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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Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

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

Results: HTML CSV LaTeX

Showing element 51 to 100 of 1892 in total

Network Comparison Type	Subtracted
Interaction Map	High confidence
Filtered	1
red	0
green	0
network_comparison	0

Rank	description	Value Type	
2768	histone h2a.x (h2a/x). [source:swissprot;acc:p16104]	Squared	
2768	histone h2a.x (h2a/x). [source:swissprot;acc:p16104]	Rooted	
2769	histone h2a.q (h2a/q) (h2a-gl101) (fragment). [source:swissprot;acc:q16777]	Measured	
2769	histone h2a.q (h2a/q) (h2a-gl101) (fragment). [source:swissprot;acc:q16777]	Ranked	
2769	histone h2a.q (h2a/q) (h2a-gl101) (fragment). [source:swissprot;acc:q16777]	Squared	
2769	histone h2a.q (h2a/q) (h2a-gl101) (fragment). [source:swissprot;acc:q16777]	Rooted	
2770	nipsnap1 protein. [source:swissprot;acc:q9bpw8]	Measured	
2770	nipsnap1 protein. [source:swissprot;acc:q9bpw8]	Ranked	
2770	nipsnap1 protein. [source:swissprot;acc:q9bpw8]	Squared	
2770	nipsnap1 protein. [source:swissprot;acc:q9bpw8]	Rooted	
2771	t-box transcription factor tbx1 (t-box protein 1) (testis-specific t-box protein). [source:swissprot;acc:o43435]	Measured	
2771	t-box transcription factor tbx1 (t-box protein 1) (testis-specific t-box protein). [source:swissprot;acc:o43435]	Ranked	
2771	t-box transcription factor tbx1 (t-box protein 1) (testis-specific t-box protein). [source:swissprot;acc:o43435]	Squared	
2771	t-box transcription factor tbx1 (t-box protein 1) (testis-specific t-box protein). [source:swissprot;acc:o43435]	Rooted	
2772	uridine diphosphate glucose pyrophosphatase. [source:refseq;acc:nm_177533]	Measured	
2772	uridine diphosphate glucose pyrophosphatase. [source:refseq;acc:nm_177533]	Ranked	
2772	uridine diphosphate glucose pyrophosphatase. [source:refseq;acc:nm_177533]	Squared	
2772	uridine diphosphate glucose pyrophosphatase. [source:refseq;acc:nm_177533]	Rooted	
2773	bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [source:swissprot;acc:p34820]	Measured	
2773	bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [source:swissprot;acc:p34820]	Ranked	
2773	bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [source:swissprot;acc:p34820]	Squared	
2773	bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [source:swissprot;acc:p34820]	Rooted	
2774	dc12 protein. [source:refseq;acc:nm_020187]	Measured	
2774	dc12 protein. [source:refseq;acc:nm_020187]	Ranked	
2774	dc12 protein. [source:refseq;acc:nm_020187]	Squared	
2774	dc12 protein. [source:refseq;acc:nm_020187]	Rooted	
2775	jerky protein homolog like (hhmjg). [source:swissprot;acc:q9y4a0]	Measured	
2775	jerky protein homolog like (hhmjg). [source:swissprot;acc:q9y4a0]	Ranked	
2775	jerky protein homolog like (hhmjg). [source:swissprot;acc:q9y4a0]	Squared	
2775	jerky protein homolog like (hhmjg). [source:swissprot;acc:q9y4a0]	Rooted	
2776	bcl-6 interacting corepressor isoform 1. [source:refseq;acc:nm_017745]	Measured	
2776	bcl-6 interacting corepressor isoform 1. [source:refseq;acc:nm_017745]	Ranked	
2776	bcl-6 interacting corepressor isoform 1. [source:refseq;acc:nm_017745]	Squared	
2776	bcl-6 interacting corepressor isoform 1. [source:refseq;acc:nm_017745]	Rooted	
2777	guanine nucleotide exchange factor mss4 (rab interacting factor). [source:swissprot;acc:p47224]	Measured	
2777	guanine nucleotide exchange factor mss4 (rab interacting factor). [source:swissprot;acc:p47224]	Ranked	
2777	guanine nucleotide exchange factor mss4 (rab interacting factor). [source:swissprot;acc:p47224]	Squared	
2777	guanine nucleotide exchange factor mss4 (rab interacting factor). [source:swissprot;acc:p47224]	Rooted	
2778	transcription factor mammalian mafa (pancreatic beta-cell specific transcriptional activator). [source:sptrembl;acc:q8nhw3]	Measured	
2778	transcription factor mammalian mafa (pancreatic beta-cell specific transcriptional activator). [source:sptrembl;acc:q8nhw3]	Ranked	
2778	transcription factor mammalian mafa (pancreatic beta-cell specific transcriptional activator). [source:sptrembl;acc:q8nhw3]	Squared	
2778	transcription factor mammalian mafa (pancreatic beta-cell specific transcriptional activator). [source:sptrembl;acc:q8nhw3]	Rooted	
2779	caveolin-3 (m-caveolin). [source:swissprot;acc:p56539]	Measured	
2779	caveolin-3 (m-caveolin). [source:swissprot;acc:p56539]	Ranked	
2779	caveolin-3 (m-caveolin). [source:swissprot;acc:p56539]	Squared	
2779	caveolin-3 (m-caveolin). [source:swissprot;acc:p56539]	Rooted	
2780	importin alpha-2 subunit (karyopherin alpha-2 subunit) (srp1-alpha) (rag cohort protein 1). [source:swissprot;acc:p52292]	Measured	
2780	importin alpha-2 subunit (karyopherin alpha-2 subunit) (srp1-alpha) (rag cohort protein 1). [source:swissprot;acc:p52292]	Ranked	
2780	importin alpha-2 subunit (karyopherin alpha-2 subunit) (srp1-alpha) (rag cohort protein 1). [source:swissprot;acc:p52292]	Squared	
2780	importin alpha-2 subunit (karyopherin alpha-2 subunit) (srp1-alpha) (rag cohort protein 1). [source:swissprot;acc:p52292]	Rooted	

Legend:
- Rank is the rank after comparing the two networks
- 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/