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 4058 to 4107 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
2029 presynaptic protein sap102 (synapse-associated protein 102) (neuroendocrine-dlg) (ne-dlg) (discs, large homolog 3). [swissprot;acc:q92796] Subtracted 5835.45 6159.46 324.01
2030 channel associated protein of synapse-110 (chapsyn-110) (discs, large homolog 2). [swissprot;acc:q15700] 5835.4 6159.4 324
histone-lysine n-methyltransferase, h3 lysine-9 specific 2 (ec 2.1.1.43) (histone h3-k9 methyltransferase 2) (h3-k9-hmtase 2) (suppressor of variegation 3-9 homolog 2) (su(var)3-9 homolog 2). [swissprot;acc:q9h5i1] Divided 5060.82 5350.93 1.05732
2031 eukaryotic translation initiation factor 2 subunit 1 (eukaryotic translation initiation factor 2 alpha subunit) (eif-2-alpha) (eif- 2alpha) (eif-2a). [swissprot;acc:p05198]
presynaptic protein sap97 (synapse-associated protein 97) (discs, large homolog 1) (hdlg). [swissprot;acc:q12959] Subtracted 5835.15 6159.11 323.96
2032 histone-lysine n-methyltransferase, h3 lysine-9 specific 1 (ec 2.1.1.43) (histone h3-k9 methyltransferase 1) (h3-k9-hmtase 1) (suppressor of variegation 3-9 homolog 1) (su(var)3-9 homolog 1). [swissprot;acc:o43463] Divided 5060.82 5350.93 1.05732
lysyl-trna synthetase (ec 6.1.1.6) (lysine--trna ligase) (lysrs). [swissprot;acc:q15046] Subtracted 4941.92 5265.09 323.17
2033 dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9] Divided 6101.12 6449.87 1.05716
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] Subtracted 5019.3 5342.36 323.06
2034 topoisomerase (dna) ii binding protein. [refseq;acc:nm_007027] Divided 6920.71 7315.59 1.05706
transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [swissprot;acc:p23193] Subtracted 5019.3 5342.36 323.06
2035 acyl-coenzyme a oxidase 1, peroxisomal (ec 1.3.3.6) (palmitoyl-coa oxidase) (aox). [swissprot;acc:q15067] Divided 6920.71 7315.59 1.05706
wilms' tumor 1-associating protein (wt1-associated protein). [swissprot;acc:q15007] Subtracted 6628.99 6952.04 323.05
2036 atp synthase f chain, mitochondrial (ec 3.6.3.14). [swissprot;acc:p56134] Divided 6920.71 7315.59 1.05706
ran-binding protein 2 (ranbp2) (nuclear pore complex protein nup358) (nucleoporin nup358) (358 kda nucleoporin) (p270). [swissprot;acc:p49792] Subtracted 5800.93 6123.38 322.45
2037 probable atp-dependent helicase ddx35 (deah-box protein 35). [swissprot;acc:q9h5z1] Divided 6920.71 7315.59 1.05706
ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260] Subtracted 5800.22 6122.6 322.38
2038 5799.84 6122.18 322.34
transcription initiation factor tfiid 70 kda subunit (tafii-70) (tafii-80) (tafii80). [swissprot;acc:p49848] Divided 7088.08 7492.23 1.05702
2039 kh-type splicing regulatory protein (fuse binding protein 2); kh-type splicing regulatory protein (fuse-binding protein 2). [refseq;acc:nm_003685] Subtracted 5817.07 6138.59 321.52
mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956] Divided 3646.01 3449.54 1.05696
2040 far upstream element-binding protein; far upstream element binding protein; fuse-binding protein. [refseq;acc:nm_003902] Subtracted 5817.41 6138.8 321.39
rho-gtpase-activating protein 8. [swissprot;acc:q9nsg0] Divided 6036.68 6379.44 1.05678
2041 fuse binding protein 3 (fragment). [sptrembl;acc:q92946] Subtracted 5817.56 6138.9 321.34
rho-gtpase-activating protein 1 (gtpase-activating protein rhoogap) (rho-related small gtpase protein activator) (cdc42 gtpase-activating protein) (p50-rhogap). [swissprot;acc:q07960] Divided 6036.68 6379.44 1.05678
2042 enthoprotin; epsin 4; clathrin interacting protein localized in the trans-golgi region. [refseq;acc:nm_014666] Subtracted 5520.26 5841.16 320.9
kinesin light chain 2 (klc 2). [swissprot;acc:q9h0b6] Divided 6036.62 6379.38 1.05678
2043 af-6 protein. [swissprot;acc:p55196] Subtracted 5746.65 6067.27 320.62
kinesin heavy chain (ubiquitous kinesin heavy chain) (ukhc). [swissprot;acc:p33176] Divided 6036.68 6379.44 1.05678
2044 kinesin heavy chain isoform 5c (kinesin heavy chain neuron-specific 2). [swissprot;acc:o60282]
solute carrier family 2, facilitated glucose transporter, member 6 (glucose transporter type 6) (glucose transporter type 9). [swissprot;acc:q9ugq3] Subtracted 5429.27 5749.69 320.42
2045 neuronal kinesin heavy chain (nkhc) (kinesin heavy chain isoform 5a) (kinesin heavy chain neuron-specific 1). [swissprot;acc:q12840] Divided 6036.68 6379.44 1.05678
solute carrier family 2, facilitated glucose transporter, member 8 (glucose transporter type 8) (glucose transporter type x1). [swissprot;acc:q9ny64] Subtracted 5429.27 5749.69 320.42
2046 kinesin light chain 1 (klc 1). [swissprot;acc:q07866] Divided 6036.73 6379.48 1.05678
putative gtp-binding protein ptd004 (pro2455). [swissprot;acc:q9ntk5] Subtracted 5775.22 6094.89 319.67
2047 alcohol dehydrogenase class iii chi chain (ec 1.1.1.1) (glutathione- dependent formaldehyde dehydrogenase) (ec 1.2.1.1) (fdh). [swissprot;acc:p11766] 6834.03 7153.66 319.63
transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664] Divided 6036.68 6379.44 1.05678
2048 esterase d (ec 3.1.1.1). [swissprot;acc:p10768] Subtracted 6834.03 7153.66 319.63
exocyst complex component sec3 (bm-012). [swissprot;acc:q9nv70] Divided 6036.68 6379.44 1.05678
2049 swi/snf-related matrix-associated actin-dependent regulator of chromatin c2 isoform a; mammalian chromatin remodeling complex brg1-associated factor 170; chromatin remodeling complex baf170 subunit; swi3-like protein; swi/snf complex 170 kda subunit. [refseq;acc:nm_003075] 5634.94 5953.19 1.05648
Subtracted 318.25
2050 adapter-related protein complex 2 beta 1 subunit (beta-adaptin) (plasma membrane adaptor ha2/ap2 adaptin beta subunit) (clathrin assembly protein complex 2 beta large chain) (ap105b). [swissprot;acc:p21851] Divided 5556.36 5870.11 1.05647
polybromo 1. [refseq;acc:nm_018165] Subtracted 5634.8 5952.7 317.9
2051 60s ribosomal protein l26. [swissprot;acc:q02877] Divided 3601.97 3409.48 1.05646
swi/snf-related matrix-associated actin-dependent regulator of chromatin a5; sucrose nonfermenting-like 5. [refseq;acc:nm_003601] Subtracted 5634.8 5952.7 317.9
2052 polybromo 1. [refseq;acc:nm_018165] Divided 1.05642
possible global transcription activator snf2l4 (snf2-beta) (brg-1 protein) (mitotic growth and transcription activator) (brahma protein homolog 1). [swissprot;acc:p51532] Subtracted 317.9
2053 possible global transcription activator snf2l1. [swissprot;acc:p28370]
swi/snf-related matrix-associated actin-dependent regulator of chromatin a5; sucrose nonfermenting-like 5. [refseq;acc:nm_003601] Divided 1.05642
2054 possible global transcription activator snf2l4 (snf2-beta) (brg-1 protein) (mitotic growth and transcription activator) (brahma protein homolog 1). [swissprot;acc:p51532]

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/