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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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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 12914 to 12963 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
1615 dna polymerase epsilon subunit b (ec 2.7.7.7) (dna polymerase ii subunit b). [swissprot;acc:p56282] Ranked Divided 246.38 242.596 1.0156
dystrobrevin alpha (dystrobrevin-alpha). [swissprot;acc:q9y4j8] Squared Subtracted 26167 28674.3 2507.3
heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [swissprot;acc:q00839] Divided 15399.5 17067.9 1.10834
lim homeobox transcription factor 1 alpha (lim/homeobox protein lmx1a) (lim-homeobox protein 1.1) (lmx-1.1). [swissprot;acc:q8te12] Measured 6035.6 6464.5 1.07106
molybdenum cofactor synthesis protein 3 (molybdopterin synthase sulfurylase) (mpt synthase sulfurylase). [swissprot;acc:o95396] Subtracted 6079.19 6503.12 423.93
monoglyceride lipase; lysophospholipase-like. [refseq;acc:nm_007283] Rooted Divided 67.8337 70.1815 1.03461
sterol regulatory element binding protein-1 (srebp-1) (sterol regulatory element-binding transcription factor 1). [swissprot;acc:p36956] Ranked Subtracted 217.446 214.2 3.246
1616 apoptosis antagonizing transcription factor. [refseq;acc:nm_012138] Measured 4078.45 4502.32 423.87
beta-1-syntrophin (59 kda dystrophin-associated protein a1, basic component 1) (dapa1b) (tax interaction protein 43) (tip-43) (syntrophin 2) (bsyn2). [swissprot;acc:q13884] Squared 26167.1 28674.2 2507.1
dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [refseq;acc:nm_016355] Rooted 61.9703 64.1936 2.2233
mitochondrial precursor proteins import receptor (translocase of outer membrane tom70). [swissprot;acc:o94826] Measured Divided 6035.6 6464.5 1.07106
n-acetylglutamate synthase. [refseq;acc:nm_153006] Ranked 223.179 226.611 1.01538
runt-related transcription factor 2 (core-binding factor, alpha 1 subunit) (cbf-alpha 1) (acute myeloid leukemia 3 protein) (oncogene aml-3) (polyomavirus enhancer binding protein 2 alpha a subunit) (pebp2-alpha a) (pea2-alpha a) (sl3-3 enhancer factor 1 alpha a subunit) (sl3/akv core-binding factor alpha a subunit) (osteoblast- specific transcription factor 2) (osf-2). [swissprot;acc:q13950] Squared 15399.5 17067.9 1.10834
twinkle; likely ortholog of mouse t7 gp4-like protein with intramitochondrial nucleoid localization. [refseq;acc:nm_021830] Rooted 62.3332 64.4896 1.03459
ubiquitin-conjugating enzyme e2 variant 1 isoform b; dna-binding protein. [refseq;acc:nm_003349] Ranked Subtracted 208.106 204.867 3.239
1617 beta-2-syntrophin (59 kda dystrophin-associated protein a1, basic component 2) (syntrophin 3) (snt3) (syntrophin-like) (sntl). [swissprot;acc:q13425] Squared 26167.1 28674.2 2507.1
e1b-55kda-associated protein 5 isoform a. [refseq;acc:nm_007040] Divided 15399.5 17067.9 1.10834
lim homeobox transcription factor 1 beta (lim/homeobox protein lmx1b) (lim-homeobox protein 1.2) (lmx-1.2). [swissprot;acc:o60663] Measured 6035.6 6464.5 1.07106
microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268] Subtracted 6298.76 6722.61 423.85
rabaptin, rab gtpase binding effector protein 1; rabaptin-5; neurocrescin. [refseq;acc:nm_004703] Rooted Divided 62.3332 64.4896 1.03459
rho-gtpase activating protein 10. [refseq;acc:nm_020824] Subtracted 61.9703 64.1936 2.2233
serine hydroxymethyltransferase, cytosolic (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [swissprot;acc:p34896] Ranked Divided 221.045 217.699 1.01537
utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [swissprot;acc:q16851] Subtracted 208.113 204.876 3.237
1618 60s ribosomal protein l18. [swissprot;acc:q07020] Squared Divided 15399.5 17067.9 1.10834
f-actin capping protein alpha-3 subunit (capz alpha-3) (germ cell- specific protein 3). [swissprot;acc:q96kx2] Rooted 64.1847 66.4025 1.03455
microtubule-associated protein rp/eb family member 3 (protein eb3). [swissprot;acc:q9upy8] Measured Subtracted 6298.77 6722.62 423.85
nitrilase 1. [refseq;acc:nm_005600] Squared 26167.1 28674.2 2507.1
proteasome subunit beta type 2 (ec 3.4.25.1) (proteasome component c7-i) (macropain subunit c7-i) (multicatalytic endopeptidase complex subunit c7-i). [swissprot;acc:p49721] Measured Divided 6035.6 6464.5 1.07106
sal-like protein 1 (zinc finger protein sall1) (spalt-like transcription factor 1) (hsal1). [swissprot;acc:q9nsc2] Rooted Subtracted 61.9705 64.1938 2.2233
transcription elongation factor a protein 2 (transcription elongation factor s-ii protein 2) (testis-specific s-ii) (transcription elongation factor tfiis.l). [swissprot;acc:q15560] Ranked Divided 227.768 231.246 1.01527
ubiquitin-conjugating enzyme e2 variant 2; 1 alpha,25-dihydroxyvitamin d3-inducible; enterocyte differentiation promoting factor; methyl methanesulfonate sensitive 2, s. cerevisiae, homolog of. [refseq;acc:nm_003350] Subtracted 208.122 204.886 3.236
1619 2-oxoisovalerate dehydrogenase beta subunit, mitochondrial precursor (ec 1.2.4.4) (branched-chain alpha-keto acid dehydrogenase e1 component beta chain) (bckdh e1-beta). [swissprot;acc:p21953] Rooted 61.9705 64.1938 2.2233
adp-ribosylation factor-like protein 1. [swissprot;acc:p40616] Measured Divided 6035.6 6464.5 1.07106
f-actin capping protein beta subunit (capz beta). [swissprot;acc:p47756] Rooted 64.1847 66.4025 1.03455
histidine-rich membrane protein ke4. [swissprot;acc:q92504] Measured Subtracted 6298.81 6722.65 423.84
serine/threonine-protein kinase dcamkl1 (ec 2.7.1.-) (doublecortin- like and cam kinase-like 1). [swissprot;acc:o15075] Squared Divided 31022.4 34382.7 1.10832
survival motor neuron protein (component of gems 1) (gemin1). [swissprot;acc:q16637] Ranked Subtracted 228.496 231.729 3.233
transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [swissprot;acc:p23193] Divided 227.768 231.246 1.01527
utrophin (dystrophin-related protein 1) (drp1) (drp). [swissprot;acc:p46939] Squared Subtracted 26167.1 28674.2 2507.1
1620 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 Divided 6296.52 6743.85 1.07104
ccr4-not transcription complex, subunit 4; not4 (negative regulator of transcription 4, yeast) homolog; ccr4-not transcription complex, subunit. [refseq;acc:nm_013316] Rooted Subtracted 61.9705 64.1938 2.2233
heat shock protein hsp 90-beta (hsp 84) (hsp 90). [swissprot;acc:p08238] Squared Divided 26833.7 29737.4 1.10821
lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitochondrial precursor (ec 2.3.1.-) (e2) (dihydrolipoamide branched chain transacylase) (bckad e2 subunit). [swissprot;acc:p11182] Subtracted 26167.1 28674.2 2507.1
microtubule-associated protein rp/eb family member 1 (apc-binding protein eb1). [swissprot;acc:q15691] Measured 6298.81 6722.65 423.84
ras-related c3 botulinum toxin substrate 1 (p21-rac1) (ras-like protein tc25). [swissprot;acc:p15154] Ranked 228.496 231.729 3.233
s-adenosylmethionine synthetase gamma form (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-ii). [swissprot;acc:p31153] Rooted Divided 64.4022 66.6218 1.03446
transcription initiation factor iib (general transcription factor tfiib) (s300-ii). [swissprot;acc:q00403] Ranked 228.611 225.185 1.01521
1621 calreticulin precursor (crp55) (calregulin) (hacbp) (erp60). [swissprot;acc:p27797] Rooted 58.9585 60.9832 1.03434
doublecortin (lissencephalin-x) (lis-x) (doublin). [swissprot;acc:o43602] Measured Subtracted 6301.03 6724.63 423.6
dystrophin. [swissprot;acc:p11532] Squared 26167.1 28674.2 2507.1

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/