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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Value Type Gene description Interaction Map Network Comparison Type Rank network_comparison green Filtered red

Results: HTML CSV LaTeX

Showing element 51 to 100 of 38536 in total

Value Type

: Measured
Network Comparison Type

: Divided

description	Interaction Map	Rank	network_comparison	green	Filtered	red
25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [swissprot;acc:o15528]	High confidence	19	11.6763	26.1599	0	305.45
	High confidence	3079	1	0.00001	1	0.00001
	Low confidence	19	1.29112	3915.4	1	3032.56
	Low confidence	171	1.22585	181.734	0	222.779
26s protease regulatory subunit 4 (p26s4). [swissprot;acc:q03527]	High confidence	1521	1.07379	6376.76	1	5938.56
	Low confidence	1881	1.03263	8422.67		8156.56
26s protease regulatory subunit 6a (tat-binding protein 1) (tbp-1) (proteasome subunit p50). [swissprot;acc:p17980]	High confidence	1527	1.07349	6362.33		5926.76
	Low confidence	2003	1.03218	8372.5		8111.49
26s protease regulatory subunit 6b (mip224) (mb67 interacting protein) (tat-binding protein-7) (tbp-7). [swissprot;acc:p43686]	High confidence	1567	1.07226	6242.94		5822.25
	Low confidence	1203	1.03623	8556.58		8257.44
26s protease regulatory subunit 7 (mss1 protein). [swissprot;acc:p35998]	High confidence	1539	1.07322	6207.5		5783.97
	Low confidence	1024	1.03794	8703.92		8385.76
26s protease regulatory subunit 8 (proteasome subunit p45) (thyroid hormone receptor interacting protein 1) (trip1) (msug1 protein) (tat-binding protein homolog 10) (tbp10) (p45/sug). [swissprot;acc:p47210]	High confidence	2651	1.00914	9234.09		9150.44
	Low confidence	3044	1.02789	8314.51		8088.94
26s protease regulatory subunit s10b (proteasome subunit p42) (p44) (conserved atpase domain protein 44) (cadp44). [swissprot;acc:q92524]	High confidence	1577	1.07181	6349.04		5923.66
	Low confidence	2711	1.02947	8326.51		8088.12
26s proteasome non-atpase regulatory subunit 1 (26s proteasome regulatory subunit s1) (26s proteasome subunit p112). [swissprot;acc:q99460]	High confidence	1883	1.06342	6195.48		5826
	Low confidence	2447	1.03046	8063.51		7825.14
26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832]	High confidence	451	1.01545	2642.79	0	2683.61
	High confidence	1609	1.07134	6242.44	1	5826.74
	Low confidence	771	1.01017	1609.88	0	1593.68
	Low confidence	2056	1.0319	8397.56	1	8137.96
26s proteasome non-atpase regulatory subunit 11 (26s proteasome regulatory subunit s9) (26s proteasome regulatory subunit p44.5). [swissprot;acc:o00231]	High confidence	1592	1.07153	6271.79		5853.1
	Low confidence	889	1.03984	8727.99		8393.58
26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232]	High confidence	474	1.00763	2263.85	0	2281.12
	High confidence	1579	1.07179	6261.87	1	5842.44
	Low confidence	785	1.00797	2331.31	0	2349.9
	Low confidence	1073	1.03739	8671.34	1	8358.82
26s proteasome non-atpase regulatory subunit 13 (26s proteasome regulatory subunit s11) (26s proteasome regulatory subunit p40.5). [swissprot;acc:q9unm6]	High confidence	1585	1.07166	6278.32		5858.48
	Low confidence	1982	1.03225	8388.54		8126.5
26s proteasome non-atpase regulatory subunit 2 (26s proteasome regulatory subunit s2) (26s proteasome subunit p97) (tumor necrosis factor type 1 receptor associated protein 2) (55.11 protein). [swissprot;acc:q13200]	High confidence	1241	1.08451	6980.13		6436.19
	Low confidence	2168	1.03153	8521.25		8260.81
26s proteasome non-atpase regulatory subunit 3 (26s proteasome regulatory subunit s3) (proteasome subunit p58). [swissprot;acc:o43242]	High confidence	1546	1.07303	6244.37		5819.39
	Low confidence	2101	1.03175	8407.98		8149.27
26s proteasome non-atpase regulatory subunit 4 (26s proteasome regulatory subunit s5a) (rpn10) (multiubiquitin chain binding protein) (antisecretory factor-1) (af) (asf). [swissprot;acc:p55036]	High confidence	1979	1.05939	5800.97		5475.74
	Low confidence	1826	1.03275	8425.82		8158.59
26s proteasome non-atpase regulatory subunit 6 (26s proteasome regulatory subunit s10) (p42a) (proteasome regulatory particle subunit p44s10). [swissprot;acc:q15008]	High confidence	1472	1.07535	6435.42		5984.47
	Low confidence	1122	1.037	8441.1		8139.9
26s proteasome non-atpase regulatory subunit 7 (26s proteasome regulatory subunit s12) (proteasome subunit p40) (mov34 protein homolog). [swissprot;acc:p51665]	High confidence	1571	1.07208	6273.4		5851.64
	Low confidence	2648	1.02973	8358.6		8117.3
26s proteasome non-atpase regulatory subunit 8 (26s proteasome regulatory subunit s14) (p31). [swissprot;acc:p48556]	High confidence	1536	1.07344	6350.53		5916.05
	Low confidence	917	1.03928	8445.39		8126.23
26s proteasome non-atpase regulatory subunit 9 (26s proteasome regulatory subunit p27). [swissprot;acc:o00233]	High confidence	1517	1.07393	6439.46		5996.14
	Low confidence	1454	1.03429	8435.4		8155.72
26s proteasome-associated pad1 homolog. [refseq;acc:nm_005805]	High confidence	1643	1.06977	6186.39		5782.92
	Low confidence	2004	1.03218	8367.09		8106.21
27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [swissprot;acc:o14653]	High confidence	2720	1.00351	5583.64		5603.24
	Low confidence	103	1.10006	5567.34		5060.92
28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235]	High confidence	2153	1.05302	3381.34		3560.63
	Low confidence	4567	1.01755	7505.02		7375.6

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/