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 1251 to 1300 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
626 putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865] Divided 6228.39 7013.19 1.126
regulator of chromosome condensation (cell cycle regulatory protein). [swissprot;acc:p18754] Subtracted 8618.32 9340.98 722.66
627 limkain b1. [refseq;acc:nm_019081] Divided 6228.39 7013.19 1.126
zinc finger homeobox protein 1b (smad interacting protein 1) (smadip1) (hrihfb2411). [swissprot;acc:o60315] Subtracted 8618.32 9340.98 722.66
628 putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:q96hn2] Divided 6228.39 7013.19 1.126
transcription factor 8 (nil-2-a zinc finger protein) (negative regulator of il2). [swissprot;acc:p37275] Subtracted 8618.32 9340.98 722.66
629 cellular repressor of e1a-stimulated genes. [refseq;acc:nm_003851] Divided 6228.39 7013.19 1.126
neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] Subtracted 5201.41 4479.76 721.65
630 adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306]
disks large-associated protein 3 (dap-3) (sap90/psd-95-associated protein 3) (sapap3) (psd-95/sap90 binding protein 3) (fragment). [swissprot;acc:o95886] Divided 6228.39 7013.19 1.126
631 adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] Subtracted 5201.41 4479.76 721.65
kininogen precursor (alpha-2-thiol proteinase inhibitor) [contains: bradykinin]. [swissprot;acc:p01042] Divided 6228.39 7013.19 1.126
632 disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6]
leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] Subtracted 5201.41 4479.76 721.65
633 fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322]
ferritin light chain (ferritin l subunit). [swissprot;acc:p02792] Divided 6228.39 7013.19 1.126
634 disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [swissprot;acc:q9y2h0]
leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] Subtracted 5201.41 4479.76 721.65
635 ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8] Divided 6228.97 7013.53 1.12595
laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047] Subtracted 5201.41 4479.76 721.65
636 proteasome subunit alpha type 5 (ec 3.4.25.1) (proteasome zeta chain) (macropain zeta chain) (multicatalytic endopeptidase complex zeta chain). [swissprot;acc:p28066] Divided 5713.41 6432.92 1.12593
thymic stromal co-transporter. [refseq;acc:nm_033051] Subtracted 5201.41 4479.76 721.65
637 l-myc-1 proto-oncogene protein. [swissprot;acc:p12524] 4889.21 5610.52 721.31
putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361] Divided 7756.51 8731.76 1.12573
638 n-myc proto-oncogene protein. [swissprot;acc:p04198] Subtracted 4889.71 5610.69 720.98
nucleoside diphosphate kinase a (ec 2.7.4.6) (ndk a) (ndp kinase a) (tumor metastatic process-associated protein) (metastasis inhibition factor nm23) (nm23-h1). [swissprot;acc:p15531] Divided 7755.69 8730.74 1.12572
639 ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546] Subtracted 4890.51 5610.95 720.44
nucleoside diphosphate kinase b (ec 2.7.4.6) (ndk b) (ndp kinase b) (nm23-h2) (c-myc purine-binding transcription factor puf). [swissprot;acc:p22392] Divided 7753.59 8728.13 1.12569
640 ga binding protein beta-2 chain (gabp-beta-2 subunit) (transcription factor e4tf1-47) (gapbp-2) (nuclear respiratory factor-2 subunit gamma). [swissprot;acc:q06545] Subtracted 4890.51 5610.95 720.44
glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712] Divided 4811.02 5414.64 1.12547
641 nadh-ubiquinone oxidoreductase 23 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-23kd) (ci-23kd) (tyky subunit). [swissprot;acc:o00217] Subtracted 4890.51 5610.95 720.44
peroxisomal n1-acetyl-spermine/spermidine oxidase. [refseq;acc:nm_152911] Divided 4810.85 5414.21 1.12542
642 atpase inhibitor, mitochondrial precursor. [swissprot;acc:q9uii2] 5414.23
elongation of very long chain fatty acids protein 1 (cgi-88). [swissprot;acc:q9bw60] Subtracted 4890.55 5610.96 720.41
643 polyamine oxidase isoform 1; polyamine oxidase; flavin-containing spermine oxidase; putative cyclin g1 interacting protein; flavin containing amine oxidase. [refseq;acc:nm_019025] Divided 4810.85 5414.23 1.12542
scratch; scratch 1. [refseq;acc:nm_031309] Subtracted 7281.6 8001.64 720.04
644 cytochrome c-type heme lyase (ec 4.4.1.17) (cchl) (holocytochrome c- type synthase). [swissprot;acc:p53701] Divided 4810.85 5414.22 1.12542
proteasome subunit alpha type 5 (ec 3.4.25.1) (proteasome zeta chain) (macropain zeta chain) (multicatalytic endopeptidase complex zeta chain). [swissprot;acc:p28066] Subtracted 5713.41 6432.92 719.51
645 glutathione s-transferase theta 1 (ec 2.5.1.18) (gst class-theta) (glutathione transferase t1-1). [swissprot;acc:p30711] Divided 4810.71 5413.89 1.12538
myc proto-oncogene protein (c-myc). [swissprot;acc:p01106] Subtracted 4892.16 5611.48 719.32
646 dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03] 7273.78 7991.72 717.94
fibrillarin (34 kda nucleolar scleroderma antigen). [swissprot;acc:p22087] Divided 4019.88 4522.61 1.12506
647 potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Subtracted 2411.93 1695.45 716.48
short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] Divided 5167.88 4594.43 1.12481
648 cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] Subtracted 2414.22 1698.12 716.1
splicing factor 3a subunit 3 (spliceosome associated protein 61) (sap 61) (sf3a60). [swissprot;acc:q12874] Divided 5248.07 5901.72 1.12455
649 potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980] Subtracted 2414.77 1698.75 716.02
splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [swissprot;acc:q15459] Divided 5248.07 5901.72 1.12455
650 golgi reassembly stacking protein 2; golgi reassembly stacking protein 2, 55 kda. [refseq;acc:nm_015530] 8362.81 9402.7 1.12435
potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] Subtracted 2416.53 1700.8 715.73

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/