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 1051 to 1100 of 16578 in total
Value Type  : Measured
Filtered  : 1
Rank
description
Network Comparison Type
Interaction Map
red
green
network_comparison
263 oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Divided Low confidence 7424.14 7877.49 1.06106
trs85 homolog. [swissprot;acc:q9y2l5] High confidence 24896.4 20431.7 1.21852
264 cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] 4987.58 4094.57 1.2181
ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812] Subtracted 12503.3 11212 1291.3
cylindromatosis (turban tumor syndrome); cylindromatosis 1, turban tumor syndrome. [refseq;acc:nm_015247] Low confidence 10008.8 9508.16 500.64
diacylglycerol kinase, theta (ec 2.7.1.107) (diglyceride kinase) (dgk- theta) (dag kinase theta). [swissprot;acc:p52824] Divided 6396.44 6786.96 1.06105
265 epsin 3. [refseq;acc:nm_017957] Subtracted 8559.94 9059.13 499.19
splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] High confidence 4638.1 5923.4 1285.3
synaptojanin 2 (ec 3.1.3.36) (synaptic inositol-1,4,5-trisphosphate 5- phosphatase 2) (fragment). [swissprot;acc:o15056] Divided Low confidence 8081.02 8573.8 1.06098
wd-repeat protein wdc146. [swissprot;acc:q9c0j8] High confidence 24806.9 20369.9 1.21782
266 carboxypeptidase a1 precursor (ec 3.4.17.1). [swissprot;acc:p15085] Low confidence 8817.03 9353.9 1.06089
cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] High confidence 24806.9 20369.9 1.21782
dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Subtracted Low confidence 7650.5 8148.73 498.23
solute carrier family 4 (anion exchanger), member 1, adaptor protein; kidney anion exchanger adaptor protein; kanadaptin; lung cancer oncogene 3. [refseq;acc:nm_018158] High confidence 11222.2 9948.93 1273.27
267 choline/ethanolaminephosphotransferase. [refseq;acc:nm_006090] Divided Low confidence 8813.83 9348.71 1.06069
cyclin-dependent kinases regulatory subunit 2 (cks-2). [swissprot;acc:p33552] Subtracted High confidence 11222.2 9948.93 1273.27
ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] Divided 14021.4 11523 1.21682
synaptojanin 1 (ec 3.1.3.36) (synaptic inositol-1,4,5-trisphosphate 5- phosphatase 1). [swissprot;acc:o43426] Subtracted Low confidence 8082.34 8579.93 497.59
268 catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [refseq;acc:nm_003798] High confidence 11222.2 9948.93 1273.27
cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] Divided 24473.9 20127.8 1.21593
reversion-inducing cysteine-rich protein with kazal motifs precursor (hreck) (suppressor of tumorigenicity 15) (st15). [swissprot;acc:o95980] Low confidence 8813.83 9348.71 1.06069
tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452] Subtracted 8940.43 9437.54 497.11
269 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] 7647.22 8143.47 496.25
choline phosphotransferase 1; cholinephosphotransferase 1 alpha; cholinephosphotransferase 1. [refseq;acc:nm_020244] Divided 8813.95 9348.9 1.06069
crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] Subtracted High confidence 4808.79 6074.21 1265.42
u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] Divided 4590.18 5575.52 1.21466
270 carboxypeptidase a5. [refseq;acc:nm_080385] Low confidence 8811.88 9345.51 1.06056
fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] High confidence 23640.2 19479.8 1.21358
putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865] Subtracted Low confidence 6846.84 6350.78 496.06
t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] High confidence 4810.22 6075.04 1264.82
271 carboxypeptidase b precursor (ec 3.4.17.2) (pancreas-specific protein) (pasp). [swissprot;acc:p15086] Divided Low confidence 8811.69 9345.26 1.06055
chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] High confidence 2554.89 3093.78 1.21092
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] Subtracted 4812.01 6076.09 1264.08
tropomyosin alpha 4 chain (tropomyosin 4) (tm30p1). [swissprot;acc:p07226] Low confidence 7630.1 8125.09 494.99
272 delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial precursor (ec 1.5.1.12) (p5c dehydrogenase). [swissprot;acc:p30038] Divided 11162 10526.2 1.0604
histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] High confidence 3858.52 4669.27 1.21012
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] Subtracted 1991.03 3221.38 1230.35
presenilins associated rhomboid-like protein. [refseq;acc:nm_018622] Low confidence 9099.15 9593.54 494.39
273 eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] Divided High confidence 3199.4 3870.8 1.20985
phospholipase a-2-activating protein (plap) (pla2p). [swissprot;acc:q9y263] Low confidence 11162 10526.2 1.0604
ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424] Subtracted High confidence 5181.2 6410.58 1229.38
tissue alpha-l-fucosidase precursor (ec 3.2.1.51) (alpha-l-fucosidase i) (alpha-l-fucoside fucohydrolase). [swissprot;acc:p04066] Low confidence 8417.28 8911.22 493.94
274 c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596] 8926.58 9420 493.42
chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286] Divided High confidence 3119.98 2579.49 1.20953
ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] Subtracted 5181.2 6410.58 1229.38
small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] Divided Low confidence 7718.85 8184.75 1.06036
275 deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (ec 3.6.1.23) (dutpase) (dutp pyrophosphatase). [swissprot;acc:p33316] Subtracted High confidence 10264.9 9043.51 1221.39
fucosidase, alpha-l- 2, plasma. [refseq;acc:nm_032020] Low confidence 8414.05 8907.06 493.01
regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795] Divided High confidence 3119.98 2579.49 1.20953
udp-glucose 4-epimerase (ec 5.1.3.2) (galactowaldenase) (udp- galactose 4-epimerase). [swissprot;acc:q14376] Low confidence 7506.19 7958.12 1.06021

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/