MK5 Microarray Data

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

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Showing element 7486 to 7535 of 8289 in total

Value Type  : Measured
Network Comparison Type  : Divided
Interaction Map  : Low confidence
Filtered  : 1

Rank	description	red	green	network_comparison
4258	gdp-mannose pyrophosphorylase b isoform 1; mannose-1-phosphate guanylyltransferase; amphoterin induced gene 3. [refseq;acc:nm_013334]	8305.6	8469.2	1.0197
4259	protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378]	7466.38	7613.31	1.01968
4260	b-lymphocyte activation-related protein. [sptrembl;acc:q96pn3]	9143.33	9323.18	1.01967
4261	zinc finger protein zfp. [refseq;acc:nm_018651]	9143.35	9323.2
4262	zinc finger protein 197 (znf20). [swissprot;acc:o14709]	9143.34	9323.19
4263	zinc finger protein mgc21738. [refseq;acc:nm_145044]
4264	zinc finger protein 75. [swissprot;acc:p51815]	9143.31	9323.17
4265	zinc finger protein 224. [swissprot;acc:q9nzl3]	9143.34	9323.19
4266	gonadotropin inducible transcription repressor-1 (giot-1). [swissprot;acc:q8taf7]	9143.35	9323.2
4267	zinc finger protein 74 (hznf7). [swissprot;acc:q16587]	9143.34	9323.19
4268	krab zinc finger protein. [sptrembl;acc:q96jc4]	9143.35	9323.2
4269	zinc finger protein 1; likely ortholog of mouse zinc finger protein 1. [refseq;acc:nm_153688]	9143.33	9323.19
4270	zinc finger protein 285. [refseq;acc:nm_152354]	9143.34
4271	zinc finger protein 257 (bone marrow zinc finger 4) (bmzf-4). [swissprot;acc:q9y2q1]
4272	krueppel-related zinc finger protein 1 (hkr1 protein). [swissprot;acc:p10072]
4273	zinnc finger protein gli4 (krueppel-related zinc finger protein 4) (hkr4 protein). [swissprot;acc:p10075]	9143.32	9323.18
4274	zinc finger protein 273 (zinc finger protein hzf9) (fragment). [swissprot;acc:q14593]	9143.34	9323.19
4275	zinc finger protein 345 (zinc finger protein hzf10). [swissprot;acc:q14585]	9143.35	9323.2
4276	zinc finger protein 121 (zinc finger protein 20) (fragment). [swissprot;acc:p58317]
4277	mesenchymal stem cell protein dsc43. [refseq;acc:nm_016643]	9143.33	9323.19
4278	zinc finger protein 73 (zinc finger protein 186) (hznf2). [swissprot;acc:o43830]	9143.34
4279	zinc finger protein zfp6 (fragment). [sptrembl;acc:q92967]	9143.33	9323.18
4280	zinc finger protein 223. [swissprot;acc:q9uk11]		9323.19
4281	zinc finger protein 354b. [refseq;acc:nm_058230]	9143.34
4282	zinc finger protein 126 (hzf-2) (fragment). [swissprot;acc:p35275]	9143.35	9323.2
4283	zinc finger protein 454. [refseq;acc:nm_182594]	9143.34	9323.19
4284	zinc finger protein 354c; krab-zinc finger protein synten. [refseq;acc:nm_014594]
4285	zinc finger protein 135. [swissprot;acc:p52742]	9143.35	9323.2
4286	zinc finger protein loc163140 (fragment). [sptrembl;acc:q86wm6]
4287	putative zinc finger protein (fragment). [sptrembl;acc:q8n692]	9143.31	9323.17
4288	zinc finger protein 169 (fragment). [swissprot;acc:q14929]	9143.33	9323.19
4289	zinc finger protein 77 (znfpt1) (fragment). [swissprot;acc:q15935]	9143.31	9323.17
4290	zinc finger protein 32 (zinc finger protein kox30) (fragment). [swissprot;acc:p17041]	9143.32	9323.18
4291	kruppel-type zinc finger protein. [refseq;acc:nm_021045]	9143.34	9323.19
4292	similar to zinc finger protein 85 (zinc finger protein hpf4) (htf1). [refseq;acc:nm_145287]	9143.35	9323.2
4293	zinc finger protein 358. [swissprot;acc:q9nw07]	9143.34	9323.19
4294	zinc finger protein 266 (zinc finger protein hzf1) (fragment). [swissprot;acc:q14584]	9143.39	9323.22
4295	zinc finger-like protein (fragment). [sptrembl;acc:q9uia8]	9143.31	9323.17
4296	zinc finger protein 80 (znfpt17). [swissprot;acc:p51504]	9143.33	9323.18
4297	krueppel-related zinc finger protein 3 (hkr3 protein). [swissprot;acc:p10074]	9143.31
4298	zinc finger protein zfd25. [swissprot;acc:q9uii5]	9143.34	9323.19
4299	zinc finger protein 431. [swissprot;acc:q8tf32]	9143.35	9323.2
4300	f23269_2. [sptrembl;acc:o75290]	9143.34	9323.19
4301	dj54b20.4 (novel krab box containing c2h2 type zinc finger protein). [sptrembl;acc:q96qh7]
4302	similar to zinc finger protein 136. [refseq;acc:nm_145295]	9143.35	9323.2
4303	zinc finger protein 44 (zinc finger protein kox7) (gonadotropin inducible transcription repressor-2) (giot-2). [swissprot;acc:p15621]	9143.34	9323.19
4304	zinc finger protein 350; zinc-finger protein zbrk1. [refseq;acc:nm_021632]	9143.33
4305	zinc finger protein 415. [refseq;acc:nm_018355]	9143.34
4306	zinc finger protein 347 (zinc finger 1111). [swissprot;acc:q96se7]	9143.35
4307	zinc finger protein 230 (zinc finger protein fdzf2). [swissprot;acc:q9uie0]	9143.34

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.