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

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/