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 318 to 367 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Value Type
Filtered
red
green
network_comparison
40 guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898] Rooted 1 40.2797 24.3705 1.65281
heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174] Squared 0 5.83408 0.742249 7.86
nanos (fragment). [sptrembl;acc:q8wy41] Measured 377 151 2.49669
41 60s ribosomal protein l21. [swissprot;acc:p46778] Ranked 9994.33 6758.83 1.47871
dystrophin. [swissprot;acc:p11532] Squared 98.4011 12.5624 7.83299
guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754] Measured 1 1836.81 907.978 2.02297
Rooted 40.2797 24.3705 1.65281
microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] Squared 144912 81155 1.78562
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] Measured 0 266 645 2.42481
protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] Ranked 1 322 253 1.27273
suppressor of actin 1. [refseq;acc:nm_014016] Rooted 0 3.30572 5.87091 1.77599
42 acyl-coa dehydrogenase, short/branched chain specific, mitochondrial precursor (ec 1.3.99.-) (sbcad) (2-methyl branched chain acyl-coa dehydrogenase) (2-mebcad) (2-methylbutyryl-coenzyme a dehydrogenase) (2-methylbutyryl-coa dehydrogenase). [swissprot;acc:p45954] 5.11118 9.0312 1.76695
adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236] Ranked 8158 5530.5 1.47509
guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775] Measured 1 1857.32 958.237 1.93827
Rooted 40.225 24.7051 1.62821
microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Squared 144911 81154.7 1.78561
nanos (fragment). [sptrembl;acc:q8wy41] 0 33.64 5.39669 6.23345
presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341] Measured 205.439 86.9525 2.36266
proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] Ranked 1 204.641 160.957 1.2714
43 40s ribosomal protein s26. [swissprot;acc:p02383] Rooted 0 9.92134 5.66499 1.75134
cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Squared 1 144876 81136.5 1.78558
elongation factor ts, mitochondrial precursor (ef-ts) (ef-tsmt). [swissprot;acc:p43897] Measured 0 263.66 587.988 2.2301
glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712] Ranked 12143.8 8356.02 1.4533
guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] Rooted 1 40.6302 25.4452 1.59677
guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520] Measured 1881.02 1027.36 1.83093
jun dimerization protein. [refseq;acc:nm_130469] Ranked 204.641 160.957 1.2714
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] Squared 0 16.747 98.4675 5.87971
44 acyl-coa dehydrogenase, short/branched chain specific, mitochondrial precursor (ec 1.3.99.-) (sbcad) (2-methyl branched chain acyl-coa dehydrogenase) (2-mebcad) (2-methylbutyryl-coenzyme a dehydrogenase) (2-methylbutyryl-coa dehydrogenase). [swissprot;acc:p45954] Measured 45.4292 98.5074 2.16837
fos-related antigen 2. [swissprot;acc:p15408] Ranked 1 204.641 161.046 1.2707
gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] Squared 139741 78454.6 1.78117
glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926] Rooted 0 11.9583 6.85565 1.7443
guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] 1 40.5691 25.4263 1.59556
guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] Measured 1931.34 1057.39 1.82652
serpin b12. [swissprot;acc:q96p63] Ranked 0 14604.2 21138.6 1.44743
tigger transposable element derived 6. [refseq;acc:nm_030953] Squared 14.8773 83.3977 5.6057
45 elongation factor ts, mitochondrial precursor (ef-ts) (ef-tsmt). [swissprot;acc:p43897] Rooted 8.79142 14.7392 1.67654
gaba-a receptor-associated protein. [sptrembl;acc:q9by60] Squared 1 129597 73157.5 1.77148
guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] Measured 1926.69 1056.02 1.82448
guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520] Rooted 40.081 25.1546 1.59339
hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8] Ranked 0 14592 21113.7 1.44694
protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] 1 204.641 161.051 1.27066
tigger transposable element derived 6. [refseq;acc:nm_030953] Measured 0 202.374 438.605 2.1673
tigger transposable element derived 7; jerky (mouse) homolog-like. [refseq;acc:nm_033208] Squared 14.8569 83.2781 5.60535
46 60s ribosomal protein l37a. [swissprot;acc:p12751] Ranked 12941.7 18499.2 1.42943
apg3p; pc3-96 protein. [refseq;acc:nm_022488] Squared 1 129597 73157.5 1.77148
deltex 2. [refseq;acc:nm_020892] Rooted 27.634 43.9629 1.5909
fos-related antigen 1 (fra-1). [swissprot;acc:p15407] Ranked 204.642 161.068 1.27053
heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174] Rooted 0 12.53 7.48331 1.67439
neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] Measured 1 779.167 1390.33 1.78438
tigger transposable element derived 1; jerky (mouse) homolog-like. [refseq;acc:nm_145702] Squared 0 14.8562 83.274 5.60534

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/