Parameters
input_file_cond1: 20101125_LUjt8_1_hg19_ensembl59_G_iCLIP_TDP-43_SH-SY5Y_bedGraph-cDNA-hits-in-genome.bed.gz
input_file_cond1_res_type: single hits in whole-genome, cDNA counts
input_file_cond2: 20101125_LUjt8_4_hg19_ensembl59_G_iCLIP_TDP-43_BrainC6_bedGraph-cDNA-hits-in-genome.bed.gz
input_file_cond2_res_type: single hits in whole-genome, cDNA counts
mapped_to: hg19
annot_ver: ensembl59
window_size: 350
MA_window_size: 10

Differential analysis

MA plots are used for differential analysis of condition 1 (cond1) vs. condition 2 (cond2).
Data (bedGraphs) from two conditions are quantile-normalized first, then put into a MA-plot.
A sliding window of 10% of A axis span is used to calculate z-scores (of M).

Positive z-score indicates over-representation of counts in condition 1.
Negative z-score indicates over-representation of counts in condition 2.

Because bedGraph format uses the sign to indicate strand, results are split into two bedGraphs. Magnitude equals to the absolute value of z-score and sign indicates strand:

A third bedGraph is also produced showing only windows centered at peaks of high-density smoothed absolute z-values.

MA plots

M=log(count_cond1/count_cond2), A=log(count_cond1)+log(count_cond2).

Top 30 regions with highest density of difference (z-scores) in counts

Click on region to automatically upload the two bedGraphs with z-scores of differential analysis and start exploring in UCSC browser.

smoothed_abs_z_score	z_score	A	M	normalized count in condition 1	normalized count in condition 2	region	gene_name	sense relative to window	seg_type	seg_biotype
98.75	13.69	3.55	7.10	137.5	1	chr1-:204194386..204195086	PLEKHA6	same	intron	protein_coding
55.03	13.00	3.41	6.81	112.5	1	chr10+:43589940..43590640	RET	same	intron	protein_coding
40.71	1.82	9.41	1.04	973	472.5	chr1+:109642572..109643272	snoU2-25	same	ncRNA	snoRNA
37.79	2.94	5.35	1.60	71	23.5	chrX-:73047366..73048066	XIST	same	ncRNA	processed_transcript
31.46	3.70	5.07	1.96	66	17	chr7-:100805600..100806300	VGF	same	3UTR	protein_coding
31.02	-10.07	1.26	-4.52	0.5	11.5	chr14+:101312607..101313307	MEG3	same	ncRNA	processed_transcript
30.14	-7.81	3.62	-3.62	3.5	43	chr10-:116193698..116194398	ABLIM1	same	3UTR	protein_coding
27.68	10.94	2.44	4.88	29.5	1	chr1-:204193550..204194250	PLEKHA6	same	intron	protein_coding
27.35	2.11	5.07	1.21	51	0	chr1-:204194796..204195496	PLEKHA6	same	intron	protein_coding
27.17	2.40	5.00	1.35	51	20	chrX-:73046829..73047529	XIST	same	intron	processed_transcript
26.71	2.69	5.06	1.49	56	20	chr2-:72356609..72357309	CYP26B1	same	3UTR	protein_coding
25.73	-8.95	1.79	-3.58	1	12	chr3+:173545093..173545793	NLGN1	same	intron	protein_coding
24.19	9.01	3.40	4.79	55.5	2	chr10+:43604036..43604736	RET	same	intron	protein_coding
22.61	2.28	4.06	1.34	26.5	10.5	chr9-:14276979..14277679	NFIB	same	intron	protein_coding
22.38	1.38	8.55	0.84	502	279.5	chr7+:98479058..98479758	TRRAP	same	intron	protein_coding
22.05	-1.73	7.58	-0.58	156.5	234.5	chr3-:160232566..160233266	snoU90	same	ncRNA	snoRNA
22.01	8.84	1.88	3.75	13.5	1	chr1+:67007730..67008430	SGIP1	same	intron	protein_coding
21.32	-5.38	2.70	-2.22	3	14	chr2+:149880731..149881431	KIF5C	same	ORF	protein_coding
20.24	-7.70	1.58	-3.17	1	9	chr16+:58546746..58547446	NDRG4	same	3UTR	protein_coding
18.63	-7.46	1.54	-3.09	1	8.5	chr3+:41281136..41281836	CTNNB1	same	3UTR	protein_coding
18.25	7.10	1.58	3.17	9	1	chr1+:211474011..211474711	RCOR3	same	intron	protein_coding
18.07	5.83	9.15	2.89	1543	208.5	chr11+:65271557..65272257	inter	same	inter
17.94	-3.87	3.14	-1.63	5	15.5	chr2-:127811348..127812048	BIN1	same	intron	protein_coding
17.72	2.60	3.58	1.55	20.5	7	chr9-:66456255..66456955	inter	same	inter
17.38	2.31	5.53	1.30	72.5	29.5	chr15-:37391069..37391769	MEIS2	same	5UTR	protein_coding
17.28	-8.51	1.04	-4.09	0.5	8.5	chr9+:124094610..124095310	GSN	same	3UTR	protein_coding
17.25	-6.66	1.40	-2.81	1	7	chr5-:81031639..81032339	SSBP2	same	intron	protein_coding
16.94	-7.11	3.20	-3.22	3	28	chr2+:45886852..45887552	PRKCE	same	intron	protein_coding
16.73	-7.52	0.85	-3.70	0.5	6.5	chr8+:91968838..91969538	NECAB1	same	3UTR	protein_coding
16.46	3.27	5.19	1.75	67	0	chr1-:204193927..204194627	PLEKHA6	same	intron	protein_coding

Download full list in tab-delimited format.

Other measures of (dis)similarity

x-links in condition 1: 165524
x-links in condition 2: 17741
All x-link positions (union): 182831
Positions shared by both conditions (intersection): 434
Jaccard index (intersection/union): 0.0024

x-link position similarity

For each x-link in condition 1 (condition 2), look for nearest x-link in condition 2 (condition 1). Draw histogram of distances to closest neighbors.

Average distances (full span), all include distance 0:

Condition 1: both sides 950.8, downstream -15604.9, upstream 16555.7
Condition 2: both sides -1053.6, downstream -70610.2, upstream 69556.5

Average distances (-200..200 window), all include distance 0:

Condition 1: both sides -0.4, downstream -23.6, upstream 23.2
Condition 2: both sides -0.3, downstream -30.9, upstream 30.6

[eps]
Download graphs in tab-delimited format.

Count similarity

For each x-link position with specific value stored in input bedGraph for condition 1 (condition 2) look if same position in bedGraph for condition 2 (condition 1) has a non-zero value.

[eps]
Download graphs in tab-delimited format.

k-mers similarity

For k-mer analyses performed with same parameters on both conditions, report on similarity of results.
Similarity is measured by correlation of z-scores of all k-mers, and number of top k-mers shared by both conditions.

Available k-mer analyses:

compared	analysis parameters	condition	analysis id
True	intervals=[(-30, -10), (10, 30)], k=5, random_perms=100, valid_region_types=['ncRNA', 'ORF', '3UTR', '5UTR', 'intron']	condition 1	52299
True	intervals=[(-30, -10), (10, 30)], k=5, random_perms=100, valid_region_types=['ncRNA', 'ORF', '3UTR', '5UTR', 'intron']	condition 2	52326
True	intervals=[(-50, 50)], k=5, random_perms=100, valid_region_types=['ncRNA', 'ORF', '3UTR', '5UTR', 'intron']	condition 1	56690
True	intervals=[(-50, 50)], k=5, random_perms=100, valid_region_types=['ncRNA', 'ORF', '3UTR', '5UTR', 'intron']	condition 2	56699

Compared (marked as compared=True above) are only results from analyses with exactly same parameter values used to analyse both conditions.

There are 2 such pairs of analyses:

intervals=[(-30, -10), (10, 30)], k=5, random_perms=100, valid_region_types=['ncRNA', 'ORF', '3UTR', '5UTR', 'intron']
k-mers with computed scores in condition 1: 1024
k-mers with computed scores in condition 2: 1024
Pearson correlation of all k-mers with score in both conditions: 0.954

top 15 k-mers in condition 1: GTGTG, TGTGT, TGTGC, CGTGT, ATGTG, GTATG, GTGTA, GTGCG, TGCGT, TGTAT, GAATG, TGTGA, TATGT, TTGTG, GCGTG
top 15 k-mers in condition 2: GTGTG, TGTGT, GTGTA, CGTGT, ATGTG, TGTAT, GTGCG, TGTGC, GTATG, GCGTG, TGCGT, TATGT, AGTGT, GTGTT, TGTGA
intersection among top 15 k-mers: (13) GTGTG, TGTGT, CGTGT, ATGTG, GTGTA, TGTGC, GTATG, GTGCG, TGTAT, TGCGT, GCGTG, TATGT, TGTGA
intersection among top 100 k-mers: 78

Top 15 k-mers with best average rank:

average rank condition 1 & 2	kmer	rank condition 1	z-score condition 1	rank condition 2	z-score condition 2
2	GTGTG	2	375.0	2	87.5
3	TGTGT	3	354.9	3	86.6
5	CGTGT	5	129.1	5	30.5
6	ATGTG	6	123.3	6	26.3
6	GTGTA	8	116.9	4	31.2
6.5	TGTGC	4	132.5	9	21.5
8.5	GTATG	7	123.1	10	21.3
8.5	GTGCG	9	114.2	8	22.3
9	TGTAT	11	98.0	7	24.4
11	TGCGT	10	104.0	12	20.6
13.5	GCGTG	16	77.3	11	20.6
13.5	TATGT	14	80.9	13	19.5
14.5	TGTGA	13	85.1	16	16.4
16	TTGTG	15	80.0	17	15.6
17.5	GAATG	12	90.6	23	13.4

intervals=[(-50, 50)], k=5, random_perms=100, valid_region_types=['ncRNA', 'ORF', '3UTR', '5UTR', 'intron']
k-mers with computed scores in condition 1: 1024
k-mers with computed scores in condition 2: 1024
Pearson correlation of all k-mers with score in both conditions: 0.928

top 15 k-mers in condition 1: GTGTG, TGTGT, GTATG, GTGTA, ATGTG, GAATG, CGTGT, TGTAT, TGCGT, TGTGC, TGAAT, GTGCG, TATGT, TTGTG, GTGTT
top 15 k-mers in condition 2: GTGTG, TGTGT, GTGTA, CGTGT, GTATG, TGCGT, GTGCG, GTGTT, ATGTG, TGTAT, TATGT, GCGTG, TGTTT, TTGTG, GAATG
intersection among top 15 k-mers: (13) GTGTG, TGTGT, GTGTA, GTATG, CGTGT, ATGTG, TGCGT, TGTAT, GTGCG, GAATG, GTGTT, TATGT, TTGTG
intersection among top 100 k-mers: 78

Top 15 k-mers with best average rank:

average rank condition 1 & 2	kmer	rank condition 1	z-score condition 1	rank condition 2	z-score condition 2
2	GTGTG	2	344.4	2	63.9
3	TGTGT	3	299.7	3	52.5
4.5	GTGTA	5	195.9	4	49.3
5	GTATG	4	233.1	6	39.4
6.5	CGTGT	8	165.6	5	40.4
8	ATGTG	6	183.6	10	31.5
8.5	TGCGT	10	145.6	7	36.7
10	TGTAT	9	154.8	11	31.0
10.5	GTGCG	13	133.5	8	34.9
11.5	GAATG	7	175.9	16	25.6
12.5	GTGTT	16	121.7	9	34.0
13	TATGT	14	131.0	12	30.3
14.5	TGTGC	11	144.1	18	22.5
15	TTGTG	15	122.5	15	26.3
16	TGAAT	12	142.0	20	21.9

Download full list(s) in tab-delimited format.

RNAmaps similarity

For RNAmap analyses performed with same parameters on both conditions, report on similarity of results.
RNAmaps are compared by normalizing them first to sum 1.0 and then taking the average squared absolute difference (units are squared abs. difference per 1000 positions).

Available RNAmap analyses:

compared	analysis parameters	condition	analysis id
True	maxD_flanking=1000, maxD_within=300, maxU_flanking=-1000, maxU_within=-300, smoothing=0	condition 1	52300
True	maxD_flanking=1000, maxD_within=300, maxU_flanking=-1000, maxU_within=-300, smoothing=0	condition 2	52327

Compared (marked as compared=True above) are only results from analyses with exactly same parameter values used to analyse both conditions.

There are 1 such pairs of analyses:

maxD_flanking=1000, maxD_within=300, maxU_flanking=-1000, maxU_within=-300, smoothing=0
Top 10 RNAmap variables ranked by increasing difference between two conditions.

squared abs difference	RNAmap	variable	map in condition 1	map in condition 2
0.0049	3-inter	[x-link sites] (same)	link	link
0.0050	3-inter	normalized [x-link sites] (same)	link	link
0.0050	3-inter	[single hits in whole-genome, cDNA counts] (same)	link	link
0.0052	3-inter	normalized [single hits in whole-genome, cDNA counts] (same)	link	link
0.0054	exon-intron	[x-link sites] (same)	link	link
0.0058	exon-intron	[single hits in whole-genome, cDNA counts] (same)	link	link
0.0065	3UTR-inter	[x-link sites] (same)	link	link
0.0066	3UTR-inter	normalized [x-link sites] (same)	link	link
0.0066	3UTR-inter	[single hits in whole-genome, cDNA counts] (same)	link	link
0.0067	3UTR-inter	normalized [single hits in whole-genome, cDNA counts] (same)	link	link

Download full list in tab-delimited format.