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 Network Type I Analysis

Type 1 network in which we propagated the absolute log regulation ratio abs(log(r/g)). We used the filtered lowest boundary of the confidence interval for the microarray measurement based and used the high confidence interaction map. Because type-I networks tend to favour highly connected proteins we tested a normalisation scheme in which we would run the network once with real values (the measured column) and once with simulated values where each measured point is set to 1 instead of the actual signal (the expected column). Afterwards we divided the measured value by the expected value. This normalisation scheme works to a certain extend but will lead to a variance that is directly related to the connectivity of each protein. In the end we dropped the use of Type-I networks due to the many technical problems they pose.

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Rank	measured	description	Gene	final	expected	Hugo

Results: HTML CSV LaTeX

Showing element 501 to 550 of 3206 in total

Rank	measured	description	final	expected	Hugo
501	0.281309	SPECTRIN SH3 DOMAIN BINDING PROTEIN 1; EPS8 BINDING PROTEIN; INTERACTOR PROTEIN ABLBP4; ABL-INTERACTOR PROTEIN 1 LONG; NAP1 BINDING PROTEIN. [RefSeq;Acc:NM_005470]	0.274126876	1.0262	ABI1
502	0.0401445		0.274068789	0.146476	CDV3
503	0.367035	EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT 7 (EIF-3 ZETA) (EIF3 P66) (EIF3D). [SWISSPROT;Acc:O15371]	0.274068294	1.33921	EIF3D
504	0.0286746	ENIGMA PROTEIN; LIM DOMAIN PROTEIN. [RefSeq;Acc:NM_005451]	0.274067631	0.104626	no value
505	0.183159	INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE 1 (EC 1.1.1.205) (IMP DEHYDROGENASE 1) (IMPDH-I) (IMPD 1). [SWISSPROT;Acc:P20839]	0.274042432	0.66836	IMPDH1
506	0.157432	INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE 2 (EC 1.1.1.205) (IMP DEHYDROGENASE 2) (IMPDH-II) (IMPD 2). [SWISSPROT;Acc:P12268]	0.274041658	0.574482	IMPDH2
507	0.348668	GMP SYNTHASE [GLUTAMINE-HYDROLYZING] (EC 6.3.5.2) (GLUTAMINE AMIDOTRANSFERASE) (GMP SYNTHETASE). [SWISSPROT;Acc:P49915]	0.274041122	1.27232	GMPS
508	0.135095	HEAT SHOCK FACTOR BINDING PROTEIN 1. [SWISSPROT;Acc:O75506]	0.273980243	0.493083	no value
509	0.0968147	"RNA, U TRANSPORTER 1; SNURPORTIN-1. [RefSeq;Acc:NM_005701]"	0.273832852	0.353554	SNUPN
510	0.250323		0.27374309	0.914445	KIAA1217
511	0.131932	PROTEIN KINASE CLK2 (EC 2.7.1.-) (CDC-LIKE KINASE 2). [SWISSPROT;Acc:P49760]	0.273350351	0.482648	CLK2
512	0.1005	PROTEIN KINASE CLK3 (EC 2.7.1.-) (CDC-LIKE KINASE 3). [SWISSPROT;Acc:P49761]	0.273287196	0.367745	CLK3
513	0.541777	NUCLEAR PROTEIN SKIP (SKI-INTERACTING PROTEIN) (SNW1 PROTEIN) (NUCLEAR RECEPTOR COACTIVATOR NCOA-62). [SWISSPROT;Acc:Q13573]	0.273064827	1.98406	SNW1
514	0.424547	RNA-BINDING PROTEIN 9 (RNA BINDING MOTIF PROTEIN 9) (HEXARIBONUCLEOTIDE BINDING PROTEIN 2) (REPRESSOR OF TAMOXIFEN TRANSCRIPTIONAL ACTIVITY). [SWISSPROT;Acc:O43251]	0.27250536	1.55794	RBM9
515	0.534301	ATAXIN 2-BINDING PROTEIN. [SWISSPROT;Acc:Q9NWB1]	0.272423252	1.96129	no value
516	0.0480412		0.272391817	0.176368	METT10D
517	0.313715		0.272390619	1.15171	UBAP2L
518	0.510382	M-PHASE INDUCER PHOSPHATASE 2 (EC 3.1.3.48) (DUAL SPECIFICITY PHOSPHATASE CDC25B). [SWISSPROT;Acc:P30305]	0.272305394	1.8743	CDC25B
519	0.0379775	"BREAST CARCINOMA AMPLIFIED SEQUENCE 2; SPLICEOSOME ASSOCIATED PROTEIN, AMPLIFIED IN BREAST CANCER. [RefSeq;Acc:NM_005872]"	0.272249901	0.139495	BCAS2
520	0.333016	"CDC5-LIKE; CDC5 (CELL DIVISION CYCLE 5, S. POMBE, HOMOLOG)-LIKE; CELL DIVISION CYCLE 5, S. POMBE, HOMOLOG-LIKE; CDC5-RELATED PROTEIN. [RefSeq;Acc:NM_001253]"	0.272249836	1.2232	CDC5L
521	0.504359	RNA-BINDING PROTEIN WITH MULTIPLE SPLICING (RBP-MS). [SWISSPROT;Acc:Q93062]	0.272032426	1.85404	RBPMS
522	0.694134	"PRE-MRNA CLEAVAGE FACTOR I, 59 KDA SUBUNIT. [RefSeq;Acc:NM_024811]"	0.271974767	2.5522	no value
523	0.142881	"1,4-ALPHA-GLUCAN BRANCHING ENZYME (EC 2.4.1.18) (GLYCOGEN BRANCHING ENZYME) (BRANCHER ENZYME). [SWISSPROT;Acc:Q04446]"	0.271904134	0.525483	GBE1
524	0.0229997	"GLYCOGEN PHOSPHORYLASE, MUSCLE FORM (EC 2.4.1.1) (MYOPHOSPHORYLASE). [SWISSPROT;Acc:P11217]"	0.27190392	0.0845876	PYGM
525	0.0231429	"GLYCOGEN PHOSPHORYLASE, BRAIN FORM (EC 2.4.1.1). [SWISSPROT;Acc:P11216]"	0.271903462	0.0851144	PYGB
526	0.0249116	MYOSIN XV (UNCONVENTIONAL MYOSIN-15). [SWISSPROT;Acc:Q9UKN7]	0.271903112	0.0916194	MYO15A
527		"GLYCOGEN PHOSPHORYLASE, LIVER FORM (EC 2.4.1.1). [SWISSPROT;Acc:P06737]"			PYGL
528	0.309836	"PROTEIN PHOSPHATASE 1, REGULATORY (INHIBITOR) SUBUNIT 12B ISOFORM A; MYOSIN PHOSPHATASE REGULATORY SUBUNIT; MYOSIN PHOSPHATASE, TARGET SUBUNIT 2. [RefSeq;Acc:NM_002481]"	0.271816962	1.13987	PPP1R12B
529	0.253813	"PROTEIN PHOSPHATASE 1, REGULATORY (INHIBITOR) SUBUNIT 12A; MYOSIN PHOSPHATASE, TARGET SUBUNIT 1. [RefSeq;Acc:NM_002480]"	0.271754795	0.933978	PPP1R12A
530	0.260139		0.271585798	0.957852	RBM24
531	0.216511	RNA-BINDING REGION CONTAINING PROTEIN 1 (HSRNASEB) (SSDNA BINDING PROTEIN SEB4) (CLL-ASSOCIATED ANTIGEN KW-5). [SWISSPROT;Acc:Q9H0Z9]	0.271570236	0.797256	RBM38
532	0.404881	"KARYOPHERIN BETA 2B, TRANSPORTIN; IMPORTIN 3. [RefSeq;Acc:NM_013433]"	0.271387971	1.49189	TNPO2
533	0.232461	SMALL NUCLEAR RIBONUCLEOPROTEIN F (SNRNP-F) (SM PROTEIN F) (SM-F) (SMF). [SWISSPROT;Acc:Q15356]	0.271367501	0.856628	SNRPF
534	0.0399967	SMALL NUCLEAR RIBONUCLEOPROTEIN E (SNRNP-E) (SM PROTEIN E) (SM-E) (SME). [SWISSPROT;Acc:P08578]	0.271366443	0.14739	no value
535	0.443276	IMPORTIN BETA-2 SUBUNIT (KARYOPHERIN BETA-2 SUBUNIT) (TRANSPORTIN) (M9 REGION INTERACTION PROTEIN) (MIP). [SWISSPROT;Acc:Q92973]	0.271206392	1.63446	TNPO1
536	0.122154	BROMODOMAIN-CONTAINING PROTEIN 3 (RING3-LIKE PROTEIN). [SWISSPROT;Acc:Q15059]	0.271112334	0.450566	BRD3
537	0.105783	BROMODOMAIN-CONTAINING PROTEIN 2 (RING3 PROTEIN) (O27.1.1). [SWISSPROT;Acc:P25440]	0.271083457	0.390223	BRD2
538	0.144761	BROMODOMAIN-CONTAINING PROTEIN 4 (HUNK1 PROTEIN). [SWISSPROT;Acc:O60885]	0.27107837	0.534019	BRD4
539	0.0778103		0.271078247	0.28704	SRBD1
540	0.0358609		0.271077935	0.13229	LRRC4B
541	0.0376313	NAG14 PROTEIN. [RefSeq;Acc:NM_022143]	0.271077863	0.138821	LRRC4
542	0.152328	PROTEIN REGULATOR OF CYTOKINESIS 1; PROTEIN REGULATING CYTOKINESIS 1. [RefSeq;Acc:NM_003981]	0.271077616	0.561935	no value
543	0.0431799		0.27107728	0.15929	LRRC4C
544	0.0996239	TESTIS-SPECIFIC BROMODOMAIN PROTEIN. [RefSeq;Acc:NM_001726]	0.27107069	0.36752	BRDT
545	0.59995	QUAKING ISOFORM 6. [SPTREMBL;Acc:Q9P0X9]	0.271065829	2.2133	QKI
546	0.0497647	ABHYDROLASE DOMAIN CONTAINING PROTEIN 2 (PROTEIN PHPS1-2). [SWISSPROT;Acc:P08910]	0.271065805	0.183589	ABHD2
547	0.24526	"CUG TRIPLET REPEAT, RNA BINDING PROTEIN 2; ELAV-TYPE RNA-BINDING PROTEIN; CUG TRIPLET REPEAT,RNA-BINDING PROTEIN 2; CUG TRIPLET REPEAT, RNA-BINDING PROTEIN 2; NEUROBLASTOMA APOPTOSIS-RELATED RNA-BINDING PROTEIN. [RefSeq;Acc:NM_006561]"	0.271003728	0.905006	CUGBP2
548	0.267337	CUG TRIPLET REPEAT RNA-BINDING PROTEIN 1 (CUG-BP1) (RNA-BINDING PROTEIN BRUNOL-2) (DEADENYLATION FACTOR CUG-BP) (50 KDA NUCLEAR POLYADENYLATED RNA-BINDING PROTEIN) (EDEN-BP). [SWISSPROT;Acc:Q92879]	0.271003405	0.986471	CUGBP1
549	0.046789	SH3 DOMAIN-BINDING GLUTAMIC ACID-RICH PROTEIN (SH3BGR PROTEIN) (21- GLUTAMIC ACID-RICH PROTEIN) (21-GARP). [SWISSPROT;Acc:P55822]	0.271000214	0.172653	SH3BGR
550		LATS HOMOLOG 1. [RefSeq;Acc:NM_004690]			LATS1

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
- Hugo is the bloody hugo identifier as demanded by the BMC Bioinformatics idiots