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 1425 to 1474 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
179 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] Measured Subtracted 4266.04 5843.51 1577.47
huntingtin interacting protein c. [refseq;acc:nm_012272] Rooted 55.0737 66.0298 10.9561
huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] Ranked Divided 226.884 194.79 1.16476
mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] Squared 25326.3 18354.1 1.37987
myosin vc (myosin 5c). [swissprot;acc:q9nqx4] Measured 21591.5 27904.5 1.29238
palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5] Rooted 50.272 43.4634 1.15665
phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439] Ranked Subtracted 227.357 254.15 26.793
spermatogenesis associated 6. [refseq;acc:nm_019073] Squared 9924.76 25146.6 15221.8
180 amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]
c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596] Measured 10872.4 12447 1574.6
egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215] Rooted Divided 50.2801 43.4779 1.15645
metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] Subtracted 88.4361 77.5112 10.9249
myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] Measured Divided 21591.5 27904.5 1.29238
plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872] Squared 25326.2 18354.1 1.37987
pp3111 protein. [refseq;acc:nm_022156] Ranked Subtracted 227.357 254.15 26.793
tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] Divided 256.228 298.438 1.16474
181 b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] 229.818 267.265 1.16294
beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] Rooted Subtracted 88.4266 77.5047 10.9219
crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] Divided 57.4432 66.3307 1.15472
eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] Measured 4068.56 5252.6 1.29102
hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] Squared 55630.4 76083.7 1.36766
musashi 2 isoform a. [refseq;acc:nm_138962] Measured Subtracted 4241.57 5810.79 1569.22
syntaxin 18. [swissprot;acc:q9p2w9] Ranked 227.357 254.15 26.793
transcription factor iib. [refseq;acc:nm_013242] Squared 64739.9 50300.6 14439.3
182 chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286] Rooted 47.6504 36.9304 10.72
deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (ec 3.6.1.23) (dutpase) (dutp pyrophosphatase). [swissprot;acc:p33316] Squared Divided 61733.5 45224.1 1.36506
histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] Ranked 277.546 240.461 1.15422
musashi 1. [refseq;acc:nm_002442] Measured Subtracted 4241.57 5810.79 1569.22
rd protein. [swissprot;acc:p18615] Ranked 227.357 254.15 26.793
rna-binding protein. [refseq;acc:nm_019027] Measured Divided 4069.83 5252.17 1.29051
splicing factor, arginine/serine-rich 8 (suppressor of white apricot protein homolog). [swissprot;acc:q12872] Squared Subtracted 64739.9 50300.6 14439.3
t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] Rooted Divided 57.45 66.332 1.1546
183 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] Ranked 228.306 198.011 1.153
acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] Squared 79779.8 108084 1.35478
anaphase-promoting complex subunit 2; anaphase-promoting complex 2. [refseq;acc:nm_013366] Subtracted 69124.3 54897.4 14226.9
apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] Measured Divided 4069.83 5252.17 1.29051
enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511] Rooted 57.4586 66.3336 1.15446
glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] Ranked Subtracted 227.357 254.15 26.793
nuclear protein ukp68. [refseq;acc:nm_024824] Measured 4241.57 5810.79 1569.22
regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795] Rooted 47.6504 36.9304 10.72
184 androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108] Ranked 227.357 254.15 26.793
cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Rooted Divided 153.602 133.195 1.15321
ns1-associated protein 1. [refseq;acc:nm_006372] Measured 4069.83 5252.17 1.29051
odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] Ranked 274.027 237.79 1.15239
putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] Rooted Subtracted 47.6504 36.9304 10.72
pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [swissprot;acc:p11498] Squared 48127.9 62245.6 14117.7
small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072] Divided 72886.3 98544.5 1.35203
tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452] Measured Subtracted 10804.7 12363.6 1558.9
185 adiponectin receptor 2. [refseq;acc:nm_024551] Ranked Divided 281.582 246.371 1.14292
atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539] Subtracted 227.357 254.15 26.793

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/