 homolog (s. cerevisiae) like; golgi snare 15 kda protein. [refseq;acc:nm_016526] 0 8270.5 3019.5 11290
fos-related antigen 1 (fra-1). [swissprot;acc:p15407] 1 183.017 19.773 202.79
67 High confidence Divided guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] 336.075 1.25805 267.14
presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341] 0 14291.5 1.32408 10793.5
Subtracted purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491] 11823.3 2890.74 8932.56
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] 1 243.677 56.219 187.458
Low confidence Divided dynamin-like 120 kda protein, mitochondrial precursor (optic atrophy 1 gene protein). [swissprot;acc:o60313] 0 14697.6 1.26309 11636.2
retinoblastoma-associated factor 600. [refseq;acc:nm_020765] 1 149.799 1.10505 165.535
Subtracted protein kinase, lysine deficient 3. [refseq;acc:nm_020922] 0 10324.5 2996 13320.5
putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865] 1 215.516 19.699 195.817
68 High confidence Divided guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] 336.075 1.25805 267.139
purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491] 0 11823.3 1.32362 8932.56
Subtracted 40s ribosomal protein s26. [swissprot;acc:p02383] 17098 2828.3 14269.7
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] 1 243.673 56.211 187.462
Low confidence Divided 60s ribosomal protein l37a. [swissprot;acc:p12751] 217.005 1.10455 239.692
repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] 0 9824.6 1.25899 7803.58
Subtracted fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] 12378.5 2929.23 9449.27
potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] 1 245.308 19.573 225.735
69 High confidence Divided collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400] 0 10174.1 1.32051 7704.7
guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488] 1 336.075 1.25805 267.14
Subtracted elongation factor ts, mitochondrial precursor (ef-ts) (ef-tsmt). [swissprot;acc:p43897] 0 13464.8 2825.9 16290.7
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] 1 228.934 55.819 284.753
Low confidence Divided testis-specific protein tex28. [swissprot;acc:o15482] 235.017 1.10425 259.517
transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [swissprot;acc:p23193] 0 12610.3 1.25855 15870.7

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/